Sat Oct 31 16:37:58 UTC 2020 I: starting to build segemehl/buster/armhf on jenkins on '2020-10-31 16:37'
Sat Oct 31 16:37:58 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_37/3393/console.log
Sat Oct 31 16:37:58 UTC 2020 I: Downloading source for buster/segemehl=0.3.4-1
--2020-10-31 16:37:58-- http://deb.debian.org/debian/pool/main/s/segemehl/segemehl_0.3.4-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2000 (2.0K)
Saving to: ‘segemehl_0.3.4-1.dsc’
0K . 100% 363M=0s
2020-10-31 16:37:58 (363 MB/s) - ‘segemehl_0.3.4-1.dsc’ saved [2000/2000]
Sat Oct 31 16:37:58 UTC 2020 I: segemehl_0.3.4-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: segemehl
Binary: segemehl
Architecture: any
Version: 0.3.4-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://www.bioinf.uni-leipzig.de/Software/segemehl/
Standards-Version: 4.3.0
Vcs-Browser: https://salsa.debian.org/med-team/segemehl
Vcs-Git: https://salsa.debian.org/med-team/segemehl.git
Build-Depends: debhelper (>= 12~), pkg-config, libhts-dev, libncurses-dev, zlib1g-dev
Package-List:
segemehl deb science optional arch=any
Checksums-Sha1:
676d5d11382bc053fb1d5ce90bfbac1aeb26a9d9 244092 segemehl_0.3.4.orig.tar.xz
d54146ab2200a9276f993ed4af95ae36d10db41a 5536 segemehl_0.3.4-1.debian.tar.xz
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e498fb23e36d45a0d0035105812a747ca901af366d07dde431c25a49ee28abbc 244092 segemehl_0.3.4.orig.tar.xz
9d4c7b7e112ea0f4997f03e1690503789c522bb03512f265d3412f53f10ef06a 5536 segemehl_0.3.4-1.debian.tar.xz
Files:
7cbc36ce09d0328089db4031663744a5 244092 segemehl_0.3.4.orig.tar.xz
9185df13b13b65722ac4f53263224bd9 5536 segemehl_0.3.4-1.debian.tar.xz
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Sat Oct 31 16:37:58 UTC 2020 I: Checking whether the package is not for us
Sat Oct 31 16:37:58 UTC 2020 I: Starting 1st build on remote node p64c-armhf-rb.debian.net.
Sat Oct 31 16:37:58 UTC 2020 I: Preparing to do remote build '1' on p64c-armhf-rb.debian.net.
Sat Oct 31 17:01:30 UTC 2020 I: Deleting $TMPDIR on p64c-armhf-rb.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Oct 31 04:38:18 -12 2020
I: pbuilder-time-stamp: 1604162298
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 [segemehl_0.3.4-1.dsc]
I: copying [./segemehl_0.3.4.orig.tar.xz]
I: copying [./segemehl_0.3.4-1.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 Fri Jan 11 09:54:08 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 ./segemehl_0.3.4-1.dsc
dpkg-source: info: extracting segemehl in segemehl-0.3.4
dpkg-source: info: unpacking segemehl_0.3.4.orig.tar.xz
dpkg-source: info: unpacking segemehl_0.3.4-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying rpath.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/7111/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3'
DISTRIBUTION=''
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='8011b681cfa847bc9b0572d9cc14981d'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='7111'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/pbuilderrc_ZFZz --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/b1 --logfile b1/build.log segemehl_0.3.4-1.dsc'
SUDO_GID='115'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:8000/'
I: uname -a
Linux p64c 4.19.0-12-arm64 #1 SMP Debian 4.19.152-1 (2020-10-18) aarch64 GNU/Linux
I: ls -l /bin
total 3328
-rwxr-xr-x 1 root root 767656 Apr 17 2019 bash
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2
-rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore
-rwxr-xr-x 1 root root 22432 Feb 28 2019 cat
-rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp
-rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod
-rwxr-xr-x 1 root root 42972 Feb 28 2019 chown
-rwxr-xr-x 1 root root 88376 Feb 28 2019 cp
-rwxr-xr-x 1 root root 75516 Jan 17 2019 dash
-rwxr-xr-x 1 root root 71648 Feb 28 2019 date
-rwxr-xr-x 1 root root 51212 Feb 28 2019 dd
-rwxr-xr-x 1 root root 55672 Feb 28 2019 df
-rwxr-xr-x 1 root root 88444 Feb 28 2019 dir
-rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg
lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname
-rwxr-xr-x 1 root root 22364 Feb 28 2019 echo
-rwxr-xr-x 1 root root 28 Jan 7 2019 egrep
-rwxr-xr-x 1 root root 18260 Feb 28 2019 false
-rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep
-rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt
-rwsr-xr-x 1 root root 21980 Apr 22 2020 fusermount
-rwxr-xr-x 1 root root 124508 Jan 7 2019 grep
-rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip
-rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe
-rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip
-rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname
-rwxr-xr-x 1 root root 43044 Feb 28 2019 ln
-rwxr-xr-x 1 root root 34932 Jul 26 2018 login
-rwxr-xr-x 1 root root 88444 Feb 28 2019 ls
-rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk
-rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir
-rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod
-rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp
-rwxr-xr-x 1 root root 26024 Jan 9 2019 more
-rwsr-xr-x 1 root root 34268 Jan 9 2019 mount
-rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint
-rwxr-xr-x 1 root root 84284 Feb 28 2019 mv
lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd
lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash
-rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink
-rwxr-xr-x 1 root root 42968 Feb 28 2019 rm
-rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir
-rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts
-rwxr-xr-x 1 root root 76012 Dec 22 2018 sed
lrwxrwxrwx 1 root root 4 Oct 20 20:31 sh -> dash
-rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep
-rwxr-xr-x 1 root root 51124 Feb 28 2019 stty
-rwsr-xr-x 1 root root 42472 Jan 9 2019 su
-rwxr-xr-x 1 root root 22392 Feb 28 2019 sync
-rwxr-xr-x 1 root root 283324 Apr 23 2019 tar
-rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile
-rwxr-xr-x 1 root root 63464 Feb 28 2019 touch
-rwxr-xr-x 1 root root 18260 Feb 28 2019 true
-rwxr-xr-x 1 root root 9636 Apr 22 2020 ulockmgr_server
-rwsr-xr-x 1 root root 21976 Jan 9 2019 umount
-rwxr-xr-x 1 root root 22380 Feb 28 2019 uname
-rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress
-rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir
-rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl
-rwxr-xr-x 1 root root 946 Jan 21 2019 which
lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat
-rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp
-rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff
-rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep
-rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep
-rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce
-rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep
-rwxr-xr-x 1 root root 2205 Jan 5 2019 zless
-rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore
-rwxr-xr-x 1 root root 4552 Jan 5 2019 znew
I: user script /srv/workspace/pbuilder/7111/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
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~), pkg-config, libhts-dev, libncurses-dev, 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 pkg-config; however:
Package pkg-config is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libncurses-dev; however:
Package libncurses-dev 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} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libcurl3-gnutls{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts2{a} libicu63{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pkg-config{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded.
Need to get 26.6 MB of archives. After unpacking 77.8 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 sensible-utils all 0.0.12 [15.8 kB]
Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB]
Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB]
Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB]
Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB]
Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB]
Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB]
Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB]
Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB]
Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB]
Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB]
Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB]
Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB]
Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB]
Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB]
Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB]
Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB]
Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB]
Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB]
Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB]
Get: 34 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB]
Get: 35 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB]
Get: 36 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB]
Get: 37 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB]
Get: 38 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB]
Get: 39 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB]
Get: 40 http://deb.debian.org/debian buster/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-1+deb10u1 [67.4 kB]
Get: 41 http://deb.debian.org/debian buster/main armhf libsasl2-2 armhf 2.1.27+dfsg-1+deb10u1 [98.9 kB]
Get: 42 http://deb.debian.org/debian buster/main armhf libldap-common all 2.4.47+dfsg-3+deb10u2 [89.7 kB]
Get: 43 http://deb.debian.org/debian buster/main armhf libldap-2.4-2 armhf 2.4.47+dfsg-3+deb10u2 [202 kB]
Get: 44 http://deb.debian.org/debian buster/main armhf libnghttp2-14 armhf 1.36.0-2+deb10u1 [74.4 kB]
Get: 45 http://deb.debian.org/debian buster/main armhf libpsl5 armhf 0.20.2-2 [52.4 kB]
Get: 46 http://deb.debian.org/debian buster/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.9 kB]
Get: 47 http://deb.debian.org/debian buster/main armhf libssh2-1 armhf 1.8.0-2.1 [129 kB]
Get: 48 http://deb.debian.org/debian buster/main armhf libcurl3-gnutls armhf 7.64.0-4+deb10u1 [295 kB]
Get: 49 http://deb.debian.org/debian buster/main armhf libdeflate0 armhf 1.2-1 [46.4 kB]
Get: 50 http://deb.debian.org/debian buster/main armhf libhts2 armhf 1.9-11 [261 kB]
Get: 51 http://deb.debian.org/debian buster/main armhf liblzma-dev armhf 5.2.4-1 [204 kB]
Get: 52 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB]
Get: 53 http://deb.debian.org/debian buster/main armhf libhts-dev armhf 1.9-11 [4289 kB]
Get: 54 http://deb.debian.org/debian buster/main armhf libncurses-dev armhf 6.1+20181013-2+deb10u2 [295 kB]
Get: 55 http://deb.debian.org/debian buster/main armhf pkg-config armhf 0.29-6 [60.7 kB]
Fetched 26.6 MB in 9s (2962 kB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libbsd0:armhf.
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Reading package lists...
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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/segemehl-0.3.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
dpkg-buildpackage: info: source package segemehl
dpkg-buildpackage: info: source version 0.3.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
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/segemehl-0.3.4'
Cleaning...
rm -f -r build segemehl haarz
make[1]: Leaving directory '/build/segemehl-0.3.4'
dh_clean
debian/rules build
dh build
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/segemehl-0.3.4'
dh_auto_build -- all
make -j3 "INSTALL=install --strip-program=true" all
make[2]: Entering directory '/build/segemehl-0.3.4'
Building... library for source build/gzidx.o
Building... library for source build/annotation.o
Building... library for source build/mappingqual.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/annotation.o libs/annotation.c
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/gzidx.o libs/gzidx.c
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mappingqual.o libs/mappingqual.c
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationitemDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:149:23: note: in expansion of macro 'FREEMEMORY'
if(item->chromname) FREEMEMORY(space, item->chromname);
^~~~~~~~~~
libs/annotation.c:149:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->chromname) FREEMEMORY(space, item->chromname);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:150:18: note: in expansion of macro 'FREEMEMORY'
if(item->name) FREEMEMORY(space, item->name);
^~~~~~~~~~
libs/annotation.c:150:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->name) FREEMEMORY(space, item->name);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:151:21: note: in expansion of macro 'FREEMEMORY'
if(item->itemRgb) FREEMEMORY(space, item->itemRgb);
^~~~~~~~~~
libs/annotation.c:151:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->itemRgb) FREEMEMORY(space, item->itemRgb);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:152:24: note: in expansion of macro 'FREEMEMORY'
if(item->blockSizes) FREEMEMORY(space, item->blockSizes);
^~~~~~~~~~
libs/annotation.c:152:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->blockSizes) FREEMEMORY(space, item->blockSizes);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:153:25: note: in expansion of macro 'FREEMEMORY'
if(item->blockStarts) FREEMEMORY(space, item->blockStarts);
^~~~~~~~~~
libs/annotation.c:153:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->blockStarts) FREEMEMORY(space, item->blockStarts);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:154:26: note: in expansion of macro 'FREEMEMORY'
if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs);
^~~~~~~~~~
libs/annotation.c:154:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->blockRefseqs) FREEMEMORY(space, item->blockRefseqs);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:155:26: note: in expansion of macro 'FREEMEMORY'
if(item->blockStrands) FREEMEMORY(space, item->blockStrands);
^~~~~~~~~~
libs/annotation.c:155:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->blockStrands) FREEMEMORY(space, item->blockStrands);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:156:20: note: in expansion of macro 'FREEMEMORY'
if(item->source) FREEMEMORY(space, item->source);
^~~~~~~~~~
libs/annotation.c:156:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(item->source) FREEMEMORY(space, item->source);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationtrackDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:409:24: note: in expansion of macro 'FREEMEMORY'
if(track->trackname) FREEMEMORY(space, track->trackname);
^~~~~~~~~~
libs/annotation.c:409:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(track->trackname) FREEMEMORY(space, track->trackname);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:410:23: note: in expansion of macro 'FREEMEMORY'
if(track->filename) FREEMEMORY(space, track->filename);
^~~~~~~~~~
libs/annotation.c:410:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(track->filename) FREEMEMORY(space, track->filename);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:411:26: note: in expansion of macro 'FREEMEMORY'
if(track->description) FREEMEMORY(space, track->description);
^~~~~~~~~~
libs/annotation.c:411:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(track->description) FREEMEMORY(space, track->description);
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:418:20: note: in expansion of macro 'FREEMEMORY'
if(track->items) FREEMEMORY(space, track->items) ;
^~~~~~~~~~
libs/annotation.c:418:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(track->items) FREEMEMORY(space, track->items) ;
^~
In file included from include/stringutils.h:27,
from libs/annotation.c:29:
libs/annotation.c: In function 'bl_annotationmultitrackDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/annotation.c:455:20: note: in expansion of macro 'FREEMEMORY'
if(track->items) FREEMEMORY(space, track->items) ;
^~~~~~~~~~
libs/annotation.c:455:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(track->items) FREEMEMORY(space, track->items) ;
^~
Building... library for source build/segemehl.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/segemehl.o libs/segemehl.c
Building... library for source build/kdseed.o
Building... library for source build/memory.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/kdseed.o libs/kdseed.c
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/memory.o libs/memory.c
Building... library for source build/samio.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/samio.o libs/samio.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestructTag':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:102:15: note: in expansion of macro 'FREEMEMORY'
if(kv->tag) FREEMEMORY(NULL, kv->tag);
^~~~~~~~~~
libs/samio.c:102:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(kv->tag) FREEMEMORY(NULL, kv->tag);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:103:15: note: in expansion of macro 'FREEMEMORY'
if(kv->val) FREEMEMORY(NULL, kv->val);
^~~~~~~~~~
libs/samio.c:103:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(kv->val) FREEMEMORY(NULL, kv->val);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:104:16: note: in expansion of macro 'FREEMEMORY'
if(kv->type) FREEMEMORY(NULL, kv->type);
^~~~~~~~~~
libs/samio.c:104:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(kv->type) FREEMEMORY(NULL, kv->type);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:105:15: note: in expansion of macro 'FREEMEMORY'
if(kv->key) FREEMEMORY(NULL, kv->key);
^~~~~~~~~~
libs/samio.c:105:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(kv->key) FREEMEMORY(NULL, kv->key);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
libs/samio.c: In function 'bl_samDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:112:21: note: in expansion of macro 'FREEMEMORY'
if(samrec->qname) FREEMEMORY(NULL, samrec->qname);
^~~~~~~~~~
libs/samio.c:112:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->qname) FREEMEMORY(NULL, samrec->qname);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:113:21: note: in expansion of macro 'FREEMEMORY'
if(samrec->rname) FREEMEMORY(NULL, samrec->rname);
^~~~~~~~~~
libs/samio.c:113:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->rname) FREEMEMORY(NULL, samrec->rname);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:114:21: note: in expansion of macro 'FREEMEMORY'
if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar);
^~~~~~~~~~
libs/samio.c:114:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->cigar) FREEMEMORY(NULL, samrec->cigar);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:115:21: note: in expansion of macro 'FREEMEMORY'
if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext);
^~~~~~~~~~
libs/samio.c:115:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->rnext) FREEMEMORY(NULL, samrec->rnext);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:116:21: note: in expansion of macro 'FREEMEMORY'
if(samrec->seq) FREEMEMORY(NULL, samrec->seq);
^~~~~~~~~~
libs/samio.c:116:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->seq) FREEMEMORY(NULL, samrec->seq);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:117:21: note: in expansion of macro 'FREEMEMORY'
if(samrec->qual) FREEMEMORY(NULL, samrec->qual);
^~~~~~~~~~
libs/samio.c:117:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->qual) FREEMEMORY(NULL, samrec->qual);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from libs/samio.c:33:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/samio.c:121:20: note: in expansion of macro 'FREEMEMORY'
if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
^~~~~~~~~~
libs/samio.c:121:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(samrec->tags) FREEMEMORY(NULL, samrec->tags);
^~
Building... library for source build/brendel.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/brendel.o libs/brendel.c
Building... library for source build/merge.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/merge.o libs/merge.c
In file included from include/stringutils.h:27,
from libs/merge.c:34:
libs/merge.c: In function 'se_mergeWorker':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/merge.c:1096:20: note: in expansion of macro 'FREEMEMORY'
if(curkey) FREEMEMORY(NULL, curkey);
^~~~~~~~~~
libs/merge.c:1096:9: note: some parts of macro expansion are not guarded by this 'if' clause
if(curkey) FREEMEMORY(NULL, curkey);
^~
In file included from include/stringutils.h:27,
from libs/merge.c:34:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/merge.c:1216:26: note: in expansion of macro 'FREEMEMORY'
if(!reads && curkey) FREEMEMORY(NULL, curkey);
^~~~~~~~~~
libs/merge.c:1216:5: note: some parts of macro expansion are not guarded by this 'if' clause
if(!reads && curkey) FREEMEMORY(NULL, curkey);
^~
Building... library for source build/bedfiles.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bedfiles.o libs/bedfiles.c
Building... library for source build/radixsort.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/radixsort.o libs/radixsort.c
Building... library for source build/bamio.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bamio.o libs/bamio.c
Building... library for source build/fileio.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/fileio.o libs/fileio.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from include/samio.h:23,
from include/bamio.h:21,
from libs/bamio.c:32:
libs/bamio.c: In function 'bl_bamCrossSectionDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/bamio.c:468:20: note: in expansion of macro 'FREEMEMORY'
if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
^~~~~~~~~~
libs/bamio.c:468:5: note: some parts of macro expansion are not guarded by this 'if' clause
if(cs->x[k].n) FREEMEMORY(NULL, cs->x[k].d);
^~
Building... library for source build/nw.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/nw.o libs/nw.c
Building... library for source build/vqueue.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vqueue.o libs/vqueue.c
Building... library for source build/haarz.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/haarz.o libs/haarz.c
Building... library for source build/matealign.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/matealign.o libs/matealign.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/locus.h:41,
from include/mapfrag.h:39,
from libs/matealign.c:32:
libs/matealign.c: In function 'bl_matealign':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/matealign.c:313:15: note: in expansion of macro 'FREEMEMORY'
if(npos[0]) FREEMEMORY(NULL, spos[0]);
^~~~~~~~~~
libs/matealign.c:313:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(npos[0]) FREEMEMORY(NULL, spos[0]);
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/locus.h:41,
from include/mapfrag.h:39,
from libs/matealign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/matealign.c:314:15: note: in expansion of macro 'FREEMEMORY'
if(npos[1]) FREEMEMORY(NULL, spos[1]);
^~~~~~~~~~
libs/matealign.c:314:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(npos[1]) FREEMEMORY(NULL, spos[1]);
^~
Building... library for source build/container.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/container.o libs/container.c
Building... library for source build/bitArray.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitArray.o libs/bitArray.c
Building... library for source build/locus.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/locus.o libs/locus.c
Building... library for source build/debug.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/debug.o libs/debug.c
Building... library for source build/stack.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/stack.o libs/stack.c
Building... library for source build/multicharseq.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/multicharseq.o libs/multicharseq.c
Building... library for source build/aluruSort.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/aluruSort.o libs/aluruSort.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
libs/multicharseq.c: In function 'destructMultiCharSeq':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/multicharseq.c:212:7: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, mseq->markpos);
^~~~~~~~~~
libs/multicharseq.c:211:2: note: some parts of macro expansion are not guarded by this 'if' clause
if (mseq->markpos != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/multicharseq.c:214:7: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, mseq->map);
^~~~~~~~~~
libs/multicharseq.c:213:2: note: some parts of macro expansion are not guarded by this 'if' clause
if (mseq->map != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/multicharseq.h:43,
from libs/multicharseq.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/multicharseq.c:216:7: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, mseq->ref);
^~~~~~~~~~
libs/multicharseq.c:215:5: note: some parts of macro expansion are not guarded by this 'if' clause
if (mseq->ref != NULL)
^~
Building... library for source build/pigeon.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/pigeon.o libs/pigeon.c
Building... library for source build/splitalign.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/splitalign.o libs/splitalign.c
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
libs/splitalign.c: In function 'bl_fixSplitAlignHoffmann':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1323:25: note: in expansion of macro 'FREEMEMORY'
if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
^~~~~~~~~~
libs/splitalign.c:1323:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1324:25: note: in expansion of macro 'FREEMEMORY'
if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
^~~~~~~~~~
libs/splitalign.c:1324:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1325:26: note: in expansion of macro 'FREEMEMORY'
if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
^~~~~~~~~~
libs/splitalign.c:1325:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1326:26: note: in expansion of macro 'FREEMEMORY'
if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
^~~~~~~~~~
libs/splitalign.c:1326:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
libs/splitalign.c: In function 'bl_fixSplitAlignBrendel':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1565:27: note: in expansion of macro 'FREEMEMORY'
if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
^~~~~~~~~~
libs/splitalign.c:1565:9: note: some parts of macro expansion are not guarded by this 'if' clause
if(leftseedno[0]) FREEMEMORY(space, leftseeds[0]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1566:27: note: in expansion of macro 'FREEMEMORY'
if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
^~~~~~~~~~
libs/splitalign.c:1566:9: note: some parts of macro expansion are not guarded by this 'if' clause
if(leftseedno[1]) FREEMEMORY(space, leftseeds[1]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1567:28: note: in expansion of macro 'FREEMEMORY'
if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
^~~~~~~~~~
libs/splitalign.c:1567:9: note: some parts of macro expansion are not guarded by this 'if' clause
if(rightseedno[0]) FREEMEMORY(space, rightseeds[0]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/bitvectoralg.h:32,
from include/splitalign.h:29,
from libs/splitalign.c:32:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/splitalign.c:1568:28: note: in expansion of macro 'FREEMEMORY'
if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
^~~~~~~~~~
libs/splitalign.c:1568:9: note: some parts of macro expansion are not guarded by this 'if' clause
if(rightseedno[1]) FREEMEMORY(space, rightseeds[1]);
^~
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/segemehl.h:44,
from libs/pigeon.c:35:
libs/pigeon.c: In function 'pigeon':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/pigeon.c:352:13: note: in expansion of macro 'FREEMEMORY'
if(check) FREEMEMORY(space, check);
^~~~~~~~~~
libs/pigeon.c:352:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(check) FREEMEMORY(space, check);
^~
Building... library for source build/mathematics.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mathematics.o libs/mathematics.c
In file included from include/mathematics.h:117,
from libs/mathematics.c:38:
libs/mathematics.c: In function 'destructVector':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/mathematics.c:251:23: note: in expansion of macro 'FREEMEMORY'
if (v->elements) FREEMEMORY(space, v->elements);
^~~~~~~~~~
libs/mathematics.c:251:6: note: some parts of macro expansion are not guarded by this 'if' clause
if (v->elements) FREEMEMORY(space, v->elements);
^~
Building... library for source build/fileBins.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/fileBins.o libs/fileBins.c
In file included from libs/fileBins.c:51:
libs/fileBins.c: In function 'bl_fileBinsSortLine':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/fileBins.c:901:18: note: in expansion of macro 'FREEMEMORY'
if(fileSort) FREEMEMORY(space, line);
^~~~~~~~~~
libs/fileBins.c:901:5: note: some parts of macro expansion are not guarded by this 'if' clause
if(fileSort) FREEMEMORY(space, line);
^~
Building... library for source build/bgzip.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bgzip.o libs/bgzip.c
Building... library for source build/samheader.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/samheader.o libs/samheader.c
Building... library for source build/portable_endian.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/portable_endian.o libs/portable_endian.c
Building... library for source build/vstack.o
Building... library for source build/bitVector.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vstack.o libs/vstack.c
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitVector.o libs/bitVector.c
Building... library for source build/manout.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/manout.o libs/manout.c
Building... library for source build/filebuffer.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/filebuffer.o libs/filebuffer.c
Building... library for source build/stringutils.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/stringutils.o libs/stringutils.c
In file included from include/stringutils.h:27,
from libs/stringutils.c:39:
libs/stringutils.c: In function 'destructStringset':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/stringutils.c:274:9: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, s->strings[i].str);
^~~~~~~~~~
libs/stringutils.c:273:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(s->strings[i].str != NULL)
^~
Building... library for source build/bitvectoralg.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/bitvectoralg.o libs/bitvectoralg.c
Building... library for source build/vtprogressbar.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/vtprogressbar.o libs/vtprogressbar.c
Building... library for source build/alignment.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/alignment.o libs/alignment.c
In file included from include/mathematics.h:117,
from libs/alignment.c:38:
libs/alignment.c: In function 'wrapAlignment':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/alignment.c:97:18: note: in expansion of macro 'FREEMEMORY'
if(al->rmvseq) FREEMEMORY(NULL, al->v);
^~~~~~~~~~
libs/alignment.c:97:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(al->rmvseq) FREEMEMORY(NULL, al->v);
^~
In file included from include/mathematics.h:117,
from libs/alignment.c:38:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/alignment.c:98:18: note: in expansion of macro 'FREEMEMORY'
if(al->rmuseq) FREEMEMORY(NULL, al->u);
^~~~~~~~~~
libs/alignment.c:98:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(al->rmuseq) FREEMEMORY(NULL, al->u);
^~
Building... library for source build/biofiles.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/biofiles.o libs/biofiles.c
Building... library for source build/segemehl_helper.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/segemehl_helper.o libs/segemehl_helper.c
Building... library for source build/mapfrag.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/mapfrag.o libs/mapfrag.c
Building... library for source build/karlin.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/karlin.o libs/karlin.c
Building... library for source build/sufarray.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sufarray.o libs/sufarray.c
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
libs/sufarray.c: In function 'destructSufArr':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:613:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->lcpctab);
^~~~~~~~~~
libs/sufarray.c:612:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (arr->lcpctab != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:615:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->inv_suftab);
^~~~~~~~~~
libs/sufarray.c:614:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (arr->inv_suftab != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:619:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->idvtab);
^~~~~~~~~~
libs/sufarray.c:618:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (arr->idvtab != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:624:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->suflink);
^~~~~~~~~~
libs/sufarray.c:620:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (arr->suflink != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:627:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->chldtab);
^~~~~~~~~~
libs/sufarray.c:626:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (arr->chldtab != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:629:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->mdfive);
^~~~~~~~~~
libs/sufarray.c:628:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (arr->mdfive)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:631:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->llvtab);
^~~~~~~~~~
libs/sufarray.c:630:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(arr->llvtab != NULL)
^~
In file included from include/stringutils.h:27,
from include/charsequence.h:43,
from include/sufarray.h:45,
from libs/sufarray.c:39:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/sufarray.c:636:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, arr->id);
^~~~~~~~~~
libs/sufarray.c:632:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(arr->id != NULL)
^~
Building... library for source build/gzip.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/gzip.o libs/gzip.c
libs/gzip.c: In function 'readCommonHeader':
libs/gzip.c:41:56: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
~~^ ~~~~~~~~~
%d
libs/gzip.c:41:71: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'unsigned int' [-Wformat=]
fprintf(stderr, "common header has a length of %ld instead of %ld - not good.\n", bytesRead, sizeof(u_CommonHeader));
~~^ ~~~~~~~~~~~~~~~~~~~~~~
%d
Building... library for source build/sort.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sort.o libs/sort.c
Building... library for source build/charsequence.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/charsequence.o libs/charsequence.c
In file included from libs/charsequence.c:26:
libs/charsequence.c: In function 'destructSequence':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:467:4: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->sequence);
^~~~~~~~~~
libs/charsequence.c:466:3: note: some parts of macro expansion are not guarded by this 'if' clause
if (sequence->sequence != NULL)
^~
In file included from libs/charsequence.c:26:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:470:5: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->alphabetname);
^~~~~~~~~~
libs/charsequence.c:469:2: note: some parts of macro expansion are not guarded by this 'if' clause
if (sequence->alphabetname != NULL)
^~
In file included from libs/charsequence.c:26:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:472:2: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->url);
^~~~~~~~~~
libs/charsequence.c:471:5: note: some parts of macro expansion are not guarded by this 'if' clause
if (sequence->url != NULL)
^~
In file included from libs/charsequence.c:26:
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/charsequence.c:474:2: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, sequence->info);
^~~~~~~~~~
libs/charsequence.c:473:5: note: some parts of macro expansion are not guarded by this 'if' clause
if (sequence->info != NULL)
^~
Building... library for source build/md5.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/md5.o libs/md5.c
Building... library for source build/queryalign.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/queryalign.o libs/queryalign.c
Building... library for source build/kdchain.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/kdchain.o libs/kdchain.c
Building... library for source build/seqclip.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/seqclip.o libs/seqclip.c
In file included from include/stringutils.h:27,
from include/biofiles.h:43,
from include/alignment.h:38,
from include/sw.h:38,
from libs/seqclip.c:44:
libs/seqclip.c: In function 'bl_Find3PrimeGreedy':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/seqclip.c:529:9: note: in expansion of macro 'FREEMEMORY'
FREEMEMORY(space, adapter);
^~~~~~~~~~
libs/seqclip.c:528:7: note: some parts of macro expansion are not guarded by this 'if' clause
if(adapter)
^~
Building... library for source build/info.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/info.o libs/info.c
libs/info.c: In function 'timestr_r':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_sec, 1900 + timeptr->tm_year);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c: In function 'infomsg':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_sec, 1900 + timeptr->tm_year);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c: In function 'nfolevel':
libs/info.c:64:50: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 12 [-Wformat-overflow=]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~
libs/info.c:64:21: note: directive argument in the range [-2147481748, 2147483647]
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
libs/info.c:64:5: note: 'sprintf' output between 16 and 67 bytes into a destination of size 26
sprintf(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
wday_name[timeptr->tm_wday], mon_name[timeptr->tm_mon],
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_mday, timeptr->tm_hour, timeptr->tm_min,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
timeptr->tm_sec, 1900 + timeptr->tm_year);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Building... library for source build/manopt.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/manopt.o libs/manopt.c
Building... library for source build/junctions.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/junctions.o libs/junctions.c
Building... library for source build/intervaltree.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/intervaltree.o libs/intervaltree.c
In file included from include/mathematics.h:117,
from libs/intervaltree.c:27:
libs/intervaltree.c: In function 'bl_intervaltreeDestruct':
include/memory.h:32:27: warning: macro expands to multiple statements [-Wmultistatement-macros]
#define FREEMEMORY(X,PTR) free(PTR); PTR=NULL
^~~~
libs/intervaltree.c:443:19: note: in expansion of macro 'FREEMEMORY'
if(root->ncoll) FREEMEMORY(NULL, root->collisions);
^~~~~~~~~~
libs/intervaltree.c:443:3: note: some parts of macro expansion are not guarded by this 'if' clause
if(root->ncoll) FREEMEMORY(NULL, root->collisions);
^~
Building... library for source build/iupac.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/iupac.o libs/iupac.c
Building... library for source build/match.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/match.o libs/match.c
Building... library for source build/sw.o
cc -g -O2 -ffile-prefix-map=/build/segemehl-0.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -std=c99 -g -O3 -DSORTEDUNMAPPED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DDBGNFO -DSHOWALIGN -DDBGLEVEL=0 -DPROGNFO -Ilibs -Ilibs/sufarray -Isamtools `pkg-config --cflags htslib` -I include -c -o build/sw.o libs/sw.c
Linking segemehl
Linking haarz
cc build/annotation.o build/gzidx.o build/mappingqual.o build/kdseed.o build/memory.o build/samio.o build/brendel.o build/merge.o build/bedfiles.o build/radixsort.o build/bamio.o build/fileio.o build/nw.o build/vqueue.o build/matealign.o build/container.o build/bitArray.o build/locus.o build/debug.o build/stack.o build/multicharseq.o build/aluruSort.o build/pigeon.o build/splitalign.o build/mathematics.o build/fileBins.o build/bgzip.o build/samheader.o build/portable_endian.o build/vstack.o build/bitVector.o build/manout.o build/filebuffer.o build/stringutils.o build/bitvectoralg.o build/vtprogressbar.o build/alignment.o build/biofiles.o build/segemehl_helper.o build/mapfrag.o build/karlin.o build/sufarray.o build/gzip.o build/sort.o build/charsequence.o build/md5.o build/queryalign.o build/kdchain.o build/seqclip.o build/info.o build/manopt.o build/junctions.o build/intervaltree.o build/iupac.o build/match.o build/sw.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now
cc build/annotation.o build/gzidx.o build/mappingqual.o build/kdseed.o build/memory.o build/samio.o build/brendel.o build/merge.o build/bedfiles.o build/radixsort.o build/bamio.o build/fileio.o build/nw.o build/vqueue.o build/matealign.o build/container.o build/bitArray.o build/locus.o build/debug.o build/stack.o build/multicharseq.o build/aluruSort.o build/pigeon.o build/splitalign.o build/mathematics.o build/fileBins.o build/bgzip.o build/samheader.o build/portable_endian.o build/vstack.o build/bitVector.o build/manout.o build/filebuffer.o build/stringutils.o build/bitvectoralg.o build/vtprogressbar.o build/alignment.o build/biofiles.o build/segemehl_helper.o build/mapfrag.o build/karlin.o build/sufarray.o build/gzip.o build/sort.o build/charsequence.o build/md5.o build/queryalign.o build/kdchain.o build/seqclip.o build/info.o build/manopt.o build/junctions.o build/intervaltree.o build/iupac.o build/match.o build/sw.o build/haarz.o -o ./haarz.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ `pkg-config --libs htslib` -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/build/segemehl-0.3.4'
make[1]: Leaving directory '/build/segemehl-0.3.4'
dh_auto_test
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
dh_auto_install
debian/rules override_dh_install
make[1]: Entering directory '/build/segemehl-0.3.4'
mv segemehl.x segemehl
mv haarz.x haarz
find . -name "*.x"
dh_install
make[1]: Leaving directory '/build/segemehl-0.3.4'
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libtinfo.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libncurses.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libform.so.6 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/segemehl/usr/bin/segemehl debian/segemehl/usr/bin/haarz were not linked against libmenu.so.6 (they use none of the library's symbols)
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'segemehl' in '../segemehl_0.3.4-1_armhf.deb'.
dpkg-deb: building package 'segemehl-dbgsym' in '../segemehl-dbgsym_0.3.4-1_armhf.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genchanges --build=binary >../segemehl_0.3.4-1_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/7111 and its subdirectories
I: Current time: Sat Oct 31 05:01:21 -12 2020
I: pbuilder-time-stamp: 1604163681
Sat Oct 31 17:01:32 UTC 2020 I: 1st build successful. Starting 2nd build on remote node cbxi4pro0-armhf-rb.debian.net.
Sat Oct 31 17:01:32 UTC 2020 I: Preparing to do remote build '2' on cbxi4pro0-armhf-rb.debian.net.
Sat Oct 31 17:05:26 UTC 2020 I: Deleting $TMPDIR on cbxi4pro0-armhf-rb.debian.net.
Sat Oct 31 17:05:28 UTC 2020 I: segemehl_0.3.4-1_armhf.changes:
Format: 1.8
Date: Fri, 11 Jan 2019 22:52:52 +0100
Source: segemehl
Binary: segemehl segemehl-dbgsym
Architecture: armhf
Version: 0.3.4-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
segemehl - short read mapping with gaps
Changes:
segemehl (0.3.4-1) unstable; urgency=medium
.
* New upstream version
* debhelper 12
* Standards-Version: 4.3.0
Checksums-Sha1:
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b54854a0520dcea0aa1063c4c5b237bde1219a77 5420 segemehl_0.3.4-1_armhf.buildinfo
e5d1f52d96bed33bc2f430f30dbf79c500d58d3f 259504 segemehl_0.3.4-1_armhf.deb
Checksums-Sha256:
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a992f0a2baf7f8f99d83df43b336af127e6e62cb59a68a41ab70038c080337c0 5420 segemehl_0.3.4-1_armhf.buildinfo
341be690ab29d245dd68f98e084dddd185a6435bd0df83c3a0bb0826e9934bab 259504 segemehl_0.3.4-1_armhf.deb
Files:
4ba825af914d89c6bebec2836a9ea3df 1558788 debug optional segemehl-dbgsym_0.3.4-1_armhf.deb
315d04e88856afc8d0b602d9dfd6ed1b 5420 science optional segemehl_0.3.4-1_armhf.buildinfo
77ef7527c8730b8192efa0ae8dfc2962 259504 science optional segemehl_0.3.4-1_armhf.deb
Sat Oct 31 17:05:30 UTC 2020 I: diffoscope 161 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/segemehl_0.3.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/segemehl_0.3.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/segemehl_0.3.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/b1/segemehl_0.3.4-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.TDZHoTwFFl/b2/segemehl_0.3.4-1_armhf.changes
## close_archive (total time: 0.001s)
0.000s 20 calls diffoscope.comparators.xz.XzContainer
0.000s 8 calls diffoscope.comparators.deb.DebTarContainer
0.000s 8 calls diffoscope.comparators.deb.DebContainer
0.000s 12 calls diffoscope.comparators.tar.TarContainer
## command (total time: 114.377s)
53.520s 213 calls diff
36.771s 1641 calls readelf
21.209s 185 calls objdump
1.683s 4 calls objcopy
0.859s 20 calls xz
0.218s 44 calls strings
0.115s 10 calls cmp
0.001s 14 calls cmp (internal)
## compare_files (cumulative) (total time: 401.504s)
74.288s 1 call abc.DotChangesFile
73.949s 2 calls abc.DebFile
73.696s 4 calls abc.XzFile
72.851s 2 calls abc.DebDataTarFile
72.285s 4 calls abc.ElfFile
30.047s 12 calls diffoscope.comparators.elf.ElfCodeSection
3.561s 50 calls diffoscope.comparators.elf.ElfSection
0.344s 3 calls diffoscope.comparators.elf.ElfStringSection
0.287s 2 calls abc.TarFile
0.090s 2 calls diffoscope.comparators.elf.MonkeyPatchedElfSection
0.059s 1 call abc.TextFile
0.049s 2 calls abc.Md5sumsFile
## container_extract (total time: 1.021s)
0.863s 20 calls diffoscope.comparators.xz.XzContainer
0.097s 22 calls diffoscope.comparators.deb.DebTarContainer
0.045s 24 calls diffoscope.comparators.deb.DebContainer
0.016s 16 calls diffoscope.comparators.tar.TarContainer
## has_same_content_as (total time: 0.122s)
0.039s 4 calls abc.ElfFile
0.033s 2 calls abc.DebFile
0.032s 4 calls abc.XzFile
0.015s 2 calls abc.DebDataTarFile
0.001s 50 calls diffoscope.comparators.elf.ElfSection
0.001s 4 calls abc.TextFile
0.001s 4 calls abc.Md5sumsFile
0.000s 2 calls abc.TarFile
0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink
0.000s 12 calls diffoscope.comparators.elf.ElfCodeSection
0.000s 1 call abc.DotChangesFile
0.000s 3 calls diffoscope.comparators.elf.ElfStringSection
0.000s 2 calls diffoscope.comparators.elf.MonkeyPatchedElfSection
## main (total time: 675.723s)
675.541s 2 calls outputs
0.182s 1 call cleanup
## open_archive (total time: 0.001s)
0.000s 20 calls diffoscope.comparators.xz.XzContainer
0.000s 12 calls diffoscope.comparators.tar.TarContainer
0.000s 8 calls diffoscope.comparators.deb.DebContainer
0.000s 8 calls diffoscope.comparators.deb.DebTarContainer
## output (total time: 600.497s)
597.696s 1 call html
1.529s 1 call text
1.272s 1 call json
## recognizes (total time: 2.000s)
0.617s 708 calls diffoscope.comparators.utils.archive.ArchiveMember
0.591s 1000 calls diffoscope.comparators.elf.ElfSection
0.492s 1672 calls diffoscope.comparators.utils.libarchive.LibarchiveMember
0.117s 240 calls diffoscope.comparators.elf.ElfCodeSection
0.098s 10 calls diffoscope.comparators.binary.FilesystemFile
0.050s 176 calls diffoscope.comparators.debian.DebControlMember
0.031s 60 calls diffoscope.comparators.elf.ElfStringSection
0.003s 40 calls diffoscope.comparators.elf.MonkeyPatchedElfSection
0.001s 28 calls abc.Md5sumsFile
0.000s 8 calls abc.DotChangesFile
0.000s 4 calls diffoscope.comparators.utils.libarchive.LibarchiveSymlink
Sat Oct 31 17:16:48 UTC 2020 E: segemehl failed to build reproducibly in buster on armhf.
Sat Oct 31 17:17:20 UTC 2020 I: Submitting .buildinfo files to external archives:
Sat Oct 31 17:17:20 UTC 2020 I: Submitting 8.0K b1/segemehl_0.3.4-1_armhf.buildinfo.asc
Sat Oct 31 17:17:22 UTC 2020 I: Submitting 8.0K b2/segemehl_0.3.4-1_armhf.buildinfo.asc
Sat Oct 31 17:17:22 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sat Oct 31 17:17:22 UTC 2020 I: Done submitting .buildinfo files.
Sat Oct 31 17:17:22 UTC 2020 I: Removing signed segemehl_0.3.4-1_armhf.buildinfo.asc files:
removed './b1/segemehl_0.3.4-1_armhf.buildinfo.asc'
removed './b2/segemehl_0.3.4-1_armhf.buildinfo.asc'