Diff of the two buildlogs: -- --- b1/build.log 2021-06-04 04:57:05.593015374 +0000 +++ b2/build.log 2021-06-04 05:06:57.561977042 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Jul 6 23:17:21 -12 2022 -I: pbuilder-time-stamp: 1657192641 +I: Current time: Fri Jun 4 18:57:12 +14 2021 +I: pbuilder-time-stamp: 1622782632 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./molmodel_3.0~svn842-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.XBhisnQt/trustedkeys.kbx': General error -gpgv: Signature made Wed Jun 17 16:27:13 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.k2cEh8k_/trustedkeys.kbx': General error +gpgv: Signature made Thu Jun 18 18:27:13 2020 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key @@ -30,137 +30,171 @@ dpkg-source: info: applying remove-failing-tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/56796/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/26336/tmp/hooks/D01_modify_environment starting +debug: Running on ionos12-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/26336/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/26336/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='e2db487e3a604d65b2f86529731d051d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='56796' - PS1='# ' - PS2='> ' + INVOCATION_ID=ee39f846728647eabeb4e290442c1e62 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=26336 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.WEOyOi3Xxn/pbuilderrc_zr7a --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WEOyOi3Xxn/b1 --logfile b1/build.log molmodel_3.0~svn842-2.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.WEOyOi3Xxn/pbuilderrc_MB2C --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.WEOyOi3Xxn/b2 --logfile b2/build.log --extrapackages usrmerge molmodel_3.0~svn842-2.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos6-i386 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux I: ls -l /bin total 5776 - -rwxr-xr-x 1 root root 1367848 Feb 24 2021 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 2021 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 2021 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 2021 more - -rwsr-xr-x 1 root root 50720 Feb 7 2021 mount - -rwxr-xr-x 1 root root 13856 Feb 7 2021 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 2021 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 6 03:47 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 2021 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 2021 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/56796/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1367848 Feb 25 10:57 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 03:23 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more + -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 10:57 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 4 18:58 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 2 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/26336/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -343,7 +377,7 @@ Get: 139 http://deb.debian.org/debian bullseye/main i386 libxmu-dev i386 2:1.1.2-2+b3 [70.3 kB] Get: 140 http://deb.debian.org/debian bullseye/main i386 libsimbody3.6 i386 3.6.1+dfsg-7 [3230 kB] Get: 141 http://deb.debian.org/debian bullseye/main i386 libsimbody-dev i386 3.6.1+dfsg-7 [2726 kB] -Fetched 87.2 MB in 6s (15.2 MB/s) +Fetched 87.2 MB in 21s (4193 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19675 files and directories currently installed.) @@ -928,8 +962,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (1464 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 26763 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/molmodel-3.0~svn842/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/molmodel-3.0~svn842/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package molmodel dpkg-buildpackage: info: source version 3.0~svn842-2 dpkg-buildpackage: info: source distribution unstable @@ -974,7 +1044,7 @@ -- Build files have been written to: /build/molmodel-3.0~svn842/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' /usr/bin/cmake -S"/build/molmodel-3.0~svn842" -B"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/CMakeFiles" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu//CMakeFiles/progress.marks" @@ -989,41 +1059,41 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f sharedTarget/CMakeFiles/SimTKmolmodel.dir/build.make sharedTarget/CMakeFiles/SimTKmolmodel.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 1%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o +[ 1%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o [ 1%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/AtomSubsystem.cpp.o -[ 2%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o +[ 2%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o [ 3%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o -c "/build/molmodel-3.0~svn842/src/Compound.cpp" cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/About.cpp.o -c "/build/molmodel-3.0~svn842/src/About.cpp" cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" 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Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o +[ 6%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/Biotype.cpp.o -c "/build/molmodel-3.0~svn842/src/Biotype.cpp" [ 6%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/BondGeometry.cpp.o -c "/build/molmodel-3.0~svn842/src/BondGeometry.cpp" +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o -c "/build/molmodel-3.0~svn842/src/DuMMForceFieldSubsystem.cpp" [ 6%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o -[ 7%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o -[ 8%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/Compound.cpp.o -c "/build/molmodel-3.0~svn842/src/Compound.cpp" cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/CompoundSystem.cpp.o -c "/build/molmodel-3.0~svn842/src/CompoundSystem.cpp" -[ 9%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o -[ 9%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystem.cpp.o -c "/build/molmodel-3.0~svn842/src/DuMMForceFieldSubsystem.cpp" -[ 10%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/DuMMForceFieldSubsystemRep.cpp.o -c "/build/molmodel-3.0~svn842/src/DuMMForceFieldSubsystemRep.cpp" cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/Element.cpp.o -c "/build/molmodel-3.0~svn842/src/Element.cpp" +[ 7%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/MolecularMechanicsSystem.cpp.o -c "/build/molmodel-3.0~svn842/src/MolecularMechanicsSystem.cpp" -[ 11%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o +[ 8%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/PDBReader.cpp.o -c "/build/molmodel-3.0~svn842/src/PDBReader.cpp" +[ 9%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/Pdb.cpp.o -c "/build/molmodel-3.0~svn842/src/Pdb.cpp" +[ 9%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/PeriodicVmdReporter.cpp.o -c "/build/molmodel-3.0~svn842/src/PeriodicVmdReporter.cpp" -[ 11%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o +[ 10%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/RiboseMobilizer.cpp.o -c "/build/molmodel-3.0~svn842/src/RiboseMobilizer.cpp" +[ 11%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/TinkerAmber99.cpp.o -c "/build/molmodel-3.0~svn842/src/TinkerAmber99.cpp" +[ 11%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/VanderWallSphere.cpp.o -c "/build/molmodel-3.0~svn842/src/VanderWallSphere.cpp" [ 12%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o -[ 13%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/VelocityRescalingThermostat.cpp.o -c "/build/molmodel-3.0~svn842/src/VelocityRescalingThermostat.cpp" +[ 13%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/VmdConnection.cpp.o -c "/build/molmodel-3.0~svn842/src/VmdConnection.cpp" [ 14%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/CpuImplicitSolvent.cpp.o -c "/build/molmodel-3.0~svn842/src/gbsa/CpuImplicitSolvent.cpp" @@ -1042,8 +1112,8 @@ [ 19%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/gbsa/cpuObcInterface.cpp.o -c "/build/molmodel-3.0~svn842/src/gbsa/cpuObcInterface.cpp" [ 19%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o -[ 20%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/mol.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/imd.cpp.o -c "/build/molmodel-3.0~svn842/src/imd.cpp" +[ 20%] Building CXX object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/mol.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/mol.cpp.o -c "/build/molmodel-3.0~svn842/src/mol.cpp" [ 21%] Building C object sharedTarget/CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.c.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/sharedTarget" && /usr/bin/cc -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_BUILDING_SHARED_LIBRARY -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -DSimTKmolmodel_EXPORTS -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/SimTKmolmodel.dir/__/src/vmdsock.c.o -c "/build/molmodel-3.0~svn842/src/vmdsock.c" @@ -1071,275 +1141,315 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' [ 21%] Built target SimTKmolmodel make -f examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/build.make examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/depend -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/DependInfo.cmake" --color= make -f examples/CMakeFiles/ExampleFoldPolyalanine.dir/build.make examples/CMakeFiles/ExampleFoldPolyalanine.dir/depend +make -f examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/build.make examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/depend +make -f examples/CMakeFiles/ExampleCreatePropane.dir/build.make examples/CMakeFiles/ExampleCreatePropane.dir/depend +make -f examples/CMakeFiles/MolmodelInstallTest.dir/build.make examples/CMakeFiles/MolmodelInstallTest.dir/depend +make -f examples/CMakeFiles/ExampleLoadPdb2.dir/build.make examples/CMakeFiles/ExampleLoadPdb2.dir/depend +make -f examples/CMakeFiles/ExampleTwoArgonAtoms.dir/build.make examples/CMakeFiles/ExampleTwoArgonAtoms.dir/depend +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/DependInfo.cmake" --color= cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/build.make examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/depend -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/depend.internal". +make -f examples/CMakeFiles/ExampleRigidProtein.dir/build.make examples/CMakeFiles/ExampleRigidProtein.dir/depend +make -f examples/CMakeFiles/ExampleSimpleProtein.dir/build.make examples/CMakeFiles/ExampleSimpleProtein.dir/depend +make -f examples/CMakeFiles/ExampleSimpleRNA.dir/build.make examples/CMakeFiles/ExampleSimpleRNA.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleCreatePropane.dir/build.make examples/CMakeFiles/ExampleCreatePropane.dir/depend -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/depend.internal". make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/DependInfo.cmake" --color= cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/MolmodelInstallTest.dir/build.make examples/CMakeFiles/MolmodelInstallTest.dir/depend +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleLoadPdb2.dir/build.make examples/CMakeFiles/ExampleLoadPdb2.dir/depend -Scanning dependencies of target ExampleAdenylateMobilitiesVMD -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/depend.internal". -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb2.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/build.make examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/build -Scanning dependencies of target ExampleFoldPolyalanine -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/depend.internal". -make -f examples/CMakeFiles/ExampleFoldPolyalanine.dir/build.make examples/CMakeFiles/ExampleFoldPolyalanine.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleTwoArgonAtoms.dir/build.make examples/CMakeFiles/ExampleTwoArgonAtoms.dir/depend +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -Scanning dependencies of target ExampleAdenylateMobilitiesViz -make -f examples/CMakeFiles/ExampleRigidProtein.dir/build.make examples/CMakeFiles/ExampleRigidProtein.dir/depend +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/DependInfo.cmake" --color= make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/DependInfo.cmake" --color= -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/depend.internal". +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleFoldPolyalanine.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb2.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb2.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb2.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTest.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleCreatePropane.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/depend.internal". +Scanning dependencies of target ExampleAdenylateMobilitiesViz make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/DependInfo.cmake" --color= make -f examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/build.make examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/build -Scanning dependencies of target ExampleCreatePropane +Scanning dependencies of target ExampleSimpleRNA make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleSimpleRNA.dir/build.make examples/CMakeFiles/ExampleSimpleRNA.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +Scanning dependencies of target ExampleSimpleProtein +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleSimpleProtein.dir/build.make examples/CMakeFiles/ExampleSimpleProtein.dir/build +Scanning dependencies of target ExampleLoadPdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleLoadPdb2.dir/build.make examples/CMakeFiles/ExampleLoadPdb2.dir/build +Scanning dependencies of target ExampleTwoArgonAtoms +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleTwoArgonAtoms.dir/build.make examples/CMakeFiles/ExampleTwoArgonAtoms.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleCreatePropane.dir/build.make examples/CMakeFiles/ExampleCreatePropane.dir/build -[ 21%] Building CXX object examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/ExampleAdenylateMobilitiesVMD.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/ExampleAdenylateMobilitiesVMD.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp" make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleSimpleProtein.dir/build.make examples/CMakeFiles/ExampleSimpleProtein.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleSimpleRNA.dir/build.make examples/CMakeFiles/ExampleSimpleRNA.dir/depend Scanning dependencies of target MolmodelInstallTest +[ 22%] Building CXX object examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/ExampleAdenylateMobilitiesViz.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleAdenylateMobilitiesViz.dir/ExampleAdenylateMobilitiesViz.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp" make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoArgonAtoms.dir/depend.internal". -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/DependInfo.cmake" --color= -Scanning dependencies of target ExampleLoadPdb2 +[ 23%] Building CXX object examples/CMakeFiles/ExampleSimpleRNA.dir/ExampleSimpleRNA.cpp.o make -f examples/CMakeFiles/MolmodelInstallTest.dir/build.make examples/CMakeFiles/MolmodelInstallTest.dir/build -[ 22%] Building CXX object examples/CMakeFiles/ExampleFoldPolyalanine.dir/ExampleFoldPolyalanine.cpp.o -[ 23%] Building CXX object examples/CMakeFiles/ExampleAdenylateMobilitiesViz.dir/ExampleAdenylateMobilitiesViz.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleSimpleRNA.dir/ExampleSimpleRNA.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp" +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +Scanning dependencies of target ExampleFoldPolyalanine +[ 24%] Building CXX object examples/CMakeFiles/ExampleTwoArgonAtoms.dir/ExampleTwoArgonAtoms.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleTwoArgonAtoms.dir/ExampleTwoArgonAtoms.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp" make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleAdenylateMobilitiesViz.dir/ExampleAdenylateMobilitiesViz.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesViz.cpp" +make -f examples/CMakeFiles/ExampleFoldPolyalanine.dir/build.make examples/CMakeFiles/ExampleFoldPolyalanine.dir/build +Scanning dependencies of target ExampleAdenylateMobilitiesVMD +[ 24%] Building CXX object examples/CMakeFiles/ExampleSimpleProtein.dir/ExampleSimpleProtein.cpp.o +[ 24%] Building CXX object examples/CMakeFiles/ExampleLoadPdb2.dir/ExampleLoadPdb2.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleLoadPdb2.dir/ExampleLoadPdb2.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp" +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleSimpleProtein.dir/ExampleSimpleProtein.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp" +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/build.make examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleLoadPdb2.dir/build.make examples/CMakeFiles/ExampleLoadPdb2.dir/build -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleRigidProtein.dir/depend.internal". -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleFoldPolyalanine.dir/ExampleFoldPolyalanine.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp" -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleProtein.dir/depend.internal". -[ 24%] Building CXX object examples/CMakeFiles/ExampleCreatePropane.dir/ExampleCreatePropane.cpp.o make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +Scanning dependencies of target ExampleRigidProtein +Scanning dependencies of target ExampleCreatePropane +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleCreatePropane.dir/build.make examples/CMakeFiles/ExampleCreatePropane.dir/build +[ 25%] Building CXX object examples/CMakeFiles/MolmodelInstallTest.dir/MolmodelInstallTest.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/MolmodelInstallTest.dir/MolmodelInstallTest.cpp.o -c "/build/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp" +make -f examples/CMakeFiles/ExampleRigidProtein.dir/build.make examples/CMakeFiles/ExampleRigidProtein.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 25%] Building CXX object examples/CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/ExampleAdenylateMobilitiesVMD.cpp.o +[ 26%] Building CXX object examples/CMakeFiles/ExampleFoldPolyalanine.dir/ExampleFoldPolyalanine.cpp.o +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleFoldPolyalanine.dir/ExampleFoldPolyalanine.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleFoldPolyalanine.cpp" +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/ExampleAdenylateMobilitiesVMD.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleAdenylateMobilitiesVMD.cpp" +[ 27%] Building CXX object examples/CMakeFiles/ExampleCreatePropane.dir/ExampleCreatePropane.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleCreatePropane.dir/ExampleCreatePropane.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleCreatePropane.cpp" +[ 28%] Building CXX object examples/CMakeFiles/ExampleRigidProtein.dir/ExampleRigidProtein.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleRigidProtein.dir/ExampleRigidProtein.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp" +[ 29%] Linking CXX executable ../ExampleTwoArgonAtoms +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleTwoArgonAtoms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleTwoArgonAtoms.dir/ExampleTwoArgonAtoms.cpp.o -o ../ExampleTwoArgonAtoms -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 30%] Linking CXX executable ../ExampleLoadPdb2 +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleLoadPdb2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleLoadPdb2.dir/ExampleLoadPdb2.cpp.o -o ../ExampleLoadPdb2 -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 30%] Built target ExampleTwoArgonAtoms make -f examples/CMakeFiles/ExampleTwoEthanes.dir/build.make examples/CMakeFiles/ExampleTwoEthanes.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/depend.internal". +Scanning dependencies of target ExampleTwoEthanes +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleTwoEthanes.dir/build.make examples/CMakeFiles/ExampleTwoEthanes.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 31%] Building CXX object examples/CMakeFiles/ExampleTwoEthanes.dir/ExampleTwoEthanes.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleTwoEthanes.dir/ExampleTwoEthanes.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp" +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 31%] Built target ExampleLoadPdb2 make -f examples/CMakeFiles/ExampleLoadPdb.dir/build.make examples/CMakeFiles/ExampleLoadPdb.dir/depend -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleSimpleRNA.dir/depend.internal". -[ 25%] Building CXX object examples/CMakeFiles/MolmodelInstallTest.dir/MolmodelInstallTest.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/MolmodelInstallTest.dir/MolmodelInstallTest.cpp.o -c "/build/molmodel-3.0~svn842/examples/MolmodelInstallTest.cpp" make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/MolmodelInstallTestNoViz.dir/build.make examples/CMakeFiles/MolmodelInstallTestNoViz.dir/depend -Scanning dependencies of target ExampleTwoArgonAtoms +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/depend.internal". +Scanning dependencies of target ExampleLoadPdb make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/ExampleLoadPdb.dir/build.make examples/CMakeFiles/ExampleLoadPdb.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTestNoViz.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleTwoArgonAtoms.dir/build.make examples/CMakeFiles/ExampleTwoArgonAtoms.dir/build -make -f tests/CMakeFiles/TestWriteSimtimePdb.dir/build.make tests/CMakeFiles/TestWriteSimtimePdb.dir/depend -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 25%] Building CXX object examples/CMakeFiles/ExampleLoadPdb2.dir/ExampleLoadPdb2.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleLoadPdb2.dir/ExampleLoadPdb2.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleLoadPdb2.cpp" -Scanning dependencies of target ExampleRigidProtein -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestWriteSimtimePdb.dir/DependInfo.cmake" --color= +[ 32%] Building CXX object examples/CMakeFiles/ExampleLoadPdb.dir/ExampleLoadPdb.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleLoadPdb.dir/ExampleLoadPdb.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp" +[ 33%] Linking CXX executable ../ExampleCreatePropane +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleCreatePropane.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleCreatePropane.dir/ExampleCreatePropane.cpp.o -o ../ExampleCreatePropane -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestTorsionPartitioner.dir/build.make tests/CMakeFiles/TestTorsionPartitioner.dir/depend +[ 33%] Built target ExampleCreatePropane +make -f examples/CMakeFiles/MolmodelInstallTestNoViz.dir/build.make examples/CMakeFiles/MolmodelInstallTestNoViz.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/DependInfo.cmake" --color= +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTestNoViz.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTestNoViz.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTestNoViz.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/MolmodelInstallTestNoViz.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleLoadPdb.dir/depend.internal". -make -f examples/CMakeFiles/ExampleRigidProtein.dir/build.make examples/CMakeFiles/ExampleRigidProtein.dir/build -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples/CMakeFiles/ExampleTwoEthanes.dir/depend.internal". -[ 26%] Building CXX object examples/CMakeFiles/ExampleTwoArgonAtoms.dir/ExampleTwoArgonAtoms.cpp.o -Scanning dependencies of target ExampleSimpleRNA +Scanning dependencies of target MolmodelInstallTestNoViz make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f examples/CMakeFiles/MolmodelInstallTestNoViz.dir/build.make examples/CMakeFiles/MolmodelInstallTestNoViz.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleSimpleRNA.dir/build.make examples/CMakeFiles/ExampleSimpleRNA.dir/build -Scanning dependencies of target ExampleSimpleProtein -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleTwoArgonAtoms.dir/ExampleTwoArgonAtoms.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleTwoArgonAtoms.cpp" -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestTinkerAmber.dir/build.make tests/CMakeFiles/TestTinkerAmber.dir/depend -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/depend.internal". -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTinkerAmber.dir/DependInfo.cmake" --color= -make -f tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build.make tests/CMakeFiles/TestVelocityRescalingThermostat.dir/depend +[ 33%] Building CXX object examples/CMakeFiles/MolmodelInstallTestNoViz.dir/MolmodelInstallTestNoViz.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/MolmodelInstallTestNoViz.dir/MolmodelInstallTestNoViz.cpp.o -c "/build/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp" +[ 34%] Linking CXX executable ../ExampleSimpleProtein +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleSimpleProtein.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleSimpleProtein.dir/ExampleSimpleProtein.cpp.o -o ../ExampleSimpleProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 34%] Linking CXX executable ../ExampleAdenylateMobilitiesViz +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleAdenylateMobilitiesViz.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleAdenylateMobilitiesViz.dir/ExampleAdenylateMobilitiesViz.cpp.o -o ../ExampleAdenylateMobilitiesViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 34%] Linking CXX executable ../ExampleSimpleRNA +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleSimpleRNA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleSimpleRNA.dir/ExampleSimpleRNA.cpp.o -o ../ExampleSimpleRNA -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 35%] Linking CXX executable ../ExampleAdenylateMobilitiesVMD +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/ExampleAdenylateMobilitiesVMD.cpp.o -o ../ExampleAdenylateMobilitiesVMD -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 35%] Built target ExampleSimpleProtein +make -f tests/CMakeFiles/TestWriteSimtimePdb.dir/build.make tests/CMakeFiles/TestWriteSimtimePdb.dir/depend +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestWriteSimtimePdb.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestWriteSimtimePdb.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestWriteSimtimePdb.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestWriteSimtimePdb.dir/depend.internal". +Scanning dependencies of target TestWriteSimtimePdb +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f tests/CMakeFiles/TestWriteSimtimePdb.dir/build.make tests/CMakeFiles/TestWriteSimtimePdb.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/DependInfo.cmake" --color= -make -f examples/CMakeFiles/ExampleSimpleProtein.dir/build.make examples/CMakeFiles/ExampleSimpleProtein.dir/build -[ 27%] Building CXX object examples/CMakeFiles/ExampleRigidProtein.dir/ExampleRigidProtein.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleRigidProtein.dir/ExampleRigidProtein.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleRigidProtein.cpp" -[ 28%] Building CXX object examples/CMakeFiles/ExampleSimpleRNA.dir/ExampleSimpleRNA.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleSimpleRNA.dir/ExampleSimpleRNA.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleSimpleRNA.cpp" -make -f tests/CMakeFiles/TestShortPdbLines.dir/build.make tests/CMakeFiles/TestShortPdbLines.dir/depend +[ 36%] Building CXX object tests/CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp" +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 36%] Built target ExampleAdenylateMobilitiesViz +make -f tests/CMakeFiles/TestTorsionPartitioner.dir/build.make tests/CMakeFiles/TestTorsionPartitioner.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -Scanning dependencies of target MolmodelInstallTestNoViz +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTorsionPartitioner.dir/depend.internal". +[ 36%] Built target ExampleSimpleRNA +make -f tests/CMakeFiles/TestTinkerAmber.dir/build.make tests/CMakeFiles/TestTinkerAmber.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/DependInfo.cmake" --color= +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTinkerAmber.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTinkerAmber.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTinkerAmber.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestTinkerAmber.dir/depend.internal". -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/MolmodelInstallTestNoViz.dir/build.make examples/CMakeFiles/MolmodelInstallTestNoViz.dir/build -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/depend.internal". -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 28%] Building CXX object examples/CMakeFiles/ExampleSimpleProtein.dir/ExampleSimpleProtein.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleSimpleProtein.dir/ExampleSimpleProtein.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleSimpleProtein.cpp" Scanning dependencies of target TestTorsionPartitioner -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/depend.internal". -Scanning dependencies of target ExampleLoadPdb make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleLoadPdb.dir/build.make examples/CMakeFiles/ExampleLoadPdb.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestTorsionPartitioner.dir/build.make tests/CMakeFiles/TestTorsionPartitioner.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -Scanning dependencies of target TestWriteSimtimePdb -Scanning dependencies of target ExampleTwoEthanes -[ 28%] Building CXX object examples/CMakeFiles/MolmodelInstallTestNoViz.dir/MolmodelInstallTestNoViz.cpp.o +[ 37%] Building CXX object tests/CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp" +Scanning dependencies of target TestTinkerAmber make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f tests/CMakeFiles/TestTinkerAmber.dir/build.make tests/CMakeFiles/TestTinkerAmber.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f examples/CMakeFiles/ExampleTwoEthanes.dir/build.make examples/CMakeFiles/ExampleTwoEthanes.dir/build -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/MolmodelInstallTestNoViz.dir/MolmodelInstallTestNoViz.cpp.o -c "/build/molmodel-3.0~svn842/examples/MolmodelInstallTestNoViz.cpp" -Scanning dependencies of target TestTinkerAmber -Scanning dependencies of target TestVelocityRescalingThermostat +[ 38%] Building CXX object tests/CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestTinkerAmber.cpp" +[ 38%] Built target ExampleAdenylateMobilitiesVMD +make -f tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build.make tests/CMakeFiles/TestVelocityRescalingThermostat.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestVelocityRescalingThermostat.dir/depend.internal". +[ 39%] Linking CXX executable ../ExampleRigidProtein +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleRigidProtein.dir/link.txt --verbose=1 +Scanning dependencies of target TestVelocityRescalingThermostat make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestWriteSimtimePdb.dir/build.make tests/CMakeFiles/TestWriteSimtimePdb.dir/build -[ 29%] Building CXX object examples/CMakeFiles/ExampleLoadPdb.dir/ExampleLoadPdb.cpp.o +make -f tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build.make tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleRigidProtein.dir/ExampleRigidProtein.cpp.o -o ../ExampleRigidProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 40%] Building CXX object tests/CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp" +[ 40%] Linking CXX executable ../ExampleFoldPolyalanine +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleFoldPolyalanine.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleFoldPolyalanine.dir/ExampleFoldPolyalanine.cpp.o -o ../ExampleFoldPolyalanine -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 41%] Linking CXX executable ../MolmodelInstallTest +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolmodelInstallTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/MolmodelInstallTest.dir/MolmodelInstallTest.cpp.o -o ../MolmodelInstallTest -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleLoadPdb.dir/ExampleLoadPdb.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleLoadPdb.cpp" -[ 30%] Building CXX object tests/CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestTorsionPartitioner.cpp" +[ 41%] Built target ExampleRigidProtein +make -f tests/CMakeFiles/TestShortPdbLines.dir/build.make tests/CMakeFiles/TestShortPdbLines.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestTinkerAmber.dir/build.make tests/CMakeFiles/TestTinkerAmber.dir/build +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestShortPdbLines.dir/depend.internal". Scanning dependencies of target TestShortPdbLines -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build.make tests/CMakeFiles/TestVelocityRescalingThermostat.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestShortPdbLines.dir/build.make tests/CMakeFiles/TestShortPdbLines.dir/build -[ 31%] Building CXX object examples/CMakeFiles/ExampleTwoEthanes.dir/ExampleTwoEthanes.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/ExampleTwoEthanes.dir/ExampleTwoEthanes.cpp.o -c "/build/molmodel-3.0~svn842/examples/ExampleTwoEthanes.cpp" -[ 32%] Building CXX object tests/CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestWriteSimtimePdb.cpp" -[ 33%] Building CXX object tests/CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestTinkerAmber.cpp" -[ 34%] Building CXX object tests/CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestVelocityRescalingThermostat.cpp" -[ 34%] Building CXX object tests/CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o +[ 41%] Building CXX object tests/CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestShortPdbLines.cpp" -[ 34%] Linking CXX executable ../TestTinkerAmber -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestTinkerAmber.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -o ../TestTinkerAmber -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 35%] Linking CXX executable ../ExampleTwoArgonAtoms -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleTwoArgonAtoms.dir/link.txt --verbose=1 -[ 35%] Linking CXX executable ../TestVelocityRescalingThermostat -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestVelocityRescalingThermostat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleTwoArgonAtoms.dir/ExampleTwoArgonAtoms.cpp.o -o ../ExampleTwoArgonAtoms -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -o ../TestVelocityRescalingThermostat -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 36%] Linking CXX executable ../ExampleLoadPdb -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleLoadPdb.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleLoadPdb.dir/ExampleLoadPdb.cpp.o -o ../ExampleLoadPdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 36%] Built target TestTinkerAmber +[ 41%] Built target MolmodelInstallTest make -f tests/CMakeFiles/TestGbsa.dir/build.make tests/CMakeFiles/TestGbsa.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGbsa.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGbsa.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGbsa.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGbsa.dir/depend.internal". -Scanning dependencies of target TestGbsa -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestGbsa.dir/build.make tests/CMakeFiles/TestGbsa.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 36%] Building CXX object tests/CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestGbsa.cpp" make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 37%] Linking CXX executable ../ExampleLoadPdb2 -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleLoadPdb2.dir/link.txt --verbose=1 -[ 37%] Built target TestVelocityRescalingThermostat +[ 41%] Built target ExampleFoldPolyalanine make -f tests/CMakeFiles/TestGetAtomName.dir/build.make tests/CMakeFiles/TestGetAtomName.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleLoadPdb2.dir/ExampleLoadPdb2.cpp.o -o ../ExampleLoadPdb2 -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGetAtomName.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGetAtomName.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGetAtomName.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestGetAtomName.dir/depend.internal". +Scanning dependencies of target TestGbsa +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f tests/CMakeFiles/TestGbsa.dir/build.make tests/CMakeFiles/TestGbsa.dir/build Scanning dependencies of target TestGetAtomName make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestGetAtomName.dir/build.make tests/CMakeFiles/TestGetAtomName.dir/build -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 38%] Building CXX object tests/CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -[ 38%] Built target ExampleTwoArgonAtoms +[ 42%] Building CXX object tests/CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o +[ 42%] Building CXX object tests/CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestGetAtomName.cpp" +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestGbsa.cpp" +[ 42%] Linking CXX executable ../ExampleTwoEthanes +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleTwoEthanes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleTwoEthanes.dir/ExampleTwoEthanes.cpp.o -o ../ExampleTwoEthanes -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 43%] Linking CXX executable ../ExampleLoadPdb +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleLoadPdb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleLoadPdb.dir/ExampleLoadPdb.cpp.o -o ../ExampleLoadPdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 43%] Built target ExampleTwoEthanes make -f tests/CMakeFiles/TestProteinDihedrals.dir/build.make tests/CMakeFiles/TestProteinDihedrals.dir/depend -[ 38%] Built target ExampleLoadPdb make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProteinDihedrals.dir/DependInfo.cmake" --color= -make -f tests/CMakeFiles/TestDuMMForces.dir/build.make tests/CMakeFiles/TestDuMMForces.dir/depend -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProteinDihedrals.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProteinDihedrals.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProteinDihedrals.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/depend.internal". Scanning dependencies of target TestProteinDihedrals make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestProteinDihedrals.dir/build.make tests/CMakeFiles/TestProteinDihedrals.dir/build -Scanning dependencies of target TestDuMMForces make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 43%] Building CXX object tests/CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestProteinDihedrals.cpp" +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 43%] Built target ExampleLoadPdb +make -f tests/CMakeFiles/TestDuMMForces.dir/build.make tests/CMakeFiles/TestDuMMForces.dir/depend +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestDuMMForces.dir/depend.internal". +Scanning dependencies of target TestDuMMForces make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestDuMMForces.dir/build.make tests/CMakeFiles/TestDuMMForces.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 38%] Building CXX object tests/CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestProteinDihedrals.cpp" -[ 38%] Building CXX object tests/CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o +[ 43%] Building CXX object tests/CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestDuMMForces.cpp" -[ 39%] Linking CXX executable ../TestShortPdbLines +[ 44%] Linking CXX executable ../TestShortPdbLines cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestShortPdbLines.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestShortPdbLines.dir/TestShortPdbLines.cpp.o -o ../TestShortPdbLines -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 44%] Linking CXX executable ../TestTinkerAmber +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestTinkerAmber.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestTinkerAmber.dir/TestTinkerAmber.cpp.o -o ../TestTinkerAmber -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 39%] Built target ExampleLoadPdb2 +[ 44%] Built target TestShortPdbLines make -f tests/CMakeFiles/TestForeignBodyIds.dir/build.make tests/CMakeFiles/TestForeignBodyIds.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestForeignBodyIds.dir/DependInfo.cmake" --color= @@ -1349,93 +1459,96 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestForeignBodyIds.dir/build.make tests/CMakeFiles/TestForeignBodyIds.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 40%] Building CXX object tests/CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o +[ 45%] Building CXX object tests/CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestForeignBodyIds.cpp" make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 40%] Built target TestShortPdbLines +[ 45%] Built target TestTinkerAmber make -f tests/CMakeFiles/TestRna.dir/build.make tests/CMakeFiles/TestRna.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestRna.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestRna.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestRna.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestRna.dir/depend.internal". -[ 40%] Linking CXX executable ../ExampleSimpleRNA -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleSimpleRNA.dir/link.txt --verbose=1 Scanning dependencies of target TestRna make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestRna.dir/build.make tests/CMakeFiles/TestRna.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleSimpleRNA.dir/ExampleSimpleRNA.cpp.o -o ../ExampleSimpleRNA -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 41%] Linking CXX executable ../ExampleCreatePropane -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleCreatePropane.dir/link.txt --verbose=1 -[ 41%] Building CXX object tests/CMakeFiles/TestRna.dir/TestRna.cpp.o +[ 45%] Building CXX object tests/CMakeFiles/TestRna.dir/TestRna.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestRna.dir/TestRna.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestRna.cpp" -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleCreatePropane.dir/ExampleCreatePropane.cpp.o -o ../ExampleCreatePropane -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 41%] Linking CXX executable ../ExampleTwoEthanes -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleTwoEthanes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleTwoEthanes.dir/ExampleTwoEthanes.cpp.o -o ../ExampleTwoEthanes -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 46%] Linking CXX executable ../MolmodelInstallTestNoViz +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolmodelInstallTestNoViz.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/MolmodelInstallTestNoViz.dir/MolmodelInstallTestNoViz.cpp.o -o ../MolmodelInstallTestNoViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 46%] Linking CXX executable ../TestVelocityRescalingThermostat +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestVelocityRescalingThermostat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestVelocityRescalingThermostat.dir/TestVelocityRescalingThermostat.cpp.o -o ../TestVelocityRescalingThermostat -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 41%] Built target ExampleSimpleRNA +[ 46%] Built target MolmodelInstallTestNoViz make -f tests/CMakeFiles/TestLoneAtomCoordinates.dir/build.make tests/CMakeFiles/TestLoneAtomCoordinates.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoneAtomCoordinates.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoneAtomCoordinates.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoneAtomCoordinates.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoneAtomCoordinates.dir/depend.internal". -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' Scanning dependencies of target TestLoneAtomCoordinates make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestLoneAtomCoordinates.dir/build.make tests/CMakeFiles/TestLoneAtomCoordinates.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 41%] Built target ExampleCreatePropane +[ 47%] Building CXX object tests/CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp" +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 47%] Built target TestVelocityRescalingThermostat make -f tests/CMakeFiles/TestCompoundTransforms.dir/build.make tests/CMakeFiles/TestCompoundTransforms.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestCompoundTransforms.dir/DependInfo.cmake" --color= -[ 42%] Building CXX object tests/CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestLoneAtomCoordinates.cpp" Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestCompoundTransforms.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestCompoundTransforms.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestCompoundTransforms.dir/depend.internal". Scanning dependencies of target TestCompoundTransforms make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestCompoundTransforms.dir/build.make tests/CMakeFiles/TestCompoundTransforms.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 43%] Building CXX object tests/CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o +[ 48%] Building CXX object tests/CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestCompoundTransforms.cpp" +[ 49%] Linking CXX executable ../TestWriteSimtimePdb +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteSimtimePdb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -o ../TestWriteSimtimePdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 43%] Built target ExampleTwoEthanes +[ 49%] Built target TestWriteSimtimePdb make -f tests/CMakeFiles/TestProtein.dir/build.make tests/CMakeFiles/TestProtein.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProtein.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProtein.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProtein.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestProtein.dir/depend.internal". -[ 43%] Linking CXX executable ../ExampleAdenylateMobilitiesViz -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleAdenylateMobilitiesViz.dir/link.txt --verbose=1 Scanning dependencies of target TestProtein make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestProtein.dir/build.make tests/CMakeFiles/TestProtein.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleAdenylateMobilitiesViz.dir/ExampleAdenylateMobilitiesViz.cpp.o -o ../ExampleAdenylateMobilitiesViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 44%] Building CXX object tests/CMakeFiles/TestProtein.dir/TestProtein.cpp.o +[ 50%] Building CXX object tests/CMakeFiles/TestProtein.dir/TestProtein.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestProtein.dir/TestProtein.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestProtein.cpp" -[ 45%] Linking CXX executable ../ExampleAdenylateMobilitiesVMD -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleAdenylateMobilitiesVMD.dir/ExampleAdenylateMobilitiesVMD.cpp.o -o ../ExampleAdenylateMobilitiesVMD -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 51%] Linking CXX executable ../TestGetAtomName +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestGetAtomName.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -o ../TestGetAtomName -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 45%] Built target ExampleAdenylateMobilitiesViz -[ 46%] Linking CXX executable ../ExampleSimpleProtein +[ 51%] Built target TestGetAtomName make -f tests/CMakeFiles/TestBiotypeSelfCode.dir/build.make tests/CMakeFiles/TestBiotypeSelfCode.dir/depend -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleSimpleProtein.dir/link.txt --verbose=1 make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBiotypeSelfCode.dir/DependInfo.cmake" --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleSimpleProtein.dir/ExampleSimpleProtein.cpp.o -o ../ExampleSimpleProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBiotypeSelfCode.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBiotypeSelfCode.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBiotypeSelfCode.dir/depend.internal". Scanning dependencies of target TestBiotypeSelfCode make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestBiotypeSelfCode.dir/build.make tests/CMakeFiles/TestBiotypeSelfCode.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 47%] Building CXX object tests/CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o +[ 52%] Building CXX object tests/CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestBiotypeSelfCode.cpp" -[ 47%] Built target ExampleAdenylateMobilitiesVMD +[ 53%] Linking CXX executable ../TestGbsa +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestGbsa.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -o ../TestGbsa -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 54%] Linking CXX executable ../TestProteinDihedrals +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestProteinDihedrals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -o ../TestProteinDihedrals -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 55%] Linking CXX executable ../TestTorsionPartitioner +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestTorsionPartitioner.dir/link.txt --verbose=1 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -o ../TestTorsionPartitioner -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 55%] Built target TestGbsa make -f tests/CMakeFiles/TestWriteDefaultPdb.dir/build.make tests/CMakeFiles/TestWriteDefaultPdb.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestWriteDefaultPdb.dir/DependInfo.cmake" --color= @@ -1445,16 +1558,10 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestWriteDefaultPdb.dir/build.make tests/CMakeFiles/TestWriteDefaultPdb.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 48%] Linking CXX executable ../MolmodelInstallTest -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolmodelInstallTest.dir/link.txt --verbose=1 -[ 49%] Building CXX object tests/CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o +[ 56%] Building CXX object tests/CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestWriteDefaultPdb.cpp" -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/MolmodelInstallTest.dir/MolmodelInstallTest.cpp.o -o ../MolmodelInstallTest -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 50%] Linking CXX executable ../ExampleRigidProtein -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleRigidProtein.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleRigidProtein.dir/ExampleRigidProtein.cpp.o -o ../ExampleRigidProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 50%] Built target ExampleSimpleProtein +[ 56%] Built target TestProteinDihedrals make -f tests/CMakeFiles/TestEthane.dir/build.make tests/CMakeFiles/TestEthane.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestEthane.dir/DependInfo.cmake" --color= @@ -1464,32 +1571,35 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestEthane.dir/build.make tests/CMakeFiles/TestEthane.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 51%] Building CXX object tests/CMakeFiles/TestEthane.dir/TestEthane.cpp.o +[ 57%] Building CXX object tests/CMakeFiles/TestEthane.dir/TestEthane.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestEthane.dir/TestEthane.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestEthane.cpp" -[ 52%] Linking CXX executable ../TestWriteSimtimePdb -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteSimtimePdb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteSimtimePdb.dir/TestWriteSimtimePdb.cpp.o -o ../TestWriteSimtimePdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 53%] Linking CXX executable ../MolmodelInstallTestNoViz -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolmodelInstallTestNoViz.dir/link.txt --verbose=1 -[ 53%] Built target MolmodelInstallTest +[ 57%] Built target TestTorsionPartitioner make -f tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/build.make tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/DependInfo.cmake" --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/MolmodelInstallTestNoViz.dir/MolmodelInstallTestNoViz.cpp.o -o ../MolmodelInstallTestNoViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/depend.internal". Scanning dependencies of target TestLoadVariantRnaAtomNames -[ 53%] Linking CXX executable ../ExampleFoldPolyalanine make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/examples" && /usr/bin/cmake -E cmake_link_script CMakeFiles/ExampleFoldPolyalanine.dir/link.txt --verbose=1 make -f tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/build.make tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/build -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/ExampleFoldPolyalanine.dir/ExampleFoldPolyalanine.cpp.o -o ../ExampleFoldPolyalanine -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu:" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 53%] Building CXX object tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -[ 53%] Built target ExampleRigidProtein +[ 57%] Building CXX object tests/CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestLoadVariantRnaAtomNames.cpp" +[ 58%] Linking CXX executable ../TestCompoundTransforms +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestCompoundTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o -o ../TestCompoundTransforms -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 59%] Linking CXX executable ../TestForeignBodyIds +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestForeignBodyIds.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o -o ../TestForeignBodyIds -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 59%] Linking CXX executable ../TestLoneAtomCoordinates +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoneAtomCoordinates.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -o ../TestLoneAtomCoordinates -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 60%] Linking CXX executable ../TestDuMMForces +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestDuMMForces.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o -o ../TestDuMMForces -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 60%] Built target TestCompoundTransforms make -f tests/CMakeFiles/TestBiopolymer.dir/build.make tests/CMakeFiles/TestBiopolymer.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBiopolymer.dir/DependInfo.cmake" --color= @@ -1497,41 +1607,38 @@ Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBiopolymer.dir/depend.internal". Scanning dependencies of target TestBiopolymer make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestBiopolymer.dir/build.make tests/CMakeFiles/TestBiopolymer.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 53%] Built target TestWriteSimtimePdb +[ 61%] Building CXX object tests/CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestBiopolymer.cpp" +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 61%] Built target TestLoneAtomCoordinates make -f tests/CMakeFiles/TestBodyIds.dir/build.make tests/CMakeFiles/TestBodyIds.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBodyIds.dir/DependInfo.cmake" --color= -[ 54%] Building CXX object tests/CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestBiopolymer.cpp" Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBodyIds.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBodyIds.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestBodyIds.dir/depend.internal". -Scanning dependencies of target TestBodyIds -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestBodyIds.dir/build.make tests/CMakeFiles/TestBodyIds.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 54%] Built target MolmodelInstallTestNoViz +[ 61%] Built target TestForeignBodyIds make -f tests/CMakeFiles/TestAtomTargetLocations.dir/build.make tests/CMakeFiles/TestAtomTargetLocations.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestAtomTargetLocations.dir/DependInfo.cmake" --color= -[ 54%] Building CXX object tests/CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestBodyIds.cpp" Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestAtomTargetLocations.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestAtomTargetLocations.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestAtomTargetLocations.dir/depend.internal". -[ 55%] Linking CXX executable ../TestTorsionPartitioner -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestTorsionPartitioner.dir/link.txt --verbose=1 +Scanning dependencies of target TestBodyIds +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f tests/CMakeFiles/TestBodyIds.dir/build.make tests/CMakeFiles/TestBodyIds.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' Scanning dependencies of target TestAtomTargetLocations make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestAtomTargetLocations.dir/build.make tests/CMakeFiles/TestAtomTargetLocations.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestTorsionPartitioner.dir/TestTorsionPartitioner.cpp.o -o ../TestTorsionPartitioner -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 56%] Building CXX object tests/CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o +[ 61%] Building CXX object tests/CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestBodyIds.cpp" +[ 62%] Building CXX object tests/CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestAtomTargetLocations.cpp" -[ 56%] Built target ExampleFoldPolyalanine +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 62%] Built target TestDuMMForces make -f tests/CMakeFiles/TestMethaneCartesian.dir/build.make tests/CMakeFiles/TestMethaneCartesian.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestMethaneCartesian.dir/DependInfo.cmake" --color= @@ -1541,10 +1648,13 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestMethaneCartesian.dir/build.make tests/CMakeFiles/TestMethaneCartesian.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 57%] Building CXX object tests/CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o +[ 63%] Building CXX object tests/CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestMethaneCartesian.cpp" +[ 64%] Linking CXX executable ../TestBiotypeSelfCode +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBiotypeSelfCode.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o -o ../TestBiotypeSelfCode -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 57%] Built target TestTorsionPartitioner +[ 64%] Built target TestBiotypeSelfCode make -f tests/CMakeFiles/TestPartitionerDihedrals.dir/build.make tests/CMakeFiles/TestPartitionerDihedrals.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPartitionerDihedrals.dir/DependInfo.cmake" --color= @@ -1554,64 +1664,64 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestPartitionerDihedrals.dir/build.make tests/CMakeFiles/TestPartitionerDihedrals.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 58%] Building CXX object tests/CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o +[ 65%] Building CXX object tests/CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestPartitionerDihedrals.cpp" -[ 59%] Linking CXX executable ../TestProteinDihedrals -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestProteinDihedrals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestProteinDihedrals.dir/TestProteinDihedrals.cpp.o -o ../TestProteinDihedrals -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 66%] Linking CXX executable ../TestRna +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestRna.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestRna.dir/TestRna.cpp.o -o ../TestRna -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 67%] Linking CXX executable ../TestProtein +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestProtein.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestProtein.dir/TestProtein.cpp.o -o ../TestProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 59%] Built target TestProteinDihedrals +[ 67%] Built target TestRna make -f tests/CMakeFiles/TestSetTorsion.dir/build.make tests/CMakeFiles/TestSetTorsion.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSetTorsion.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSetTorsion.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSetTorsion.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSetTorsion.dir/depend.internal". -Scanning dependencies of target TestSetTorsion -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestSetTorsion.dir/build.make tests/CMakeFiles/TestSetTorsion.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 60%] Building CXX object tests/CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestSetTorsion.cpp" -[ 61%] Linking CXX executable ../TestBiotypeSelfCode -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBiotypeSelfCode.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestBiotypeSelfCode.dir/TestBiotypeSelfCode.cpp.o -o ../TestBiotypeSelfCode -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 62%] Linking CXX executable ../TestGetAtomName -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestGetAtomName.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestGetAtomName.dir/TestGetAtomName.cpp.o -o ../TestGetAtomName -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 62%] Linking CXX executable ../TestLoneAtomCoordinates -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoneAtomCoordinates.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 62%] Built target TestBiotypeSelfCode +[ 67%] Built target TestProtein make -f tests/CMakeFiles/TestNoseHooverThermostat.dir/build.make tests/CMakeFiles/TestNoseHooverThermostat.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNoseHooverThermostat.dir/DependInfo.cmake" --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestLoneAtomCoordinates.dir/TestLoneAtomCoordinates.cpp.o -o ../TestLoneAtomCoordinates -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +Scanning dependencies of target TestSetTorsion +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f tests/CMakeFiles/TestSetTorsion.dir/build.make tests/CMakeFiles/TestSetTorsion.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNoseHooverThermostat.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNoseHooverThermostat.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNoseHooverThermostat.dir/depend.internal". +[ 68%] Building CXX object tests/CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestSetTorsion.cpp" Scanning dependencies of target TestNoseHooverThermostat make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestNoseHooverThermostat.dir/build.make tests/CMakeFiles/TestNoseHooverThermostat.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 62%] Building CXX object tests/CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o +[ 68%] Building CXX object tests/CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestNoseHooverThermostat.cpp" +[ 69%] Linking CXX executable ../TestWriteDefaultPdb +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteDefaultPdb.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o -o ../TestWriteDefaultPdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 62%] Built target TestGetAtomName +[ 69%] Built target TestWriteDefaultPdb make -f tests/CMakeFiles/TestNucleotide2.dir/build.make tests/CMakeFiles/TestNucleotide2.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNucleotide2.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNucleotide2.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNucleotide2.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestNucleotide2.dir/depend.internal". -[ 63%] Linking CXX executable ../TestForeignBodyIds -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestForeignBodyIds.dir/link.txt --verbose=1 Scanning dependencies of target TestNucleotide2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestNucleotide2.dir/build.make tests/CMakeFiles/TestNucleotide2.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestForeignBodyIds.dir/TestForeignBodyIds.cpp.o -o ../TestForeignBodyIds -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 64%] Building CXX object tests/CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o +[ 70%] Building CXX object tests/CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestNucleotide2.cpp" +[ 71%] Linking CXX executable ../TestLoadVariantRnaAtomNames +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoadVariantRnaAtomNames.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -o ../TestLoadVariantRnaAtomNames -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 72%] Linking CXX executable ../TestMethaneCartesian +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMethaneCartesian.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o -o ../TestMethaneCartesian -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 64%] Built target TestLoneAtomCoordinates +[ 72%] Built target TestLoadVariantRnaAtomNames make -f tests/CMakeFiles/TestRiboseMobilizer.dir/build.make tests/CMakeFiles/TestRiboseMobilizer.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestRiboseMobilizer.dir/DependInfo.cmake" --color= @@ -1619,15 +1729,12 @@ Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestRiboseMobilizer.dir/depend.internal". Scanning dependencies of target TestRiboseMobilizer make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 65%] Linking CXX executable ../TestGbsa -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestGbsa.dir/link.txt --verbose=1 make -f tests/CMakeFiles/TestRiboseMobilizer.dir/build.make tests/CMakeFiles/TestRiboseMobilizer.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestGbsa.dir/TestGbsa.cpp.o -o ../TestGbsa -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 66%] Building CXX object tests/CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o +[ 73%] Building CXX object tests/CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestRiboseMobilizer.cpp" make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 66%] Built target TestForeignBodyIds +[ 73%] Built target TestMethaneCartesian make -f tests/CMakeFiles/TestMethanol.dir/build.make tests/CMakeFiles/TestMethanol.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestMethanol.dir/DependInfo.cmake" --color= @@ -1636,14 +1743,14 @@ Scanning dependencies of target TestMethanol make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestMethanol.dir/build.make tests/CMakeFiles/TestMethanol.dir/build -[ 67%] Linking CXX executable ../TestCompoundTransforms make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestCompoundTransforms.dir/link.txt --verbose=1 -[ 68%] Building CXX object tests/CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o +[ 74%] Building CXX object tests/CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestMethanol.cpp" -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestCompoundTransforms.dir/TestCompoundTransforms.cpp.o -o ../TestCompoundTransforms -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 74%] Linking CXX executable ../TestBiopolymer +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBiopolymer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -o ../TestBiopolymer -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 68%] Built target TestGbsa +[ 74%] Built target TestBiopolymer make -f tests/CMakeFiles/TestOxygenMolecule.dir/build.make tests/CMakeFiles/TestOxygenMolecule.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestOxygenMolecule.dir/DependInfo.cmake" --color= @@ -1653,65 +1760,65 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestOxygenMolecule.dir/build.make tests/CMakeFiles/TestOxygenMolecule.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 68%] Building CXX object tests/CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o +[ 74%] Building CXX object tests/CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestOxygenMolecule.cpp" +[ 75%] Linking CXX executable ../TestBodyIds +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBodyIds.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -o ../TestBodyIds -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 76%] Linking CXX executable ../TestAtomTargetLocations +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestAtomTargetLocations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o -o ../TestAtomTargetLocations -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 68%] Built target TestCompoundTransforms +[ 76%] Built target TestBodyIds make -f tests/CMakeFiles/TestPartitioner.dir/build.make tests/CMakeFiles/TestPartitioner.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPartitioner.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPartitioner.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPartitioner.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPartitioner.dir/depend.internal". -Scanning dependencies of target TestPartitioner make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/CMakeFiles/TestPartitioner.dir/build.make tests/CMakeFiles/TestPartitioner.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 69%] Building CXX object tests/CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestPartitioner.cpp" -[ 70%] Linking CXX executable ../TestProtein -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestProtein.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestProtein.dir/TestProtein.cpp.o -o ../TestProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 71%] Linking CXX executable ../TestDuMMForces -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestDuMMForces.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestDuMMForces.dir/TestDuMMForces.cpp.o -o ../TestDuMMForces -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 72%] Linking CXX executable ../TestRna -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestRna.dir/link.txt --verbose=1 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestRna.dir/TestRna.cpp.o -o ../TestRna -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 72%] Built target TestProtein +[ 76%] Built target TestAtomTargetLocations make -f tests/CMakeFiles/TestFitMagnesiums.dir/build.make tests/CMakeFiles/TestFitMagnesiums.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestFitMagnesiums.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestFitMagnesiums.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestFitMagnesiums.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestFitMagnesiums.dir/depend.internal". +Scanning dependencies of target TestPartitioner +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +make -f tests/CMakeFiles/TestPartitioner.dir/build.make tests/CMakeFiles/TestPartitioner.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' Scanning dependencies of target TestFitMagnesiums make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestFitMagnesiums.dir/build.make tests/CMakeFiles/TestFitMagnesiums.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 73%] Building CXX object tests/CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o +[ 77%] Building CXX object tests/CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestPartitioner.cpp" +[ 78%] Building CXX object tests/CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o +[ 78%] Linking CXX executable ../TestEthane +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestEthane.dir/link.txt --verbose=1 cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestFitMagnesiums.cpp" -[ 74%] Linking CXX executable ../TestWriteDefaultPdb -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteDefaultPdb.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteDefaultPdb.dir/TestWriteDefaultPdb.cpp.o -o ../TestWriteDefaultPdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 75%] Linking CXX executable ../TestMethaneCartesian -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMethaneCartesian.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestMethaneCartesian.dir/TestMethaneCartesian.cpp.o -o ../TestMethaneCartesian -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestEthane.dir/TestEthane.cpp.o -o ../TestEthane -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 75%] Built target TestDuMMForces +[ 78%] Built target TestEthane make -f tests/CMakeFiles/TestPositiveControl.dir/build.make tests/CMakeFiles/TestPositiveControl.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPositiveControl.dir/DependInfo.cmake" --color= -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPositiveControl.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPositiveControl.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestPositiveControl.dir/depend.internal". Scanning dependencies of target TestPositiveControl make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestPositiveControl.dir/build.make tests/CMakeFiles/TestPositiveControl.dir/build -[ 75%] Built target TestRna -make -f tests/CMakeFiles/TestMgSolvationEnergy.dir/build.make tests/CMakeFiles/TestMgSolvationEnergy.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 76%] Building CXX object tests/CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o +[ 79%] Building CXX object tests/CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestPositiveControl.cpp" +[ 80%] Linking CXX executable ../TestPartitionerDihedrals +[ 80%] Linking CXX executable ../TestPositiveControl +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPositiveControl.dir/link.txt --verbose=1 +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPartitionerDihedrals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o -o ../TestPositiveControl -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o -o ../TestPartitionerDihedrals -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 80%] Built target TestPositiveControl +make -f tests/CMakeFiles/TestMgSolvationEnergy.dir/build.make tests/CMakeFiles/TestMgSolvationEnergy.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestMgSolvationEnergy.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestMgSolvationEnergy.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestMgSolvationEnergy.dir/depend.internal". @@ -1719,120 +1826,123 @@ Scanning dependencies of target TestMgSolvationEnergy make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestMgSolvationEnergy.dir/build.make tests/CMakeFiles/TestMgSolvationEnergy.dir/build -[ 76%] Linking CXX executable ../TestBiopolymer make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBiopolymer.dir/link.txt --verbose=1 -[ 77%] Building CXX object tests/CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o +[ 81%] Building CXX object tests/CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestMgSolvationEnergy.cpp" -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestBiopolymer.dir/TestBiopolymer.cpp.o -o ../TestBiopolymer -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 77%] Built target TestMethaneCartesian +[ 81%] Built target TestPartitionerDihedrals make -f tests/CMakeFiles/TestSanityDuMM.dir/build.make tests/CMakeFiles/TestSanityDuMM.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSanityDuMM.dir/DependInfo.cmake" --color= -[ 77%] Built target TestWriteDefaultPdb -make -f tests/CMakeFiles/TestSerine.dir/build.make tests/CMakeFiles/TestSerine.dir/depend -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSanityDuMM.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSanityDuMM.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSanityDuMM.dir/depend.internal". Scanning dependencies of target TestSanityDuMM -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/depend.internal". -Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/depend.internal". make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestSanityDuMM.dir/build.make tests/CMakeFiles/TestSanityDuMM.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 78%] Building CXX object tests/CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o +[ 82%] Building CXX object tests/CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestSanityDuMM.cpp" -[ 78%] Linking CXX executable ../TestPositiveControl -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPositiveControl.dir/link.txt --verbose=1 +[ 83%] Linking CXX executable ../TestNoseHooverThermostat +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestNoseHooverThermostat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o -o ../TestNoseHooverThermostat -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 83%] Built target TestNoseHooverThermostat +make -f tests/CMakeFiles/TestSerine.dir/build.make tests/CMakeFiles/TestSerine.dir/depend +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/DependInfo.cmake" --color= +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/depend.internal". +Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/CMakeFiles/TestSerine.dir/depend.internal". Scanning dependencies of target TestSerine make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/CMakeFiles/TestSerine.dir/build.make tests/CMakeFiles/TestSerine.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestPositiveControl.dir/TestPositiveControl.cpp.o -o ../TestPositiveControl -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 79%] Building CXX object tests/CMakeFiles/TestSerine.dir/TestSerine.cpp.o +[ 84%] Building CXX object tests/CMakeFiles/TestSerine.dir/TestSerine.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSerine.dir/TestSerine.cpp.o -c "/build/molmodel-3.0~svn842/tests/TestSerine.cpp" -[ 79%] Built target TestBiopolymer +[ 85%] Linking CXX executable ../TestOxygenMolecule +[ 86%] Linking CXX executable ../TestNucleotide2 +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestOxygenMolecule.dir/link.txt --verbose=1 +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestNucleotide2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o -o ../TestNucleotide2 -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o -o ../TestOxygenMolecule -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 86%] Linking CXX executable ../TestMethanol +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMethanol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o -o ../TestMethanol -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 87%] Linking CXX executable ../TestSetTorsion +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSetTorsion.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -o ../TestSetTorsion -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 88%] Linking CXX executable ../TestRiboseMobilizer +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestRiboseMobilizer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o -o ../TestRiboseMobilizer -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 88%] Built target TestOxygenMolecule make -f tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/depend +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/DependInfo.cmake" --color= +[ 88%] Built target TestMethanol Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/depend.internal". -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -Scanning dependencies of target RemoveMassCenterDrift -[ 79%] Built target TestPositiveControl -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build.make tests/adhoc/CMakeFiles/TestSimpleProtein.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSimpleProtein.dir/DependInfo.cmake" --color= -make -f tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 80%] Building CXX object tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp" Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSimpleProtein.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSimpleProtein.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSimpleProtein.dir/depend.internal". -Scanning dependencies of target TestSimpleProtein make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -make -f tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build.make tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build -[ 81%] Linking CXX executable ../TestPartitionerDihedrals -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPartitionerDihedrals.dir/link.txt --verbose=1 -[ 82%] Building CXX object tests/adhoc/CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp" -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestPartitionerDihedrals.dir/TestPartitionerDihedrals.cpp.o -o ../TestPartitionerDihedrals -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 83%] Linking CXX executable ../TestBodyIds -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestBodyIds.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestBodyIds.dir/TestBodyIds.cpp.o -o ../TestBodyIds -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +Scanning dependencies of target RemoveMassCenterDrift make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 83%] Built target TestPartitionerDihedrals +make -f tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/build +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 88%] Built target TestNucleotide2 make -f tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/DependInfo.cmake" --color= +Scanning dependencies of target TestSimpleProtein +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 89%] Building CXX object tests/adhoc/CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o +make -f tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build.make tests/adhoc/CMakeFiles/TestSimpleProtein.dir/build +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDrift.cpp" +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/depend.internal". -[ 84%] Linking CXX executable ../TestLoadVariantRnaAtomNames -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestLoadVariantRnaAtomNames.dir/link.txt --verbose=1 +[ 90%] Building CXX object tests/adhoc/CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestSimpleProtein.cpp" make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestLoadVariantRnaAtomNames.dir/TestLoadVariantRnaAtomNames.cpp.o -o ../TestLoadVariantRnaAtomNames -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 Scanning dependencies of target RemoveMassCenterDriftWithOptimizer make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 84%] Built target TestBodyIds make -f tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/build.make tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/build +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 90%] Built target TestRiboseMobilizer make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSerineWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSerineWithViz.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSerineWithViz.dir/DependInfo.cmake" --color= -[ 84%] Building CXX object tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o +[ 90%] Building CXX object tests/adhoc/CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp" +[ 90%] Built target TestSetTorsion +make -f tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build.make tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/depend Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSerineWithViz.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSerineWithViz.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSerineWithViz.dir/depend.internal". +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/DependInfo.cmake" --color= Scanning dependencies of target TestSerineWithViz make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSerineWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSerineWithViz.dir/build -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 85%] Building CXX object tests/adhoc/CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp" -[ 86%] Linking CXX executable ../TestAtomTargetLocations -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestAtomTargetLocations.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestAtomTargetLocations.dir/TestAtomTargetLocations.cpp.o -o ../TestAtomTargetLocations -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 86%] Built target TestLoadVariantRnaAtomNames -make -f tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build.make tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/depend -make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/DependInfo.cmake" --color= Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/DependInfo.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/depend.internal". Dependee "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/depend.internal". +make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 91%] Building CXX object tests/adhoc/CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestSerineWithViz.cpp" Scanning dependencies of target TestWriteLargerPdb make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build.make tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 86%] Building CXX object tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o +[ 91%] Building CXX object tests/adhoc/CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestWriteLargerPdb.cpp" +[ 91%] Linking CXX executable ../TestSanityDuMM +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSanityDuMM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o -o ../TestSanityDuMM -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 86%] Built target TestAtomTargetLocations +[ 91%] Built target TestSanityDuMM make -f tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/build.make tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/DependInfo.cmake" --color= @@ -1842,13 +1952,13 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/build.make tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 87%] Building CXX object tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o +[ 92%] Building CXX object tests/adhoc/CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestEthaneFromSimbody.cpp" -[ 87%] Linking CXX executable ../TestEthane -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestEthane.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestEthane.dir/TestEthane.cpp.o -o ../TestEthane -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 93%] Linking CXX executable ../TestMgSolvationEnergy +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMgSolvationEnergy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o -o ../TestMgSolvationEnergy -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 87%] Built target TestEthane +[ 93%] Built target TestMgSolvationEnergy make -f tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/depend make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" && /usr/bin/cmake -E cmake_depends "Unix Makefiles" "/build/molmodel-3.0~svn842" "/build/molmodel-3.0~svn842/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/DependInfo.cmake" --color= @@ -1858,105 +1968,65 @@ make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' make -f tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/build.make tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/build make[3]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 87%] Building CXX object tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o +[ 93%] Building CXX object tests/adhoc/CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/c++ -DMMDB2_LIB_USAGE -DSimTK_MOLMODEL_AUTHORS=\"Christopher.Bruns_Michael.Sherman\" -DSimTK_MOLMODEL_COPYRIGHT_YEARS=\"2006-12\" -DSimTK_MOLMODEL_LIBRARY_NAME=SimTKmolmodel -DSimTK_MOLMODEL_MAJOR_VERSION=3 -DSimTK_MOLMODEL_MINOR_VERSION=0 -DSimTK_MOLMODEL_PATCH_VERSION=0 -DSimTK_MOLMODEL_SVN_REVISION=\"unknown\" -I"/build/molmodel-3.0~svn842/src" -I"/build/molmodel-3.0~svn842/./include" -isystem /usr/include/simbody -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -o CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o -c "/build/molmodel-3.0~svn842/tests/adhoc/TestSodiumWithViz.cpp" -[ 88%] Linking CXX executable ../TestRiboseMobilizer -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestRiboseMobilizer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestRiboseMobilizer.dir/TestRiboseMobilizer.cpp.o -o ../TestRiboseMobilizer -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 88%] Linking CXX executable ../TestMethanol -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMethanol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestMethanol.dir/TestMethanol.cpp.o -o ../TestMethanol -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 88%] Built target TestRiboseMobilizer -[ 89%] Linking CXX executable ../TestOxygenMolecule -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestOxygenMolecule.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestOxygenMolecule.dir/TestOxygenMolecule.cpp.o -o ../TestOxygenMolecule -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 89%] Built target TestMethanol -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 89%] Built target TestOxygenMolecule -[ 89%] Linking CXX executable ../TestSanityDuMM -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSanityDuMM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSanityDuMM.dir/TestSanityDuMM.cpp.o -o ../TestSanityDuMM -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 90%] Linking CXX executable ../TestSetTorsion -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSetTorsion.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSetTorsion.dir/TestSetTorsion.cpp.o -o ../TestSetTorsion -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 91%] Linking CXX executable ../TestNoseHooverThermostat -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestNoseHooverThermostat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestNoseHooverThermostat.dir/TestNoseHooverThermostat.cpp.o -o ../TestNoseHooverThermostat -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 92%] Linking CXX executable ../TestMgSolvationEnergy -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestMgSolvationEnergy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestMgSolvationEnergy.dir/TestMgSolvationEnergy.cpp.o -o ../TestMgSolvationEnergy -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 92%] Built target TestSanityDuMM -[ 93%] Linking CXX executable ../TestNucleotide2 -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestNucleotide2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestNucleotide2.dir/TestNucleotide2.cpp.o -o ../TestNucleotide2 -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 93%] Built target TestSetTorsion -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 93%] Built target TestMgSolvationEnergy +[ 93%] Linking CXX executable ../TestFitMagnesiums +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestFitMagnesiums.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o -o ../TestFitMagnesiums -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 93%] Built target TestNoseHooverThermostat +[ 93%] Built target TestFitMagnesiums +[ 93%] Linking CXX executable ../TestPartitioner +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPartitioner.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -o ../TestPartitioner -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 93%] Built target TestNucleotide2 +[ 93%] Built target TestPartitioner [ 94%] Linking CXX executable ../TestSerine cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSerine.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSerine.dir/TestSerine.cpp.o -o ../TestSerine -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 94%] Linking CXX executable ../../TestSerineWithViz +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSerineWithViz.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -o ../../TestSerineWithViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' [ 94%] Built target TestSerine -[ 94%] Linking CXX executable ../TestPartitioner -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestPartitioner.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestPartitioner.dir/TestPartitioner.cpp.o -o ../TestPartitioner -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 94%] Built target TestPartitioner +[ 94%] Built target TestSerineWithViz [ 95%] Linking CXX executable ../../TestSodiumWithViz cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSodiumWithViz.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSodiumWithViz.dir/TestSodiumWithViz.cpp.o -o ../../TestSodiumWithViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 95%] Linking CXX executable ../../TestSerineWithViz -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSerineWithViz.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSerineWithViz.dir/TestSerineWithViz.cpp.o -o ../../TestSerineWithViz -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 96%] Linking CXX executable ../../RemoveMassCenterDrift -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/RemoveMassCenterDrift.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -o ../../RemoveMassCenterDrift -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 96%] Linking CXX executable ../TestFitMagnesiums -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestFitMagnesiums.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestFitMagnesiums.dir/TestFitMagnesiums.cpp.o -o ../TestFitMagnesiums -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -[ 97%] Linking CXX executable ../../TestWriteLargerPdb +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[ 95%] Built target TestSodiumWithViz +[ 96%] Linking CXX executable ../../TestWriteLargerPdb cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestWriteLargerPdb.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestWriteLargerPdb.dir/TestWriteLargerPdb.cpp.o -o ../../TestWriteLargerPdb -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 97%] Linking CXX executable ../../RemoveMassCenterDrift +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/RemoveMassCenterDrift.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/RemoveMassCenterDrift.dir/RemoveMassCenterDrift.cpp.o -o ../../RemoveMassCenterDrift -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +[ 98%] Linking CXX executable ../../TestEthaneFromSimbody +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestEthaneFromSimbody.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o -o ../../TestEthaneFromSimbody -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 97%] Built target TestSodiumWithViz -[ 98%] Linking CXX executable ../../TestSimpleProtein -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSimpleProtein.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -o ../../TestSimpleProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 98%] Built target TestSerineWithViz make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' [ 98%] Built target RemoveMassCenterDrift -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 98%] Built target TestFitMagnesiums -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' [ 98%] Built target TestWriteLargerPdb -make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' -[ 98%] Built target TestSimpleProtein -[ 99%] Linking CXX executable ../../TestEthaneFromSimbody -cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestEthaneFromSimbody.dir/link.txt --verbose=1 -[100%] Linking CXX executable ../../RemoveMassCenterDriftWithOptimizer +[ 99%] Linking CXX executable ../../RemoveMassCenterDriftWithOptimizer +[100%] Linking CXX executable ../../TestSimpleProtein cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/link.txt --verbose=1 +cd "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/tests/adhoc" && /usr/bin/cmake -E cmake_link_script CMakeFiles/TestSimpleProtein.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/RemoveMassCenterDriftWithOptimizer.dir/RemoveMassCenterDriftWithOptimizer.cpp.o -o ../../RemoveMassCenterDriftWithOptimizer -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestEthaneFromSimbody.dir/TestEthaneFromSimbody.cpp.o -o ../../TestEthaneFromSimbody -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/molmodel-3.0~svn842=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wl,-z,relro -rdynamic CMakeFiles/TestSimpleProtein.dir/TestSimpleProtein.cpp.o -o ../../TestSimpleProtein -Wl,-rpath,"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" ../../libSimTKmolmodel.so.3.0 /usr/lib/i386-linux-gnu/libSimTKsimbody.so.3.6 /usr/lib/i386-linux-gnu/libSimTKmath.so.3.6 /usr/lib/i386-linux-gnu/libSimTKcommon.so.3.6 -lblas -llapack -lblas -llapack -lpthread -lrt -ldl -lm -lmmdb2 make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[100%] Built target TestEthaneFromSimbody +make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' +[100%] Built target TestSimpleProtein make[3]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' [100%] Built target RemoveMassCenterDriftWithOptimizer -[100%] Built target TestEthaneFromSimbody make[2]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start "/build/molmodel-3.0~svn842/obj-i686-linux-gnu/CMakeFiles" 0 make[1]: Leaving directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/molmodel-3.0\~svn842/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/molmodel-3.0\~svn842/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/molmodel-3.0~svn842/obj-i686-linux-gnu' /usr/bin/cmake -S"/build/molmodel-3.0~svn842" -B"/build/molmodel-3.0~svn842/obj-i686-linux-gnu" --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2084,20 +2154,22 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'libsimtkmolmodel-dev' in '../libsimtkmolmodel-dev_3.0~svn842-2_i386.deb'. -dpkg-deb: building package 'libsimtkmolmodel3.0' in '../libsimtkmolmodel3.0_3.0~svn842-2_i386.deb'. dpkg-deb: building package 'libsimtkmolmodel3.0-dbgsym' in '../libsimtkmolmodel3.0-dbgsym_3.0~svn842-2_i386.deb'. +dpkg-deb: building package 'libsimtkmolmodel3.0' in '../libsimtkmolmodel3.0_3.0~svn842-2_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../molmodel_3.0~svn842-2_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/26336/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/26336/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/56796 and its subdirectories -I: Current time: Wed Jul 6 23:20:04 -12 2022 -I: pbuilder-time-stamp: 1657192804 +I: removing directory /srv/workspace/pbuilder/26336 and its subdirectories +I: Current time: Fri Jun 4 19:06:57 +14 2021 +I: pbuilder-time-stamp: 1622783217