gff2aplot →
2.0-13 →
armhf → 2020-07-28 06:52:18
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| gff2aplot 2.0-13 (armhf) Tue, 28 Jul 2020 06:48:20 +0000 |
+==============================================================================+
Package: gff2aplot
Version: 2.0-13
Source Version: 2.0-13
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-87ad2df7-ff74-458b-adc1-568f9c4baf35' with '<<CHROOT>>'
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| Update chroot |
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Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
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| Fetch source files |
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Check APT
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Checking available source versions...
Download source files with APT
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Reading package lists...
NOTICE: 'gff2aplot' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/gff2aplot.git
Please use:
git clone https://salsa.debian.org/med-team/gff2aplot.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 351 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gff2aplot 2.0-13 (dsc) [2044 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gff2aplot 2.0-13 (tar) [328 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main gff2aplot 2.0-13 (diff) [20.6 kB]
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I: NOTICE: Log filtering will replace 'build/gff2aplot-RQcsLe/gff2aplot-2.0' with '<<PKGBUILDDIR>>'
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| Install build-essential |
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Merged Build-Depends: build-essential, fakeroot
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dpkg-scanpackages: warning: Packages in archive but missing from override file:
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gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
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gpg: Total number processed: 1
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gpg: secret keys read: 1
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gpg: using "Sbuild Signer" as default secret key for signing
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Install core build dependencies (apt-based resolver)
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The following packages were automatically installed and are no longer required:
bsdextrautils dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1
libjson-c4 libpam-cap libssl1.1 netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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| Install package build dependencies |
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Setup apt archive
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Merged Build-Depends: debhelper-compat (= 13)
Filtered Build-Depends: debhelper-compat (= 13)
dpkg-deb: building package 'sbuild-build-depends-gff2aplot-dummy' in '/<<BUILDDIR>>/resolver-P6MYL5/apt_archive/sbuild-build-depends-gff2aplot-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
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dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
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Install gff2aplot build dependencies (apt-based resolver)
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Installing build dependencies
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Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dmsetup libargon2-1 libcryptsetup12 libdevmapper1.02.1 libjson-c4 libpam-cap
libssl1.1 netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu67 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-gff2aplot-dummy
sensible-utils
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.34.90.20200706-1+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-14+rpi1 gcc-9_9.3.0-14+rpi1 libc6-dev_2.31-1+rpi1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 linux-libc-dev_5.7.6-1+rpi1
Package versions: adduser_3.118 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34.90.20200706-1+rpi1 binutils-arm-linux-gnueabihf_2.34.90.20200706-1+rpi1 binutils-common_2.34.90.20200706-1+rpi1 bsdextrautils_2.35.2-7 bsdutils_1:2.35.2-7 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-14+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dmsetup_2:1.02.167-1+b2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.2-7 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-14+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-4+rpi1 gcc-9_9.3.0-14+rpi1 gcc-9-base_9.3.0-14+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-14+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-4+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34.90.20200706-1+rpi1 libblkid1_2.35.2-7 libbz2-1.0_1.0.8-3 libc-bin_2.31-1+rpi1 libc-dev-bin_2.31-1+rpi1 libc6_2.31-1+rpi1 libc6-dev_2.31-1+rpi1 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcap2-bin_1:2.36-1 libcc1-0_10.1.0-4+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libcryptsetup12_2:2.3.3-1 libctf-nobfd0_2.34.90.20200706-1+rpi1 libctf0_2.34.90.20200706-1+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdevmapper1.02.1_2:1.02.167-1+b2 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.2-7 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-14+rpi1 libgcc-s1_10.1.0-4+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.1.0-4+rpi1 libgpg-error0_1.38-2 libhogweed6_3.6-2 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1+b1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-7 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-cap_1:2.36-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2 libsmartcols1_2.35.2-7 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-14+rpi1 libstdc++6_10.1.0-4+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1+b1 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-4+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1+b1 libunistring2_0.9.10-4 libuuid1_2.35.2-7 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.7.6-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.35.2-7 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gff2aplot-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.2-7 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jun 15 16:23:00 2020 UTC
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 ./gff2aplot_2.0-13.dsc
dpkg-source: info: extracting gff2aplot in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz
dpkg-source: info: unpacking gff2aplot_2.0-13.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying non_lexical_loop_iterator.patch
dpkg-source: info: applying 02-blat2gff.diff
dpkg-source: info: applying 03-parseblast.diff
dpkg-source: info: applying use-dpkg-buildflags.patch
dpkg-source: info: applying mayhem.patch
dpkg-source: info: applying fis-privacy-breach.patch
dpkg-source: info: applying perl_5.28.patch
dpkg-source: info: applying fix_install_ali2gff.patch
dpkg-source: info: applying enhance_sprintf_buffer.patch
dpkg-source: info: applying fix_README_used_for_test.patch
dpkg-source: info: applying fix_gff_comments.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-87ad2df7-ff74-458b-adc1-568f9c4baf35
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gff2aplot
dpkg-buildpackage: info: source version 2.0-13
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f src/ali2gff/ali2gff bin/ali2gff
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
###
### RUNNING MAKEFILE
###
### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl"
### Tue Jul 28 06:52:05 UTC 2020 -- buildd
###
### Finishing PERL script from "src/parseblast.pl" -> "bin/parseblast.pl"
### Finishing PERL script from "src/blat2gff.pl" -> "bin/blat2gff.pl"
### Finishing PERL script from "src/sim2gff.pl" -> "bin/sim2gff.pl"
### Making ALI2GFF...
###
### MAKEFILE DONE...
make[2]: Entering directory '/<<PKGBUILDDIR>>/src/ali2gff'
###
ali2gff.c: In function 'main':
ali2gff.c:88:8: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
88 | char *ptr;
| ^~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:355:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
355 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", xName,yName,source,xb,yb,xe,ye,scores,strands,frames);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 25 and 5063 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:354:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
354 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",xName,yName,source,xb,yb,xe,ye,score ,strands,frames);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 30 and 3378 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:351:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
351 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", xName,yName,source,xb,yb,xe,ye,scores,strands,frames,cptr);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 5027) into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:350:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
350 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",xName,yName,source,xb,yb,xe,ye,score ,strands,frames,cptr);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 3033) into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:300:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
300 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\n", yName,xName,source,yb,xb,ye,xe,scores,strands,frames);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 25 and 5063 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:299:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
299 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\n",yName,xName,source,yb,xb,ye,xe,score,strands,frames);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 30 and 3378 bytes into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:296:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
296 | else sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%s\t%s\t%s\t%s", yName,xName,source,yb,xb,ye,xe,scores,strands,frames,cptr);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 5027) into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:295:71: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
295 | if (sscanf(scores,"%f",&score) == 1) sprintf(aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%s\t%s\t%s",yName,xName,source,yb,xb,ye,xe,score,strands,frames,cptr);
| ^~ ~~~~~
In file included from /usr/include/stdio.h:867,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 3033) into a destination of size 1000
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processMumfile':
ali2gff.c:732:12: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
732 | score = (score - errCount)/score; // match percentage
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processSimfile':
ali2gff.c:1073:15: warning: 'yrev' may be used uninitialized in this function [-Wmaybe-uninitialized]
1073 | ye = yrev-ye;
| ~~~~^~~
ali2gff.c:1064:41: warning: 'yseqLen_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) {
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:1064:15: warning: 'xseqLen_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) {
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from ali2gff.h:22,
from ali2gff.c:64:
In function 'strncpy',
inlined from 'main' at ali2gff.c:135:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src/ali2gff'
mkdir -p ./bin
cp ./src/ali2gff/ali2gff \
./bin/ali2gff
mode of 'bin/gff2aplot.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x)
mode of 'bin/parseblast.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x)
mode of 'bin/blat2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x)
mode of 'bin/sim2gff.pl' changed from 0644 (rw-r--r--) to 0755 (rwxr-xr-x)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
### SORRY !!! Tests were not implemented yet...
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
for script in `find bin -name "*.pl"` ; do mv $script bin/`basename $script .pl` ; done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_installexamples
# Fix path names, silence GS
find debian/*/usr/share/doc/*/examples -name README -exec sed -i \
-e 's?^$BIN/\([0-9a-z]\+\)\.pl?\1?' \
-e 's?^$BIN/\([0-9a-z]\+\) ?\1 ?' \
-e 's?^GS=.*;?GS="gs -q" ;?' \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gff2aplot/usr/bin/ali2gff was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-13_armhf.deb'.
dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-13_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../gff2aplot_2.0-13_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-07-28T06:52:16Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gff2aplot_2.0-13_armhf.changes:
-------------------------------
Format: 1.8
Date: Sun, 14 Jun 2020 11:51:26 +0530
Source: gff2aplot
Binary: gff2aplot gff2aplot-dbgsym
Architecture: armhf
Version: 2.0-13
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Pranav Ballaney <ballaneypranav@gmail.com>
Description:
gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript
Closes: 962553
Changes:
gff2aplot (2.0-13) unstable; urgency=medium
.
* Team upload.
* Replace tabs in gff files with spaces (Closes: #962553)
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615ba343e371cde5c6bafde3ae989597 4551 science optional gff2aplot_2.0-13_armhf.buildinfo
047f0608b1712befad58b399503c7999 243692 science optional gff2aplot_2.0-13_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gff2aplot-dbgsym_2.0-13_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 25664 bytes: control archive=536 bytes.
375 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gff2aplot-dbgsym
Source: gff2aplot
Version: 2.0-13
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 39
Depends: gff2aplot (= 2.0-13)
Section: debug
Priority: optional
Description: debug symbols for gff2aplot
Build-Ids: 11b4b512237a4e4da71846e42044158f54578f31
drwxr-xr-x root/root 0 2020-06-14 06:21 ./
drwxr-xr-x root/root 0 2020-06-14 06:21 ./usr/
drwxr-xr-x root/root 0 2020-06-14 06:21 ./usr/lib/
drwxr-xr-x root/root 0 2020-06-14 06:21 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-06-14 06:21 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2020-06-14 06:21 ./usr/share/
drwxr-xr-x root/root 0 2020-06-14 06:21 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-06-14 06:21 ./usr/share/doc/gff2aplot-dbgsym -> gff2aplot
gff2aplot_2.0-13_armhf.deb
--------------------------
new Debian package, version 2.0.
size 243692 bytes: control archive=3404 bytes.
2842 bytes, 49 lines control
5626 bytes, 66 lines md5sums
Package: gff2aplot
Version: 2.0-13
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1443
Depends: libc6 (>= 2.7), perl:any
Recommends: graphicsmagick | imagemagick, ghostscript
Suggests: postscript-viewer, gff2ps
Section: science
Priority: optional
Homepage: http://genome.imim.es/software/gfftools/GFF2APLOT.html
Description: pair-wise alignment-plots for genomic sequences in PostScript
A program to visualize the alignment of two genomic sequences together with
their annotations. From GFF-format input files it produces PostScript figures
for that alignment.
The following menu lists many features of gff2aplot:
* Comprehensive alignment plots for any GFF-feature. Attributes are defined
separately so you can modify only whatsoever attributes for a given file or
share same customization across different data-sets.
* All parameters are set by default within the program, but it can be also
fully configured via gff2ps-like flexible customization files. Program can
handle several of such files, summarizing all the settings before producing
the corresponding figure. Moreover, all customization parameters can be set
via command-line switches, which allows users to play with those parameters
before adding any to a customization file.
* Source order is taken from input files, if you swap file order you can
visualize alignment and its annotation with the new input arrangement.
* All alignment scores can be visualized in a PiP box below gff2aplot area,
using grey-color scale, user-defined color scale or score-dependent
gradients.
* Scalable fonts, which can also be chosen among the basic PostScript default
fonts. Feature and group labels can be rotated to improve readability in
both annotation axes.
* The program is still defined as a Unix filter so it can handle data from
files, redirections and pipes, writing output to standard-output and
warnings to standard error.
* gff2aplot is able to manage many physical page formats (from A0 to A10, and
more -see available page sizes in its manual-), including user-defined ones.
This allows, for instance, the generation of poster size genomic maps, or
the use of a continuous-paper supporting plotting device, either in portrait
or landscape.
* You can draw different alignments on same alignment plot and distinguish
them by using different colors for each.
* Shape dictionary has been expanded, so that further feature shapes are now
available (see manual).
* Annotation projections through alignment plots (so called ribbons) emulate
transparencies via complementary color fill patterns. This feature allows
one to show color pseudo-blending when horizontal and vertical ribbons
overlap.
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 4912
Build-Time: 13
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 203
Job: gff2aplot_2.0-13
Machine Architecture: armhf
Package: gff2aplot
Package-Time: 236
Source-Version: 2.0-13
Space: 4912
Status: successful
Version: 2.0-13
--------------------------------------------------------------------------------
Finished at 2020-07-28T06:52:16Z
Build needed 00:03:56, 4912k disk space