gff2aplot →
2.0-15 →
armhf → 2024-02-08 07:00:19
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| gff2aplot 2.0-15 (armhf) Thu, 08 Feb 2024 06:52:29 +0000 |
+==============================================================================+
Package: gff2aplot
Version: 2.0-15
Source Version: 2.0-15
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-6e4ec574-9128-4920-8434-d9b14cec3b11' with '<<CHROOT>>'
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| Update chroot |
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Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
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W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
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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://172.17.4.1/private trixie-staging/main gff2aplot 2.0-15 (dsc) [2044 B]
Get:2 http://172.17.4.1/private trixie-staging/main gff2aplot 2.0-15 (tar) [328 kB]
Get:3 http://172.17.4.1/private trixie-staging/main gff2aplot 2.0-15 (diff) [20.8 kB]
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I: NOTICE: Log filtering will replace 'build/gff2aplot-FVSIL8/gff2aplot-2.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gff2aplot-FVSIL8' with '<<BUILDDIR>>'
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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: /<<BUILDDIR>>/resolver-BE9Qfr/gpg/trustdb.gpg: trustdb created
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
gpg: key 37145E60F90AF620: secret key imported
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:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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| Check architectures |
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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-BE9Qfr/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.
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Install gff2aplot build dependencies (apt-based resolver)
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Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1
libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf
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 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1
libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1
libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-gff2aplot-dummy
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Get:21 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
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Get:26 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
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Get:28 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
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| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.2+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-13+rpi1 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.9 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.83 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.2+rpi1 dpkg-dev_1.22.2+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-6 libapt-pkg6.0_2.7.9 libarchive-zip-perl_1.68-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.1-5 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-13+rpi1 libc-dev-bin_2.37-13+rpi1 libc6_2.37-13+rpi1 libc6-dev_2.37-13+rpi1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-9+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdpkg-perl_1.22.2+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.33-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.3-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1+b1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libreadline8_8.2-3 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1+b1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 mount_2.39.3-6 nano_7.2-2 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gff2aplot-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.08-5 tar_1.35+dfsg-3 tzdata_2023d-1 usrmerge_38 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Mon Feb 5 11:39:37 2024 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./gff2aplot_2.0-15.dsc: no acceptable signature found
dpkg-source: info: extracting gff2aplot in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz
dpkg-source: info: unpacking gff2aplot_2.0-15.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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-6e4ec574-9128-4920-8434-d9b14cec3b11
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gff2aplot
dpkg-buildpackage: info: source version 2.0-15
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/*
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"
### Thu Feb 8 06:59:54 UTC 2024 -- 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:88:15: warning: variable 'ptr' set but not used [-Wunused-but-set-variable]
88 | char *ptr;
| ^~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:355:113: 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:906,
from ali2gff.h:20,
from ali2gff.c:64:
In function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:355:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:354:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:354:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:351:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:351:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:350:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:350:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:300:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:300:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:299:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:299:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:296:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:296:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4028) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processGFFfile':
ali2gff.c:295:113: 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 function 'sprintf',
inlined from 'processGFFfile' at ali2gff.c:295:44:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output 30 or more bytes (assuming 2034) into a destination of size 1000
30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
31 | __glibc_objsize (__s), __fmt,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
32 | __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processMumfile':
ali2gff.c:732:40: warning: 'score' may be used uninitialized [-Wmaybe-uninitialized]
732 | score = (score - errCount)/score; // match percentage
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:420:15: note: 'score' was declared here
420 | float score;
| ^~~~~
ali2gff.c:421:27: warning: 'fxb' may be used uninitialized [-Wmaybe-uninitialized]
421 | unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps
| ^~~
ali2gff.c:421:37: warning: 'fyb' may be used uninitialized [-Wmaybe-uninitialized]
421 | unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps
| ^~~
ali2gff.c: In function 'processSimfile':
ali2gff.c:1064:36: warning: 'xseqLen_4' may be used uninitialized [-Wmaybe-uninitialized]
1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) {
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:997:27: note: 'xseqLen_4' was declared here
997 | unsigned long int xseqLen_4; /* length of x sequence -5 */
| ^~~~~~~~~
ali2gff.c:1064:62: warning: 'yseqLen_4' may be used uninitialized [-Wmaybe-uninitialized]
1064 | if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) {
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:998:27: note: 'yseqLen_4' was declared here
998 | unsigned long int yseqLen_4; /* length of y sequence -5 */
| ^~~~~~~~~
ali2gff.c: In function 'main':
ali2gff.c:135:9: warning: '__builtin_strncpy' specified bound 1000 equals destination size [-Wstringop-truncation]
135 | strncpy(infile,argv[1],MAXSTRING);
| ^
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_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
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dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-15_armhf.deb'.
dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-15_armhf.deb'.
dpkg-genbuildinfo --build=any -O../gff2aplot_2.0-15_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../gff2aplot_2.0-15_armhf.changes
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dpkg-source --after-build .
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| Changes |
+------------------------------------------------------------------------------+
gff2aplot_2.0-15_armhf.changes:
-------------------------------
Format: 1.8
Date: Mon, 05 Feb 2024 12:09:38 +0100
Source: gff2aplot
Binary: gff2aplot gff2aplot-dbgsym
Architecture: armhf
Version: 2.0-15
Distribution: trixie-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript
Closes: 1044834
Changes:
gff2aplot (2.0-15) unstable; urgency=medium
.
* Fix clean target
Closes: #1044834
* Standards-Version: 4.6.2 (routine-update)
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gff2aplot-dbgsym_2.0-15_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 24692 bytes: control archive=536 bytes.
375 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gff2aplot-dbgsym
Source: gff2aplot
Version: 2.0-15
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 38
Depends: gff2aplot (= 2.0-15)
Section: debug
Priority: optional
Description: debug symbols for gff2aplot
Build-Ids: 6834259dcf85dbd169fcd92b8d411fb86f80750d
drwxr-xr-x root/root 0 2024-02-05 11:09 ./
drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/
drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/
drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/share/
drwxr-xr-x root/root 0 2024-02-05 11:09 ./usr/share/doc/
lrwxrwxrwx root/root 0 2024-02-05 11:09 ./usr/share/doc/gff2aplot-dbgsym -> gff2aplot
gff2aplot_2.0-15_armhf.deb
--------------------------
new Debian package, version 2.0.
size 242740 bytes: control archive=3404 bytes.
2843 bytes, 49 lines control
5626 bytes, 66 lines md5sums
Package: gff2aplot
Version: 2.0-15
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1442
Depends: libc6 (>= 2.34), perl:any
Recommends: graphicsmagick | imagemagick, ghostscript
Suggests: postscript-viewer, gff2ps
Section: science
Priority: optional
Homepage: https://genome.crg.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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| Cleanup |
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 4896
Build-Time: 25
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 416
Job: gff2aplot_2.0-15
Machine Architecture: armhf
Package: gff2aplot
Package-Time: 466
Source-Version: 2.0-15
Space: 4896
Status: successful
Version: 2.0-15
--------------------------------------------------------------------------------
Finished at 2024-02-08T07:00:15Z
Build needed 00:07:46, 4896k disk space