gff2aplot →
2.0-14 →
armhf → 2021-09-19 17:44:57
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| gff2aplot 2.0-14 (armhf) Sun, 19 Sep 2021 17:38:44 +0000 |
+==============================================================================+
Package: gff2aplot
Version: 2.0-14
Source Version: 2.0-14
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-f0c726b4-2bf6-4a18-8d22-589e93edf416' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
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Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.4 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 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
------------------------------
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 bookworm-staging/main gff2aplot 2.0-14 (dsc) [2044 B]
Get:2 http://172.17.0.1/private bookworm-staging/main gff2aplot 2.0-14 (tar) [328 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main gff2aplot 2.0-14 (diff) [20.7 kB]
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I: NOTICE: Log filtering will replace 'build/gff2aplot-kRu3HO/gff2aplot-2.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gff2aplot-kRu3HO' with '<<BUILDDIR>>'
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| Install build-essential |
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dpkg-scanpackages: warning: Packages in archive but missing from override file:
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gpg: keybox '/<<BUILDDIR>>/resolver-bxDw6W/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-bxDw6W/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
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gpg: using "Sbuild Signer" as default secret key for signing
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W: copy:///<<BUILDDIR>>/resolver-bxDw6W/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-bxDw6W/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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Install core build dependencies (apt-based resolver)
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Installing build dependencies
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Building dependency tree...
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The following package was automatically installed and is no longer required:
netbase
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The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 78 not upgraded.
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| Check architectures |
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13)
Filtered Build-Depends: debhelper-compat (= 13)
dpkg-deb: building package 'sbuild-build-depends-gff2aplot-dummy' in '/<<BUILDDIR>>/resolver-bxDw6W/apt_archive/sbuild-build-depends-gff2aplot-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gff2aplot-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
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W: copy:///<<BUILDDIR>>/resolver-bxDw6W/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-bxDw6W/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install gff2aplot build dependencies (apt-based resolver)
---------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
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 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 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 libicu67 libmagic-mgc libmagic1
libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2
m4 man-db po-debconf sbuild-build-depends-gff2aplot-dummy sensible-utils
0 upgraded, 32 newly installed, 0 to remove and 78 not upgraded.
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Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
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Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.5.1 [1056 kB]
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Processing triggers for libc-bin (2.31-13+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.5.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.1 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.3 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gff2aplot-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.17 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.OOnCoWAg/trustedkeys.kbx': General error
gpgv: Signature made Thu Sep 9 05:00:38 2021 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_2.0-14.dsc
dpkg-source: info: extracting gff2aplot in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz
dpkg-source: info: unpacking gff2aplot_2.0-14.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 disc 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=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-f0c726b4-2bf6-4a18-8d22-589e93edf416
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gff2aplot
dpkg-buildpackage: info: source version 2.0-14
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"
### Sun Sep 19 17:44:16 UTC 2021 -- 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 25 or more bytes (assuming 4028) 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 30 or more bytes (assuming 2034) 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 4028) 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 2034) 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 25 or more bytes (assuming 4028) 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 30 or more bytes (assuming 2034) 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 4028) 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 2034) 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_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-dbgsym' in '../gff2aplot-dbgsym_2.0-14_armhf.deb'.
dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-14_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../gff2aplot_2.0-14_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 2021-09-19T17:44:52Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gff2aplot_2.0-14_armhf.changes:
-------------------------------
Format: 1.8
Date: Thu, 09 Sep 2021 06:58:51 +0200
Source: gff2aplot
Binary: gff2aplot gff2aplot-dbgsym
Architecture: armhf
Version: 2.0-14
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript
Changes:
gff2aplot (2.0-14) unstable; urgency=medium
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[ Andreas Tille ]
* Fix homepage
* Define HOME=/tmp to enable salsa-ci building this package
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[ Diane Trout ]
* Update watch file to new upsream location
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[ Andreas Tille ]
* Standards-Version: 4.6.0 (routine-update)
* No tab in license text (routine-update)
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Files:
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gff2aplot-dbgsym_2.0-14_armhf.deb
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new Debian package, version 2.0.
size 25388 bytes: control archive=536 bytes.
375 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gff2aplot-dbgsym
Source: gff2aplot
Version: 2.0-14
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 39
Depends: gff2aplot (= 2.0-14)
Section: debug
Priority: optional
Description: debug symbols for gff2aplot
Build-Ids: 1c3d86f7c29be47cac4e16db4151899ee3d5ca0e
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gff2aplot_2.0-14_armhf.deb
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new Debian package, version 2.0.
size 244420 bytes: control archive=3404 bytes.
2842 bytes, 49 lines control
5626 bytes, 66 lines md5sums
Package: gff2aplot
Version: 2.0-14
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: 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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Build Architecture: armhf
Build-Space: 4916
Build-Time: 44
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 273
Job: gff2aplot_2.0-14
Machine Architecture: armhf
Package: gff2aplot
Package-Time: 368
Source-Version: 2.0-14
Space: 4916
Status: successful
Version: 2.0-14
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Finished at 2021-09-19T17:44:52Z
Build needed 00:06:08, 4916k disc space