I: pbuilder: network access will be disabled during build I: Current time: Tue Aug 11 09:14:48 +14 2020 I: pbuilder-time-stamp: 1597086888 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bedops_2.4.35+dfsg-1.dsc] I: copying [./bedops_2.4.35+dfsg.orig.tar.xz] I: copying [./bedops_2.4.35+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu May 24 05:54:16 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bedops_2.4.35+dfsg-1.dsc dpkg-source: info: extracting bedops in bedops-2.4.35+dfsg dpkg-source: info: unpacking bedops_2.4.35+dfsg.orig.tar.xz dpkg-source: info: unpacking bedops_2.4.35+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_libs dpkg-source: info: applying hardening.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1595/tmp/hooks/D01_modify_environment starting debug: Running on codethink-sled10-arm64. 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/1595/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1595/tmp/hooks/D02_print_environment starting I: set 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]="0" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=1595 PS4='+ ' 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.Dg8Saxt7PD/pbuilderrc_su59 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Dg8Saxt7PD/b2 --logfile b2/build.log bedops_2.4.35+dfsg-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.4.0-186-generic #216-Ubuntu SMP Wed Jul 1 05:35:21 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 18 2019 bash -rwxr-xr-x 3 root root 34808 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 35576 Mar 1 2019 cat -rwxr-xr-x 1 root root 60256 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 56096 Mar 1 2019 chmod -rwxr-xr-x 1 root root 64368 Mar 1 2019 chown -rwxr-xr-x 1 root root 134632 Mar 1 2019 cp -rwxr-xr-x 1 root root 129536 Jan 18 2019 dash -rwxr-xr-x 1 root root 97136 Mar 1 2019 date -rwxr-xr-x 1 root root 76736 Mar 1 2019 dd -rwxr-xr-x 1 root root 93752 Mar 1 2019 df -rwxr-xr-x 1 root root 138848 Mar 1 2019 dir -rwxr-xr-x 1 root root 75984 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 27256 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 6 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 27 2018 hostname -rwxr-xr-x 1 root root 64472 Mar 1 2019 ln -rwxr-xr-x 1 root root 52544 Jul 27 2018 login -rwxr-xr-x 1 root root 138848 Mar 1 2019 ls -rwxr-xr-x 1 root root 108552 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 76840 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 64480 Mar 1 2019 mknod -rwxr-xr-x 1 root root 39736 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 10 2019 more -rwsr-xr-x 1 root root 47112 Jan 10 2019 mount -rwxr-xr-x 1 root root 14344 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138736 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68440 Mar 1 2019 rm -rwxr-xr-x 1 root root 39624 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 11 09:14 sh -> bash lrwxrwxrwx 1 root root 4 Aug 9 22:26 sh.distrib -> dash -rwxr-xr-x 1 root root 31384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 72480 Mar 1 2019 stty -rwsr-xr-x 1 root root 59424 Jan 10 2019 su -rwxr-xr-x 1 root root 31416 Mar 1 2019 sync -rwxr-xr-x 1 root root 449416 Apr 24 2019 tar -rwxr-xr-x 1 root root 10560 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 88968 Mar 1 2019 touch -rwxr-xr-x 1 root root 27256 Mar 1 2019 true -rwxr-xr-x 1 root root 14264 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 10 2019 umount -rwxr-xr-x 1 root root 31384 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138848 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/1595/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), help2man, libbz2-dev, libjansson-dev, libjs-mathjax, python3-distutils, python3-sphinx, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libjansson-dev; however: Package libjansson-dev is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on python3-distutils; however: Package python3-distutils is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} docutils-common{a} dwz{a} file{a} fonts-mathjax{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libbz2-dev{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libjansson-dev{a} libjansson4{a} libjs-jquery{a} libjs-mathjax{a} libjs-sphinxdoc{a} libjs-underscore{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libpipeline1{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} openssl{a} po-debconf{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-babel{a} python3-certifi{a} python3-chardet{a} python3-distutils{a} python3-docutils{a} python3-idna{a} python3-imagesize{a} python3-jinja2{a} python3-lib2to3{a} python3-markupsafe{a} python3-minimal{a} python3-packaging{a} python3-pkg-resources{a} python3-pygments{a} python3-pyparsing{a} python3-requests{a} python3-roman{a} python3-six{a} python3-sphinx{a} python3-tz{a} python3-urllib3{a} python3.7{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} xml-core{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl javascript-common libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils lynx python3-pil shared-mime-info wget xdg-user-dirs 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 41.8 MB of archives. After unpacking 189 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 liblocale-gettext-perl arm64 1.07-3+b4 [18.8 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libpython3.7-minimal arm64 3.7.3-2+deb10u2 [588 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 python3.7-minimal arm64 3.7.3-2+deb10u2 [1404 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 python3-minimal arm64 3.7.3-1 [36.6 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 libmpdec2 arm64 2.4.2-2 [77.7 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 libpython3.7-stdlib arm64 3.7.3-2+deb10u2 [1641 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 python3.7 arm64 3.7.3-2+deb10u2 [330 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython3-stdlib arm64 3.7.3-1 [20.0 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python3 arm64 3.7.3-1 [61.5 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 sgml-base all 1.29 [14.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 openssl arm64 1.1.1d-0+deb10u3 [823 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 ca-certificates all 20190110 [157 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 docutils-common all 0.14+dfsg-4 [167 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 fonts-mathjax all 2.7.4+dfsg-1 [2209 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 help2man arm64 1.47.8 [177 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 libbz2-dev arm64 1.0.6-9.2~deb10u1 [30.9 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 libjansson4 arm64 2.12-1 [37.5 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 libjansson-dev arm64 2.12-1 [40.7 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libjs-mathjax all 2.7.4+dfsg-1 [5658 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 python3-alabaster all 0.7.8-1 [18.4 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 python3-tz all 2019.1-1 [27.1 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 python3-babel all 2.6.0+dfsg.1-1 [96.7 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 python3-certifi all 2018.8.24-1 [140 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 python3-chardet all 3.0.4-3 [80.5 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 python3-distutils all 3.7.3-1 [142 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 python3-roman all 2.0.0-3 [8768 B] Get: 72 http://deb.debian.org/debian buster/main arm64 python3-docutils all 0.14+dfsg-4 [378 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 python3-idna all 2.6-1 [34.3 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 python3-imagesize all 1.0.0-1 [4960 B] Get: 75 http://deb.debian.org/debian buster/main arm64 python3-markupsafe arm64 1.1.0-1 [14.8 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 python3-jinja2 all 2.10-2 [106 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 python3-six all 1.12.0-1 [15.7 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 python3-packaging all 19.0-1 [20.5 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 python3-pygments all 2.3.1+dfsg-1 [594 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 python3-urllib3 all 1.24.1-1 [97.1 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 python3-requests all 2.21.0-1 [66.9 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 sphinx-common all 1.8.4-1 [500 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 python3-sphinx all 1.8.4-1 [481 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 41.8 MB in 2s (20.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. 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Setting up autotools-dev (20180224.1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up sgml-base (1.29) ... Setting up libmpdec2:arm64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libjansson-dev:arm64 (2.12-1) ... Setting up liblocale-gettext-perl (1.07-3+b4) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libjs-underscore (1.9.1~dfsg-1) ... Setting up libbz2-dev:arm64 (1.0.6-9.2~deb10u1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:arm64 (3.7.3-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up m4 (1.4.18-2) ... Setting up help2man (1.47.8) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libcroco3:arm64 (0.6.12-3) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libpython3-stdlib:arm64 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u2) ... Setting up gettext (0.19.8.1-9) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (1.1.0-1) ... Setting up python3-tz (2019.1-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up python3-roman (2.0.0-3) ... Setting up python3-jinja2 (2.10-2) ... Setting up python3-pygments (2.3.1+dfsg-1) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-certifi (2018.8.24-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up python3-idna (2.6-1) ... Setting up python3-urllib3 (1.24.1-1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-imagesize (1.0.0-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up python3-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up python3-alabaster (0.7.8-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-packaging (19.0-1) ... Setting up python3-chardet (3.0.4-3) ... Setting up python3-requests (2.21.0-1) ... Setting up dh-autoreconf (19) ... Setting up debhelper (12.1.1) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python3-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python3/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python3/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python3-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python3/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/bedops-2.4.35+dfsg/ && 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 bedops dpkg-buildpackage: info: source version 2.4.35+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with sphinxdoc dh_auto_clean make -j8 clean make[1]: Entering directory '/build/bedops-2.4.35+dfsg' make clean -j 8 -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-2.4.35+dfsg' make[2]: warning: -j8 forced in submake: resetting jobserver mode. rm -rf bin rm -rf bin rm -rf bin make -C applications/bed/bedmap/src -f Makefile clean make -C applications/bed/sort-bed/src -f Makefile clean make -C applications/bed/bedops/src -f Makefile clean make -C applications/bed/closestfeats/src -f Makefile clean rm -rf modules make -C applications/bed/bedextract/src -f Makefile clean make -C applications/bed/starch/src -f Makefile clean make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' make -C applications/bed/conversion/src -f Makefile clean make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' rm -rf objects-typical rm -rf objects_typical make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' rm -rf objects_typical rm -rf objects_typical make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' rm -rf ../bin make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' rm -rf objects_typical make[3]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' rm -rf ../lib rm -rf ../bin rm -rf ../bin rm -f ../lib/libstarch_debug.a rm -rf objects make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' rm -f ../lib/libstarch_gprof.a rm -rf ../bin rm -rf ../bin rm -rf *.so *~ rm -rf objects rm -rf ../bin make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' rm -rf ../bin make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' rm -rf third-party/bzip2-1.0.6 rm -f third-party/bzip2 rm -rf third-party/jansson-2.6 rm -f third-party/jansson rm -rf third-party/zlib-1.2.7 rm -f third-party/zlib rm -rf bin make[2]: Leaving directory '/build/bedops-2.4.35+dfsg' make[1]: Leaving directory '/build/bedops-2.4.35+dfsg' dh_clean debian/rules build dh build --with sphinxdoc dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-2.4.35+dfsg' make -j 8 -f system.mk/Makefile.linux make[2]: Entering directory '/build/bedops-2.4.35+dfsg' make[2]: warning: -j8 forced in submake: resetting jobserver mode. #bzcat | tar -x -C third-party #bzcat | tar -x -C third-party #cd third-party/jansson-2.6 && ./configure --prefix=/build/bedops-2.4.35+dfsg/third-party/jansson-2.6 && make && make install && cd /build/bedops-2.4.35+dfsg && rm -f jansson && ln -sf jansson-2.6 third-party/jansson #bzcat | tar -x -C third-party #cd third-party/bzip2-1.0.6 && make libbz2.a && cd /build/bedops-2.4.35+dfsg && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2 #cd third-party/zlib-1.2.7 && ./configure --static && make && cd /build/bedops-2.4.35+dfsg && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib make build -f /build/bedops-2.4.35+dfsg/system.mk/Makefile.linux make[3]: Entering directory '/build/bedops-2.4.35+dfsg' make -C applications/bed/bedmap/src -f Makefile build make -C applications/bed/sort-bed/src -f Makefile build make -C applications/bed/bedops/src -f Makefile build make -C applications/bed/closestfeats/src -f Makefile build make -C applications/bed/bedextract/src -f Makefile build make -C applications/bed/starch/src -f Makefile build make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' mkdir -p objects mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2094:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2096:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( mdSha1BufferLength )); ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2385:105: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2387:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here strncpy(*chr, s, strlen(s) + 1); ~~~~~~^~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here strncpy(*chr, s, strlen(s) + 1); ~~~~~~^~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here strncpy(*chr, s, strlen(s) + 1); ~~~~~~^~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recFilename, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recFilename, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here strncpy(*chr, s, strlen(s) + 1); ~~~~~~^~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here strncpy(*chr, s, strlen(s) + 1); ~~~~~~^~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)': ../../../../interfaces/src/data/starch/starchHelpers.c:330:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:330:87: note: length computed here strncpy(*chr, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*chr, s, strlen(s) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:354:48: note: length computed here strncpy(*chr, s, strlen(s) + 1); ~~~~~~^~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:456:77: note: length computed here strncpy(*remainder, reinterpret_cast( buffer ), strlen(buffer) + 1); ~~~~~~^~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:982:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] } while (currC != EOF); ^ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:856:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:856:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:893:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)': ../../../../interfaces/src/data/starch/starchHelpers.c:1281:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:1281:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recFilename, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:2204:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2204:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:28: warning: 'char* strncat(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:2239:98: note: length computed here strncat(nonCoordLineBuf, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/bedops-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && g++ -o ../bin/bedmap-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchHelpers.c: In function 'int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)': ../../../../interfaces/src/data/starch/starchHelpers.c:3363:28: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchHelpers.c:3363:97: note: length computed here strncpy(prevChromosome, reinterpret_cast( chromosome ), strlen(chromosome) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recFilename, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'void starch::UNSTARCH_printMetadataSignature(const unsigned char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2094:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2096:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( mdSha1BufferLength )); ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2385:105: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ ../../../../interfaces/src/data/starch/unstarchHelpers.c:2387:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); ^ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recFilename, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1542:83: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1569:75: note: length computed here strncpy(elemTok2, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c:1558:75: note: length computed here strncpy(elemTok1, reinterpret_cast( buffer ), strlen(reinterpret_cast( buffer )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:184:32: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:982:24: warning: comparison is always true due to limited range of data type [-Wtype-limits] } while (currC != EOF); ^ mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../.. ../../../../interfaces/src/data/starch/unstarchHelpers.c: In function 'char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)': ../../../../interfaces/src/data/starch/unstarchHelpers.c:2316:40: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf ))); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mkdir -p objects g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../.. mkdir -p ../bin && g++ -o ../bin/bedextract-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp mkdir -p ../bin && g++ -o ../bin/closest-features-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -pedantic -O3 -std=c++11 objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:282:47: note: length computed here strncpy(iter->filename, fn, strlen(fn) + 1); ~~~~~~^~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:297:59: note: length computed here strncpy(iter->signature, signature, strlen(signature) + 1); ~~~~~~^~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers mkdir -p ../bin cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical mkdir -p ../bin cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical mkdir -p ../bin cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical mkdir -p ../bin cp starch-diff.py ../bin/starch-diff-typical mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1844:57: note: length computed here strncpy(recTokBuf, token, strlen(token) + 1); ~~~~~~^~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1860:65: note: length computed here strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1); ~~~~~~^~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:32: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(recFilename, token, strlen(token) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1872:59: note: length computed here strncpy(recFilename, token, strlen(token) + 1); ~~~~~~^~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers ../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function 'int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)': ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1349:50: note: length computed here strncpy(*note, streamNote, strlen(streamNote) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1332:52: note: length computed here strncpy(*cTime, streamCTime, strlen(streamCTime) + 1); ~~~~~~^~~~~~~~~~~~~ mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical make -C applications/bed/conversion/src -f Makefile build make[4]: Entering directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -O3 -iquote"/build/bedops-2.4.35+dfsg/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" convert2bed.c -o ../bin/convert2bed-typical -lpthread mkdir -p ../lib ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../.. starch.c: In function 'int main(int, char**)': starch.c:97:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( type ), ^ starch.c:112:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( type ), ^ starch.c:114:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( kStarchFinalizeTransformTrue ), ^ starch.c:137:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( type ), ^ starch.c:152:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( type ), ^ starch.c:154:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( kStarchFinalizeTransformTrue ), ^ starch.c:182:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( type ), ^ starch.c:185:95: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( bedGeneratePerChrSignatureFlag ), ^ starch.c:186:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( bedHeaderFlag ), ^ starch.c:187:86: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( bedReportProgressFlag ), ^ starch.c:188:89: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( bedReportProgressN )) != STARCH_EXIT_SUCCESS) ^ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::listJSONMetadata(FILE*, FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1219:93: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( getArchiveType() ), ^ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1223:91: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( getArchiveHeaderFlag() ), ^ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1224:96: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( getArchiveShowNewlineFlag() )); ^ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractAllData(const string&, FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1989:102: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( getArchiveHeaderFlag() )) != 0 ) { ^ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:2000:101: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( getArchiveHeaderFlag() )) != 0 ) { ^ g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../.. SortDetails.cpp: In function 'ChromBedData* initializeChromBedData(char*, double*)': SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(chrom->chromName, chromBuf, chromBufLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:249:25: note: length computed here chromBufLen = strlen(chromBuf); // we know >= 1 ~~~~~~^~~~~~~~~~ unstarch.c: In function 'int main(int, char**)': unstarch.c:373:113: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( metadataOffset ), ^ unstarch.c:374:98: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( headerFlag )) != 0) { ^ unstarch.c:394:112: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( metadataOffset ), ^ unstarch.c:395:97: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( headerFlag )) != 0) { ^ unstarch.c:424:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sizeof(starchRevision2HeaderBytes) ), ^ unstarch.c:425:98: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( headerFlag )) != 0) { ^ unstarch.c:445:132: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sizeof(starchRevision2HeaderBytes) ), ^ unstarch.c:446:97: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( headerFlag )) != 0) { ^ unstarch.c:539:80: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_printCompressionType(static_cast( type )); ^ unstarch.c:770:152: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sizeof(starchRevision2HeaderBytes) ), ^ unstarch.c:781:156: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sizeof(starchRevision2HeaderBytes) ), ^ unstarch.c: In function 'void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)': unstarch.c:1287:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ unstarch.c:1289:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( sha1BufferLength )); ^ SortDetails.cpp: In function 'void lexSortBedData(BedData*)': SortDetails.cpp:1327:20: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp:1326:33: note: length computed here chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1 ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'ChromBedData* initializeChromBedData(char*, double*)', inlined from 'int processData(const char**, unsigned int, double, char*, bool, bool)' at SortDetails.cpp:909:59: SortDetails.cpp:250:12: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] strncpy(chrom->chromName, chromBuf, chromBufLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SortDetails.cpp: In function 'int processData(const char**, unsigned int, double, char*, bool, bool)': SortDetails.cpp:249:25: note: length computed here chromBufLen = strlen(chromBuf); // we know >= 1 ~~~~~~^~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchcat.c:6672:5: warning: this use of "defined" may not be portable [-Wexpansion-to-defined] #if CLANG_COMPILER ^~~~~~~~~~~~~~ starchcat.c:6678:5: warning: this use of "defined" may not be portable [-Wexpansion-to-defined] #if CLANG_COMPILER ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/cassert:44, from starchcat.c:33: starchcat.c: In function 'int main(int, char**)': starchcat.c:126:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast( numRecords ) ) ); ^ starchcat.c:127:119: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast( numRecords ) ) ); ^ starchcat.c:128:130: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); ^ starchcat.c:128:162: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast( firstArgc ), static_cast( argc ), const_cast( argv ) ) ); ^ starchcat.c:129:119: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast( numRecords ) ) ); ^ starchcat.c:130:189: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast( mdRecords ), static_cast( numRecords ) ) ); ^ starchcat.c:131:117: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast( numChromosomes ) ) ); ^ starchcat.c:132:168: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); ^ starchcat.c:132:261: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast( mdRecords ), static_cast( numRecords ), const_cast( chromosomes ), static_cast( numChromosomes ) ) ); ^ starchcat.c:133:119: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast( numChromosomes ) ) ); ^ starchcat.c:134:175: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast( summary ), static_cast( numChromosomes ) ) ); ^ starchcat.c:154:108: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:168:108: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:213:104: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast( numRecords ) ) ); ^ starchcat.c:223:112: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast( numRecords ) ) ); ^ mkdir -p ../bin g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../.. starchcat.c: In function 'int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)': starchcat.c:1253:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), ^ starchcat.c:1714:115: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_reverseTransformCoordinates( static_cast( t_lineIdx ), ^ starchcat.c: In function 'int starch::STARCHCAT_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*)': starchcat.c:2284:70: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( inRec->mdOffset ), ^ starchcat.c:2285:66: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( inRec->hFlag )) != 0 ) { ^ starchcat.c:2305:73: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( inRec->mdOffset ), ^ starchcat.c:2306:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( inRec->hFlag )) != 0 ) { ^ starchcat.c:2339:67: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outType ), ^ starchcat.c:2341:81: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( kStarchFinalizeTransformFalse ), ^ starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)': starchcat.c:2921:90: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] if (STARCHCAT2_setupBzip2InputStream(static_cast( inRecIdx ), ^ starchcat.c:3081:116: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( summary->numRecords ), ^ starchcat.c:3220:122: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( flushZStreamFlag ), ^ starchcat.c: In function 'int starch::STARCHCAT_mergeInputRecordsToOutput(starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*)': starchcat.c:3884:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outType ), ^ starchcat.c:3886:101: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( kStarchFinalizeTransformFalse ), ^ In file included from /usr/include/c++/8/cassert:44, from starchcat.c:33: starchcat.c: In function 'int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)': starchcat.c:4007:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:4025:110: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:4052:104: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:4084:73: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( hFlag ), ^ starchcat.c: In function 'int starch::STARCHCAT_freeChromosomeSummaries(starch::ChromosomeSummaries**)': starchcat.c:4142:122: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast( (*chrSums)->numChromosomes )); ^ In file included from /usr/include/c++/8/cassert:44, from starchcat.c:33: starchcat.c: In function 'int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)': starchcat.c:5284:108: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:5311:111: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:5334:111: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:5372:106: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( outputType ), ^ starchcat.c:5407:72: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( hFlag ), ^ starchcat.c:5435:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ starchcat.c:5437:70: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); ^ starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(starch::Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, starch::TransformState*)': starchcat.c:6014:103: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), ^ starchcat.c: In function 'int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(starch::Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, starch::TransformState*)': starchcat.c:6325:107: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] UNSTARCH_reverseTransformCoordinates( static_cast( *t_lineIdxPtr ), ^ starchstrip.c: In function 'void starch::STARCHSTRIP_write_updated_metadata(FILE*)': starchstrip.c:116:85: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ), ^ starchstrip.c:118:70: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers] static_cast( STARCH2_MD_FOOTER_SHA1_LENGTH )); ^ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~^~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from ExtractRows.cpp:43: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1514:82: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1698:86: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1744:40: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1755:45: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1609:40: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1617:45: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1565:86: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentRemainder(char*)', inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~^~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1617:45: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentRemainder(char*)', inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~^~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1465:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1445:22: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1465:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1500:22: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~^~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from ClosestFeature.cpp:38: In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::iterateArchiveMdIter()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentRemainder(char*)', inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~^~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1445:22: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1465:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ starchcat.c: In function 'int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)': starchcat.c:4815:20: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:4815:53: note: length computed here strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)', inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, inlined from 'static bool starch::Starch::isStarch(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, inlined from 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~^~~~~~~~~~~~ In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)', inlined from 'static bool starch::Starch::hasStarchRevision1LegacyHeader(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:634:52, inlined from 'static bool starch::Starch::isStarch(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:698:56, inlined from 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:92:90: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44, from CheckSort.cpp:28: In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ starchcat.c: In function 'int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)': starchcat.c:2892:16: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ starchcat.c:2892:78: note: length computed here strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1); ~~~~~~^~~~~~~ rm -rf objects make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/conversion/src' g++ -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now rm -rf objects make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/starch/src' In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor 'Bed::bed_check_iterator::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory&, const string&, bool) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'Bed::bed_check_iterator Bed::bed_check_iterator::operator++(int) [with BedType = Bed::BasicCoords; long unsigned int SZ = 16]' at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:267:24, inlined from 'int checkSort(const char**, unsigned int)' at CheckSort.cpp:51:28: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function 'int checkSort(const char**, unsigned int)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~^~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42, from Bedops.cpp:41: In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::iterateArchiveMdIter()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -g -O2 -ffile-prefix-map=/build/bedops-2.4.35+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2 ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm -rf objects-typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/sort-bed/src' In member function 'void starch::Starch::setCurrentRemainder(char*)', inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~^~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'const char* starch::Starch::getCurrentChromosome()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130, inlined from 'bool starch::Starch::isEOF()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1445:22: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ In member function 'void starch::Starch::setCurrentChromosome(char*)', inlined from 'void starch::Starch::iterateArchiveMdIter()' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:867:37, inlined from 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1465:37: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'bool starch::Starch::extractBEDLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedextract/src' rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/closestfeats/src' rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedops/src' In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:35: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function 'static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here std::strncpy(_recTokBuf, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1); ~~~~~~~~~~~^~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here std::strncpy(_recFilename, _token, strlen(_token) + 1); ~~~~~~^~~~~~~~ In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39, from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27, from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91, from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31, from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27, from Bedmap.cpp:35: ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'void starch::Starch::setCurrentChromosome(char*)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:880:55: note: length computed here strncpy(currentChromosome, _cC, strlen(_cC) + 1); ~~~~~~^~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::zReadLine()': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1899:118: note: length computed here strncpy(reinterpret_cast( zLineBuf ), reinterpret_cast( zRemainderBuf ), strlen(reinterpret_cast( zRemainderBuf )) + 1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void starch::Starch::setCurrentRemainder(char*)', inlined from 'int starch::Starch::extractLine(std::__cxx11::string&)' at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1796:36: ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:24: warning: 'char* strncpy(char*, const char*, size_t)' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function 'int starch::Starch::extractLine(std::__cxx11::string&)': ../../../../interfaces/general-headers/data/starch/starchApi.hpp:892:61: note: length computed here strncpy(currentRemainder, _remainder, strlen(_remainder) + 1); ~~~~~~^~~~~~~~~~~~ rm -rf objects_typical make[4]: Leaving directory '/build/bedops-2.4.35+dfsg/applications/bed/bedmap/src' make[3]: Leaving directory '/build/bedops-2.4.35+dfsg' make[2]: Leaving directory '/build/bedops-2.4.35+dfsg' make[1]: Leaving directory '/build/bedops-2.4.35+dfsg' dh_auto_test create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with sphinxdoc dh_testroot dh_prep dh_auto_install make -j8 install DESTDIR=/build/bedops-2.4.35\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bedops-2.4.35+dfsg' mkdir -p bin cp applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/wig2starch applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/gtf2bed bin cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates cp applications/bed/bedops/bin/bedops-typical bin/bedops cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract cp applications/bed/starch/bin/starch-typical bin/starch cp applications/bed/starch/bin/unstarch-typical bin/unstarch cp applications/bed/starch/bin/starchcat-typical bin/starchcat cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed make[1]: Leaving directory '/build/bedops-2.4.35+dfsg' debian/rules override_dh_install-arch make[1]: Entering directory '/build/bedops-2.4.35+dfsg' dh_install -a sed -i 's:/bin/tcsh:/usr/bin/tcsh:g' bin/* mv bin/starch bin/bedops-starch mkdir -p debian/bedops/usr/bin/ cp bin/* debian/bedops/usr/bin/ make[1]: Leaving directory '/build/bedops-2.4.35+dfsg' debian/rules override_dh_installdocs-indep make[1]: Entering directory '/build/bedops-2.4.35+dfsg' cd docs && make html make[2]: Entering directory '/build/bedops-2.4.35+dfsg/docs' sphinx-build -b html -d _build/doctrees . _build/html Running Sphinx v1.8.4 making output directory... loading intersphinx inventory from http://docs.python.org/objects.inv... 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The HTML pages are in _build/html. make[2]: Leaving directory '/build/bedops-2.4.35+dfsg/docs' mkdir -p debian/bedops-doc/usr/share/doc/bedops cp -r docs/_build/html debian/bedops-doc/usr/share/doc/bedops find debian/bedops-doc/usr/share/doc/bedops/html/content/usage-examples -type f | xargs sed -i 's;https://cdn[js]*\..*/MathJax.js;../../_static/mathjax.js;g' find debian/bedops-doc/usr/share/doc/bedops/html/content -type f | xargs sed -i 's;https://cdn[js]*\..*//MathJax.js;../_static/mathjax.js;g' find debian/bedops-doc/usr/share/doc/bedops/html -type f | xargs sed -i 's;https://cdn[js]*\..*/MathJax.js;_static/mathjax.js;g' ln -s /usr/share/javascript/mathjax/MathJax.js debian/bedops-doc/usr/share/doc/bedops/html/_static/mathjax.js dh_installdocs -i make[1]: Leaving directory '/build/bedops-2.4.35+dfsg' dh_installdocs -Nbedops-doc dh_sphinxdoc dh_sphinxdoc: ignoring unknown JavaScript code: debian/bedops-doc/usr/share/doc/bedops/html/_static/mathjax.js dh_installchangelogs debian/rules override_dh_installman-arch make[1]: Entering directory '/build/bedops-2.4.35+dfsg' cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.35+dfsg" -o $f.1 ./$f; done help2man: can't get `--help' info from ./bam2bed_gnuParallel help2man: can't get `--help' info from ./bam2bed_sge help2man: can't get `--help' info from ./bam2bed_slurm help2man: can't get `--help' info from ./bam2starch_gnuParallel help2man: can't get `--help' info from ./bam2starch_sge help2man: can't get `--help' info from ./bam2starch_slurm help2man: can't get `--help' info from ./starchcluster_gnuParallel help2man: can't get `--help' info from ./starchcluster_sge help2man: can't get `--help' info from ./starchcluster_slurm dh_installman -a make[1]: Leaving directory '/build/bedops-2.4.35+dfsg' dh_installman -Nbedops dh_perl dh_link dh_strip_nondeterminism debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadatachecksum.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_notelementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_stagger_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_static/logo_with_label_v3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_bedmap_ops.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_unstarch_extractiontime.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_complement_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_padding.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/SNP_DHS_matrix_diseaseSorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_icon.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_difference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_grok_tests.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_mechanism1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_independent_grok.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_inputs.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_symmetricdifference_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_macosx_installer_screen_v2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/BEDOPS_Presentation_starch_efficiency.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedextract_nested_elements.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_all.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starchcluster_mechanism.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_intersect_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_inputs@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_merge_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref1.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_magicbytes.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_merge_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_everything@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_gcc_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_complement_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref2.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_chromosomestreams.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_partition_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_elementof_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/bedops_cygwin_installer_git_screen.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_intersect_sorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref3.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadata.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_chop_ab@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_setops_bedops_elementof_ba@2x.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/performance_bedops_merge_unsorted.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/starch_specification_metadataoffset.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. debian/bedops-doc/usr/share/doc/bedops/html/_images/reference_bedmap_mapref_ref3_padded.png: 1 bytes of garbage after IEND chunk at /usr/share/perl5/File/StripNondeterminism/handlers/png.pm line 155. dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package bedops-doc: substitution variable ${sphinxdoc:Built-Using} unused, but is defined dpkg-gencontrol: warning: package bedops-doc: substitution variable ${sphinxdoc:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.35+dfsg-1_arm64.deb'. dpkg-deb: building package 'bedops-doc' in '../bedops-doc_2.4.35+dfsg-1_all.deb'. dpkg-deb: building package 'bedops' in '../bedops_2.4.35+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bedops_2.4.35+dfsg-1_arm64.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/1595/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1595/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/1595 and its subdirectories I: Current time: Tue Aug 11 09:31:19 +14 2020 I: pbuilder-time-stamp: 1597087879