Sun May 17 06:23:04 UTC 2020 I: starting to build last-align/buster/armhf on jenkins on '2020-05-17 06:22' Sun May 17 06:23:04 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_52/2220/console.log Sun May 17 06:23:04 UTC 2020 I: Downloading source for buster/last-align=963-2 --2020-05-17 06:23:04-- http://deb.debian.org/debian/pool/main/l/last-align/last-align_963-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2049 (2.0K) Saving to: ‘last-align_963-2.dsc’ 0K .. 100% 136M=0s 2020-05-17 06:23:04 (136 MB/s) - ‘last-align_963-2.dsc’ saved [2049/2049] Sun May 17 06:23:04 UTC 2020 I: last-align_963-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: last-align Binary: last-align Architecture: any Version: 963-2 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: http://last.cbrc.jp/ Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/last-align Vcs-Git: https://salsa.debian.org/med-team/last-align.git Testsuite: autopkgtest Testsuite-Triggers: python-pil Build-Depends: debhelper (>= 12~), help2man, python-pil, zlib1g-dev Package-List: last-align deb science optional arch=any Checksums-Sha1: ff194bab0d9d7556e7d3a87212c73f15e6610eaf 398348 last-align_963.orig.tar.xz 6773fc858cbd2e345b7030edda5573271ddeaf78 9584 last-align_963-2.debian.tar.xz Checksums-Sha256: 2f83d5754706477cbeb553b252b102aa25145c5baa4e58d2a70116e1418e81e8 398348 last-align_963.orig.tar.xz 4b019eadf942082a98659c9a9a1abd7b8b63f0c780c83479ae76582cc32ac525 9584 last-align_963-2.debian.tar.xz Files: e9581f7fd6494bfc22be3f96f781c2a2 398348 last-align_963.orig.tar.xz 525e09a36d0beacadd6e1a9f8e87e733 9584 last-align_963-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxAWMcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEOaw//WACPYeU1SX9jgZ7Ae7A3RFIVtr5Fj/49 zkoLLn9oXvLSY33wyT/1/aXLha+WpMJ80vKnjlonWZgBfaA/fbCvrH0sphxbHoXt nPNZlw32zHSIDhob8IDkTGt+kFKjTdAaXsvhA4J67cq86xHCW2mS/vdV9Zv6eBdy QUBgqPHAVP41cl8rDWjqjw8QIi9za/YtZsBBNxNwgnbW4y0/hiVR771TmGpDo7Ce jvPAsnyJYugenhM1KM/Nq3v6EcL8o2e2E6sKgxlDgo+U9Ikr4RqD/z9uJql2Thjt xvCJUG2k5X1SCgWCdCQF+dks4sgrNQ2gpHWuJ5H/IFVINgVoQclyQtF7ioC24AqJ sKe/6jmuYzWYsPL+5Fzw2U3v2f63lDOylq8RZBz8cC/effFaNUcQ6zY1+KCh3s8x 0vvqCkwuSXxN/gQJxQo6OzRYUlh9dpygeZPaqAcIxWyl8kvAZOfAKbPjOpIahdYk WPtbmK3/IMt7tgXQHh5f2orNFEG1dAw8JH7Yct3I6jRox2UabcMdG6nOxDOK7sIS 6j5Q6teHkCD7+3cpXy0wk20a7RFw3y/B5XosMbVuxuCsP8hYAR1Xbp59iLrXE7AR VWcmXUKp9cldpPnBBfaDhd5X2xJNYJ5vbDv8Asb/jsn9n3e7tDxfWquOjLBhofag TvLVU837wyc= =1ylN -----END PGP SIGNATURE----- Sun May 17 06:23:04 UTC 2020 I: Checking whether the package is not for us Sun May 17 06:23:05 UTC 2020 I: Starting 1st build on remote node jtx1c-armhf-rb.debian.net. Sun May 17 06:23:05 UTC 2020 I: Preparing to do remote build '1' on jtx1c-armhf-rb.debian.net. Sun May 17 06:32:45 UTC 2020 I: Deleting $TMPDIR on jtx1c-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat May 16 18:23:11 -12 2020 I: pbuilder-time-stamp: 1589696591 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 [last-align_963-2.dsc] I: copying [./last-align_963.orig.tar.xz] I: copying [./last-align_963-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jan 16 22:28:23 2019 -12 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 ./last-align_963-2.dsc dpkg-source: info: extracting last-align in last-align-963 dpkg-source: info: unpacking last-align_963.orig.tar.xz dpkg-source: info: unpacking last-align_963-2.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf 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 (>= 12~), help2man, python-pil, 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 ... 18932 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 (>= 12~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on python-pil; however: Package python-pil 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libglib2.0-0{a} libicu63{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblcms2-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libpng16-16{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxml2{a} m4{a} man-db{a} mime-support{a} po-debconf{a} python{a} python-minimal{a} python-pil{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx python-olefile shared-mime-info wget xdg-user-dirs 0 packages upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 26.0 MB of archives. After unpacking 86.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf liblocale-gettext-perl armhf 1.07-3+b4 [18.4 kB] Get: 23 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 26 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 27 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 29 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 30 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 31 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 32 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 33 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 40 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 47 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main armhf help2man armhf 1.47.8 [176 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libimagequant0 armhf 2.12.2-1.1 [27.2 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libjbig0 armhf 2.1-3.1+b2 [28.4 kB] Get: 55 http://deb.debian.org/debian buster/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [112 kB] Get: 56 http://deb.debian.org/debian buster/main armhf liblcms2-2 armhf 2.9-3 [119 kB] Get: 57 http://deb.debian.org/debian buster/main armhf libwebp6 armhf 0.6.1-2 [229 kB] Get: 58 http://deb.debian.org/debian buster/main armhf libtiff5 armhf 4.1.0+git191117-2~deb10u1 [252 kB] Get: 59 http://deb.debian.org/debian buster/main armhf libwebpdemux2 armhf 0.6.1-2 [86.6 kB] Get: 60 http://deb.debian.org/debian buster/main armhf libwebpmux3 armhf 0.6.1-2 [94.1 kB] Get: 61 http://deb.debian.org/debian buster/main armhf python-pil armhf 5.4.1-2+deb10u1 [367 kB] Get: 62 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Fetched 26.0 MB in 3s (8706 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:armhf. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_armhf.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_armhf.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:armhf. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_armhf.deb ... Unpacking libssl1.1:armhf (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_armhf.deb ... Unpacking libexpat1:armhf (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:armhf. Preparing to unpack .../14-libreadline7_7.0-5_armhf.deb ... Unpacking libreadline7:armhf (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:armhf. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:armhf. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython2-stdlib:armhf (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:armhf. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_armhf.deb ... Unpacking libpython-stdlib:armhf (2.7.16-1) ... Setting up libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20430 files and directories currently installed.) Preparing to unpack .../00-python_2.7.16-1_armhf.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-3+b4_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... 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Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up po-debconf (1.0.21) ... Setting up python-pil:armhf (5.4.1-2+deb10u1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... Processing triggers for libc-bin (2.28-10) ... 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/last-align-963/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package last-align dpkg-buildpackage: info: source version 963-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/last-align-963' make[2]: Entering directory '/build/last-align-963/src' rm -f lastdb lastal last-split last-merge-batches last-pair-probs lastdb8 lastal8 last-split8 *.o* */*.o* make[2]: Leaving directory '/build/last-align-963/src' make[1]: Leaving directory '/build/last-align-963' dh_clean debian/rules build make: 'build' is up to date. fakeroot debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/last-align-963' make all CXXFLAGS="-g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11" CFLAGS="-g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security" CPPFLAGS="-Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS" LDFLAGS="-Wl,-z,relro -Wl,-z,now -pthread" make[2]: Entering directory '/build/last-align-963' make[3]: Entering directory '/build/last-align-963/src' g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Alphabet.o Alphabet.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o CyclicSubsetSeed.o CyclicSubsetSeed.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LambdaCalculator.o LambdaCalculator.cc In file included from /usr/include/c++/8/vector:69, from LambdaCalculator.hh:16, from LambdaCalculator.cc:3: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o ScoreMatrix.o ScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetMinimizerFinder.o SubsetMinimizerFinder.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o TantanMasker.o TantanMasker.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o fileMap.o fileMap.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o tantan.o tantan.cc if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LastdbArguments.o LastdbArguments.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o MultiSequence.o MultiSequence.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o MultiSequenceQual.o MultiSequenceQual.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArray.o SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArraySort.o SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o lastdb.o lastdb.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o lastdb Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o tantan.o LastdbArguments.o MultiSequence.o MultiSequenceQual.o SubsetSuffixArray.o SubsetSuffixArraySort.o lastdb.o -lz g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LastalArguments.o LastalArguments.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAligner.o GappedXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAlignerPssm.o GappedXdropAlignerPssm.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAligner2qual.o GappedXdropAligner2qual.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GappedXdropAligner3frame.o GappedXdropAligner3frame.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GeneralizedAffineGapCosts.o GeneralizedAffineGapCosts.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GeneticCode.o GeneticCode.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o GreedyXdropAligner.o GreedyXdropAligner.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o LastEvaluer.o LastEvaluer.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o OneQualityScoreMatrix.o OneQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o QualityPssmMaker.o QualityPssmMaker.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o TwoQualityScoreMatrix.o TwoQualityScoreMatrix.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o gaplessXdrop.o gaplessXdrop.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o gaplessPssmXdrop.o gaplessPssmXdrop.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o gaplessTwoQualityXdrop.o gaplessTwoQualityXdrop.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alignment_evaluer.o alp/sls_alignment_evaluer.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/sls_alignment_evaluer.cpp:44: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~ alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/sls_alignment_evaluer.cpp:44: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~ alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from alp/sls_pvalues.hpp:41, from alp/sls_alignment_evaluer.hpp:39, from alp/sls_alignment_evaluer.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_pvalues.o alp/sls_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp_sim.o alp/sls_alp_sim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp_regression.o alp/sls_alp_regression.cpp In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_regression.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:78:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_regression.cpp:36: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_regression.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In static member function 'static void Sls::alp_reg::find_tetta_general(double (*)(double, void*), void*, double, double, long int, double, std::vector&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In static member function 'static double Sls::alp_reg::median(long int, double*)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_regression.cpp:36: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_regression.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1921:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In static member function 'static double Sls::alp_reg::robust_sum(double*, long int, long int, bool*&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp_data.o alp/sls_alp_data.cpp In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_data.hpp:62, from alp/sls_alp_data.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_data.hpp:62, from alp/sls_alp_data.cpp:36: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_alp_data.hpp:62, from alp/sls_alp_data.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In constructor 'Sls::importance_sampling::importance_sampling(Sls::alp_data*, long int, long int, double, long int, long int**, double*, double*)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_alp.o alp/sls_alp.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_basic.o alp/sls_basic.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstatmatrix.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~ alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatmatrix.cpp:37: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~ alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_localmaxstat.o alp/njn_localmaxstat.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~ alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstat.cpp:42: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~ alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_localmaxstatutil.o alp/njn_localmaxstatutil.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatutil.cpp:37: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~ alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/njn_localmaxstatutil.cpp:37: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~ alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_dynprogprob.o alp/njn_dynprogprob.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_dynprogprobproto.o alp/njn_dynprogprobproto.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_dynprogproblim.o alp/njn_dynprogproblim.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_ioutil.o alp/njn_ioutil.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/njn_random.o alp/njn_random.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_falp_alignment_evaluer.o alp/sls_falp_alignment_evaluer.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/sls_falp_alignment_evaluer.cpp:43: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~ alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/sls_falp_alignment_evaluer.cpp:43: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~ alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from alp/sls_fsa1_pvalues.hpp:41, from alp/sls_falp_alignment_evaluer.hpp:40, from alp/sls_falp_alignment_evaluer.cpp:37: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1_pvalues.o alp/sls_fsa1_pvalues.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1_utils.o alp/sls_fsa1_utils.cpp In file included from /usr/include/c++/8/vector:69, from alp/sls_fsa1_utils.hpp:40, from alp/sls_fsa1_utils.cpp:36: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from alp/sls_fsa1_utils.hpp:40, from alp/sls_fsa1_utils.cpp:36: /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void Sls::FSA_utils::multiply_matrices(const std::vector >&, const std::vector >&, std::vector >&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In static member function 'static void Sls::FSA_utils::multiply_matrix_and_vector(const std::vector >&, const std::vector&, std::vector&)': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1.o alp/sls_fsa1.cpp In file included from alp/njn_matrix.hpp:43, from alp/njn_localmaxstatutil.hpp:39, from alp/sls_fsa1.hpp:45, from alp/sls_fsa1.cpp:36: alp/njn_vector.hpp: In member function 'virtual void Njn::Vector::free2()': alp/njn_vector.hpp:333:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~ alp/njn_vector.hpp:333:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (getM () > 0) delete [] d_vector_p; d_vector_p = 0; ^~~~~~~~~~ In file included from alp/njn_localmaxstatutil.hpp:39, from alp/sls_fsa1.hpp:45, from alp/sls_fsa1.cpp:36: alp/njn_matrix.hpp: In member function 'virtual void Njn::Matrix::free2()': alp/njn_matrix.hpp:600:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~ alp/njn_matrix.hpp:600:54: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (this->getM () > 0) delete [] d_matrix_p; d_matrix_p = 0; ^~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from alp/sls_alp_regression.hpp:43, from alp/sls_fsa1.hpp:39, from alp/sls_fsa1.cpp:36: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from alp/sls_alp_regression.hpp:43, from alp/sls_fsa1.hpp:39, from alp/sls_fsa1.cpp:36: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void Sls::IS1_general_simulation::calculate_weight_W1_for_fixed_lengths_using_recursions(long int, long int, double&, bool, std::vector >*, std::vector >*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_fsa1.hpp:39, from alp/sls_fsa1.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __final_insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1880:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + int(_S_threshold), __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algo.h:61, from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_fsa1.hpp:39, from alp/sls_fsa1.cpp:36: /usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, ^~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from alp/sls_alp_regression.hpp:46, from alp/sls_fsa1.hpp:39, from alp/sls_fsa1.cpp:36: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __introsort_loop(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__cut, __last, __depth_limit, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In static member function 'static void Sls::test::calculate_ungapped_lambda(long int, double*, double*, long int**, double&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In static member function 'static void Sls::test::calculate_ungapped_lambda_general(double (*)(double, void*), void*, double&)': /usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__introsort_loop(__first, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__lg(__last - __first) * 2, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1971:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__final_insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from alp/sls_alp_regression.hpp:43, from alp/sls_fsa1.hpp:39, from alp/sls_fsa1.cpp:36: /usr/include/c++/8/bits/stl_vector.h: In member function 'void Sls::test::FSA_IS(bool, long int, long int, const long int*, const long int* const*, const double*, const double*, long int, long int, long int, long int, long int, long int, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, double, double, bool, double, double, long int, long int, long int, bool, bool, double, Sls::FALP_set_of_parameters&, Sls::par_test1_type*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -c -o alp/sls_fsa1_parameters.o alp/sls_fsa1_parameters.cpp g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Alignment.o Alignment.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o AlignmentPot.o AlignmentPot.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o AlignmentWrite.o AlignmentWrite.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Centroid.o Centroid.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o DiagonalTable.o DiagonalTable.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SegmentPair.o SegmentPair.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SegmentPairPot.o SegmentPairPot.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArraySearch.o SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o lastal.o lastal.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o lastal Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GeneralizedAffineGapCosts.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o AlignmentPot.o AlignmentWrite.o Centroid.o DiagonalTable.o MultiSequence.o MultiSequenceQual.o SegmentPair.o SegmentPairPot.o SubsetSuffixArray.o SubsetSuffixArraySearch.o lastal.o -lz g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_linalg.o split/cbrc_linalg.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_unsplit_alignment.o split/cbrc_unsplit_alignment.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/last-split-main.o split/last-split-main.cc g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_split_aligner.o split/cbrc_split_aligner.cc split/cbrc_split_aligner.cc: In member function 'void cbrc::SplitAligner::initSpliceSignals(unsigned int)': split/cbrc_split_aligner.cc:729:14: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if (a.rend > chromEnd - chromBeg) ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from split/cbrc_unsplit_alignment.hh:12, from split/cbrc_split_aligner.hh:7, from split/cbrc_split_aligner.cc:4: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from split/cbrc_unsplit_alignment.hh:12, from split/cbrc_split_aligner.hh:7, from split/cbrc_split_aligner.cc:4: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/last-split.o split/last-split.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o last-split Alphabet.o fileMap.o split/cbrc_linalg.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o split/cbrc_split_aligner.o split/last-split.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -c -o last-merge-batches.o last-merge-batches.c cc -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread -o last-merge-batches last-merge-batches.o g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o last-pair-probs.o last-pair-probs.cc In file included from /usr/include/c++/8/vector:69, from last-pair-probs.hh:28, from last-pair-probs.cc:4: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Alignment}; _Tp = Alignment; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/algorithm:62, from last-pair-probs.cc:9: /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __unguarded_linear_insert(_RandomAccessIterator __last, ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __insertion_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from last-pair-probs.hh:27, from last-pair-probs.cc:4: /usr/include/c++/8/bits/stl_algobase.h: In function '_ForwardIterator std::__lower_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Alignment; _Compare = __gnu_cxx::__ops::_Iter_less_val]': /usr/include/c++/8/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __lower_bound(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:946:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/algorithm:62, from last-pair-probs.cc:9: /usr/include/c++/8/bits/stl_algo.h: In function '_ForwardIterator std::__upper_bound(_ForwardIterator, _ForwardIterator, const _Tp&, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = Alignment; _Compare = __gnu_cxx::__ops::_Val_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __upper_bound(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2039:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__move_merge_adaptive_backward(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator2, _BidirectionalIterator2, _BidirectionalIterator3, _Compare) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Alignment*; _BidirectionalIterator3 = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge_adaptive_backward(_BidirectionalIterator1 __first1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2330:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function '_RandomAccessIterator std::_V2::__rotate(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate(_RandomAccessIterator __first, ^~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_without_buffer(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_without_buffer(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2476:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2501:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__lower_bound(__middle, __last, *__first_cut, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_comp_val(__comp)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2510:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__upper_bound(__first, __middle, *__second_cut, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_comp_iter(__comp)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2518:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __first_cut, __new_middle, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len11, __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2520:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len2 - __len22, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__inplace_stable_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __inplace_stable_sort(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2761:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2766:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2770:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __middle, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2771:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__middle, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2772:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_without_buffer(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ __middle - __first, ~~~~~~~~~~~~~~~~~~~ __last - __middle, ~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function '_BidirectionalIterator1 std::__rotate_adaptive(_BidirectionalIterator1, _BidirectionalIterator1, _BidirectionalIterator1, _Distance, _Distance, _BidirectionalIterator2, _Distance) [with _BidirectionalIterator1 = __gnu_cxx::__normal_iterator >; _BidirectionalIterator2 = Alignment*; _Distance = int]': /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __rotate_adaptive(_BidirectionalIterator1 __first, ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2373:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:1443:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__rotate(__first, __middle, __last, ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_adaptive(_BidirectionalIterator, _BidirectionalIterator, _BidirectionalIterator, _Distance, _Distance, _Pointer, _Distance, _Compare) [with _BidirectionalIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_adaptive(_BidirectionalIterator __first, ^~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2415:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2431:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge_adaptive_backward(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_end, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2431:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2445:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__lower_bound(__middle, __last, *__first_cut, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__iter_comp_val(__comp)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2454:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__upper_bound(__first, __middle, *__second_cut, ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __gnu_cxx::__ops::__val_comp_iter(__comp)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2460:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__rotate_adaptive(__first_cut, __middle, __second_cut, ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size); ~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2463:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __first_cut, __new_middle, __len11, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len22, __buffer, __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2465:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__new_middle, __second_cut, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __len1 - __len11, ~~~~~~~~~~~~~~~~~ __len2 - __len22, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = __gnu_cxx::__normal_iterator >; _OutputIterator = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __move_merge(_InputIterator __first1, _InputIterator __last1, ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function '_OutputIterator std::__move_merge(_InputIterator, _InputIterator, _InputIterator, _InputIterator, _OutputIterator, _Compare) [with _InputIterator = Alignment*; _OutputIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2639:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__merge_sort_with_buffer(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Alignment*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __merge_sort_with_buffer(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2705:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2695:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __first + __chunk_size, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2674:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __result = std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, ~~~~~~~~~~~~~~~~~~~~~~ __first + __two_step, ~~~~~~~~~~~~~~~~~~~~~ __result, __comp); ~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__move_merge(__first, __first + __step_size, ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __first + __step_size, __last, __result, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2682:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2698:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__insertion_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'void std::__stable_sort_adaptive(_RandomAccessIterator, _RandomAccessIterator, _Pointer, _Distance, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Pointer = Alignment*; _Distance = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __stable_sort_adaptive(_RandomAccessIterator __first, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2732:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algo.h:2741:31: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __middle, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2743:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__middle, __last, __buffer, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer_size, __comp); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2748:33: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__first, __middle, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2749:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_sort_with_buffer(__middle, __last, __buffer, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:2751:28: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__merge_adaptive(__first, __middle, __last, ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__middle - __first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _Distance(__last - __middle), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __buffer, __buffer_size, ~~~~~~~~~~~~~~~~~~~~~~~~ __comp); ~~~~~~~ /usr/include/c++/8/bits/stl_algo.h: In function 'bool readBatch(std::istream&, char, double, const std::set >&, std::vector&, std::vector&, std::vector&)': /usr/include/c++/8/bits/stl_algo.h:5004:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__inplace_stable_sort(__first, __last, __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algo.h:5006:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__stable_sort_adaptive(__first, __last, __buf.begin(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _DistanceType(__buf.size()), __comp); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=unsigned -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o last-pair-probs-main.o last-pair-probs-main.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o last-pair-probs last-pair-probs.o last-pair-probs-main.o -lz g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o MultiSequence.o8 MultiSequence.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o MultiSequenceQual.o8 MultiSequenceQual.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArray.o8 SubsetSuffixArray.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArraySort.o8 SubsetSuffixArraySort.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o lastdb.o8 lastdb.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o lastdb8 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o tantan.o LastdbArguments.o MultiSequence.o8 MultiSequenceQual.o8 SubsetSuffixArray.o8 SubsetSuffixArraySort.o8 lastdb.o8 -lz g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Alignment.o8 Alignment.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o AlignmentPot.o8 AlignmentPot.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o AlignmentWrite.o8 AlignmentWrite.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o Centroid.o8 Centroid.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o DiagonalTable.o8 DiagonalTable.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SegmentPair.o8 SegmentPair.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SegmentPairPot.o8 SegmentPairPot.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o SubsetSuffixArraySearch.o8 SubsetSuffixArraySearch.cc g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o lastal.o8 lastal.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o lastal8 Alphabet.o CyclicSubsetSeed.o LambdaCalculator.o ScoreMatrix.o SubsetMinimizerFinder.o TantanMasker.o fileMap.o tantan.o LastalArguments.o GappedXdropAligner.o GappedXdropAlignerPssm.o GappedXdropAligner2qual.o GappedXdropAligner3frame.o GeneralizedAffineGapCosts.o GeneticCode.o GreedyXdropAligner.o LastEvaluer.o OneQualityScoreMatrix.o QualityPssmMaker.o TwoQualityScoreMatrix.o gaplessXdrop.o gaplessPssmXdrop.o gaplessTwoQualityXdrop.o alp/sls_alignment_evaluer.o alp/sls_pvalues.o alp/sls_alp_sim.o alp/sls_alp_regression.o alp/sls_alp_data.o alp/sls_alp.o alp/sls_basic.o alp/njn_localmaxstatmatrix.o alp/njn_localmaxstat.o alp/njn_localmaxstatutil.o alp/njn_dynprogprob.o alp/njn_dynprogprobproto.o alp/njn_dynprogproblim.o alp/njn_ioutil.o alp/njn_random.o alp/sls_falp_alignment_evaluer.o alp/sls_fsa1_pvalues.o alp/sls_fsa1_utils.o alp/sls_fsa1.o alp/sls_fsa1_parameters.o Alignment.o8 AlignmentPot.o8 AlignmentWrite.o8 Centroid.o8 DiagonalTable.o8 MultiSequence.o8 MultiSequenceQual.o8 SegmentPair.o8 SegmentPairPot.o8 SubsetSuffixArray.o8 SubsetSuffixArraySearch.o8 lastal.o8 -lz g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/cbrc_split_aligner.o8 split/cbrc_split_aligner.cc split/cbrc_split_aligner.cc: In member function 'void cbrc::SplitAligner::initSpliceSignals(unsigned int)': split/cbrc_split_aligner.cc:729:14: warning: comparison of integer expressions of different signedness: 'const unsigned int' and 'int' [-Wsign-compare] if (a.rend > chromEnd - chromBeg) ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from split/cbrc_unsplit_alignment.hh:12, from split/cbrc_split_aligner.hh:7, from split/cbrc_split_aligner.cc:4: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from split/cbrc_unsplit_alignment.hh:12, from split/cbrc_split_aligner.hh:7, from split/cbrc_split_aligner.cc:4: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector cbrc::SplitAligner::marginalProbs(unsigned int, unsigned int, unsigned int, unsigned int) const': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ g++ -DLAST_INT_TYPE=size_t -Wdate-time -D_FORTIFY_SOURCE=2 -DHAS_CXX_THREADS -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -I. -c -o split/last-split.o8 split/last-split.cc g++ -g -O2 -ffile-prefix-map=/build/last-align-963=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wcast-qual -Wswitch-enum -Wundef -Wcast-align -Wno-long-long -ansi -pedantic -std=c++11 -Wl,-z,relro -Wl,-z,now -pthread -o last-split8 Alphabet.o fileMap.o split/cbrc_linalg.o split/cbrc_unsplit_alignment.o split/last-split-main.o MultiSequence.o8 split/cbrc_split_aligner.o8 split/last-split.o8 make[3]: Leaving directory '/build/last-align-963/src' make[2]: Leaving directory '/build/last-align-963' make[1]: Leaving directory '/build/last-align-963' dh_auto_test create-stamp debian/debhelper-build-stamp dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/last-align-963' make install prefix=/build/last-align-963/debian/last-align/usr make[2]: Entering directory '/build/last-align-963' make[3]: Entering directory '/build/last-align-963/src' if test -e ../.hg ; \ then echo \"`hg id -n`\" | cmp -s version.hh - || echo \"`hg id -n`\" > version.hh ; \ elif test -e ../.hg_archival.txt ; \ then echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" | cmp -s version.hh - || echo \"`grep latesttagdistance ../.hg_archival.txt | cut -d' ' -f2`\" > version.hh ; \ else test -e version.hh || echo \"UNKNOWN\" > version.hh ; \ fi make[3]: Leaving directory '/build/last-align-963/src' mkdir -p /build/last-align-963/debian/last-align/usr/bin cp src/lastdb src/lastal src/last-split src/last-merge-batches src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8 scripts/* /build/last-align-963/debian/last-align/usr/bin make[2]: Leaving directory '/build/last-align-963' make[1]: Leaving directory '/build/last-align-963' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/last-align-963' dh_installchangelogs ChangeLog.txt make[1]: Leaving directory '/build/last-align-963' dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/last-align-963' dh_installman help2man --no-info --version-string="963" \ --name='make a dotplot, a.k.a. Oxford Grid, of alignments in LAST tabular format' \ /build/last-align-963/scripts/last-dotplot > /build/last-align-963/debian/last-align/usr/share/man/man1//last-dotplot.1 help2man --no-info --version-string="963" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /build/last-align-963/src/lastal > /build/last-align-963/debian/last-align/usr/share/man/man1//lastal.1 help2man --no-info --version-string="963" \ --name="genome-scale comparison of biological sequences" \ --help-option="-h" \ /build/last-align-963/src/lastal8 > /build/last-align-963/debian/last-align/usr/share/man/man1//lastal8.1 #help2man --no-info --version-string="963" \ # --name="genome-scale comparison of biological sequences" \ # --help-option="-h" \ # /build/last-align-963/src/lastdb > /build/last-align-963/debian/last-align/usr/share/man/man1//lastdb.1 help2man --no-info --version-string="963" \ --name="Sort MAF-format alignments by sequence name" \ /build/last-align-963/scripts/maf-sort > /build/last-align-963/debian/last-align/usr/share/man/man1//maf-sort.1 help2man --no-info --version-string="963" \ --name="changes the order of the sequences in MAF-format alignments" \ /build/last-align-963/scripts/maf-swap > /build/last-align-963/debian/last-align/usr/share/man/man1//maf-swap.1 #help2man --no-info --version-string="963" \ # --name="Add extra column with mapping probabilities" \ # /build/last-align-963/scripts/last-map-probs > /build/last-align-963/debian/last-align/usr/share/man/man1//last-map-probs.1 # This script has not enough to put in a manual page. #help2man --no-info --version-string="963" \ # --name="Read files of lastal output, merge corresponding batches, and write them." \ # /build/last-align-963/scripts/last-merge-batches > /build/last-align-963/debian/last-align/usr/share/man/man1//last-merge-batches.1 #help2man --no-info --version-string="963" \ # --name="Clean up MAF-format alignments" \ # /build/last-align-963/scripts/last-reduce-alignments > /build/last-align-963/debian/last-align/usr/share/man/man1//last-reduce-alignments.1 #help2man --no-info --version-string="963" \ # --name='Remove MAF-format alignments which are "dominated" by others' \ # /build/last-align-963/scripts/last-remove-dominated > /build/last-align-963/debian/last-align/usr/share/man/man1//last-remove-dominated.1 help2man --no-info --version-string="963" \ --name='Estimates "split" or "spliced" alignments.' \ /build/last-align-963/src/last-split > /build/last-align-963/debian/last-align/usr/share/man/man1//last-split.1 help2man --no-info --version-string="963" \ --name='Estimates "split" or "spliced" alignments.' \ /build/last-align-963/src/last-split8 > /build/last-align-963/debian/last-align/usr/share/man/man1//last-split8.1 help2man --no-info --version-string="963" \ --name="Join two or more sets of MAF-format multiple alignments" \ /build/last-align-963/scripts/maf-join > /build/last-align-963/debian/last-align/usr/share/man/man1//maf-join.1 help2man --no-info --version-string="963" \ --name="Convert MAF-format alignments to tabular format" \ /build/last-align-963/scripts/maf-convert > /build/last-align-963/debian/last-align/usr/share/man/man1//maf-convert.1 help2man --no-info --version-string="963" \ --name="Read 2 fastq files, and write them interleaved" \ /build/last-align-963/scripts/fastq-interleave > /build/last-align-963/debian/last-align/usr/share/man/man1//fastq-interleave.1 help2man --no-info --version-string="963" \ --name="Read files of lastal output, merge corresponding batches, and write them" \ /build/last-align-963/src/last-merge-batches > /build/last-align-963/debian/last-align/usr/share/man/man1//last-merge-batches.1 #help2man --no-info --version-string="963" \ # --name="Read alignments of paired DNA reads to a genome, and do estimations" \ # /build/last-align-963/src/last-pair-probs > /build/last-align-963/debian/last-align/usr/share/man/man1//last-pair-probs.1 help2man --no-info --version-string="963" \ --name="Get alignments that have a segment with score >= threshold, with gentle masking of lowercase letters" \ /build/last-align-963/scripts/last-postmask > /build/last-align-963/debian/last-align/usr/share/man/man1//last-postmask.1 help2man --no-info --version-string="963" \ --name="Try to find suitable score parameters for aligning the given sequences" \ /build/last-align-963/scripts/last-train > /build/last-align-963/debian/last-align/usr/share/man/man1//last-train.1 make[1]: Leaving directory '/build/last-align-963' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split8 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal8 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb8 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastdb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-split contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/lastal contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/last-align/usr/bin/last-pair-probs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'last-align-dbgsym' in '../last-align-dbgsym_963-2_armhf.deb'. dpkg-deb: building package 'last-align' in '../last-align_963-2_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../last-align_963-2_armhf.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: 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/12719 and its subdirectories I: Current time: Sat May 16 18:32:26 -12 2020 I: pbuilder-time-stamp: 1589697146 Sun May 17 06:32:48 UTC 2020 I: 1st build successful. Starting 2nd build on remote node odu3a-armhf-rb.debian.net. Sun May 17 06:32:48 UTC 2020 I: Preparing to do remote build '2' on odu3a-armhf-rb.debian.net. Sun May 17 06:50:54 UTC 2020 I: Deleting $TMPDIR on odu3a-armhf-rb.debian.net. Sun May 17 06:50:57 UTC 2020 I: last-align_963-2_armhf.changes: Format: 1.8 Date: Thu, 17 Jan 2019 11:21:30 +0100 Source: last-align Binary: last-align last-align-dbgsym Architecture: armhf Version: 963-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: last-align - genome-scale comparison of biological sequences Closes: 919556 Changes: last-align (963-2) unstable; urgency=medium . * Example files are not compressed any more - adapt autopkgtest Closes: #919556 Checksums-Sha1: 7875763b3b80debdc9921c8638d0b9a8756bf9aa 9392436 last-align-dbgsym_963-2_armhf.deb 06b15071a3c6f0e1ebd0414b85d997c676a1232b 5436 last-align_963-2_armhf.buildinfo df486efc2cd783fec1dbb636a471cc2d10cf174d 590696 last-align_963-2_armhf.deb Checksums-Sha256: fcf45db7778f4bebe5be3afaf47992ca46a5e32b09d8aaf0a24965182f1d4322 9392436 last-align-dbgsym_963-2_armhf.deb 3789bce219a624b92b7dea71dca7ef5bd00cb9ff0fe5462717469025779e78e4 5436 last-align_963-2_armhf.buildinfo 7778ac0b95c230a80dd9e96198588bed6cc86bf5eb90a455962d7dd9772bf377 590696 last-align_963-2_armhf.deb Files: 850b131cf0ae035178ff1d4db6b3c999 9392436 debug optional last-align-dbgsym_963-2_armhf.deb 56d19012cea25cf88632ca184027a9fe 5436 science optional last-align_963-2_armhf.buildinfo 27aaffee260dc27235d44dc2d0cbddc7 590696 science optional last-align_963-2_armhf.deb Sun May 17 06:50:59 UTC 2020 I: diffoscope 144 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.Ovx8QeyBpM/last-align_963-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.Ovx8QeyBpM/last-align_963-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.Ovx8QeyBpM/last-align_963-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.Ovx8QeyBpM/b1/last-align_963-2_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.Ovx8QeyBpM/b2/last-align_963-2_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.367s) 0.367s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.141s) 0.141s 10 calls diffoscope.comparators.binary.FilesystemFile Sun May 17 06:51:01 UTC 2020 I: diffoscope 144 found no differences in the changes files, and a .buildinfo file also exists. Sun May 17 06:51:01 UTC 2020 I: last-align from buster built successfully and reproducibly on armhf. Sun May 17 06:51:03 UTC 2020 I: Submitting .buildinfo files to external archives: Sun May 17 06:51:03 UTC 2020 I: Submitting 8.0K b1/last-align_963-2_armhf.buildinfo.asc Sun May 17 06:51:03 UTC 2020 I: Submitting 8.0K b2/last-align_963-2_armhf.buildinfo.asc Sun May 17 06:51:04 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun May 17 06:51:04 UTC 2020 I: Done submitting .buildinfo files. Sun May 17 06:51:04 UTC 2020 I: Removing signed last-align_963-2_armhf.buildinfo.asc files: removed './b1/last-align_963-2_armhf.buildinfo.asc' removed './b2/last-align_963-2_armhf.buildinfo.asc'