gff2aplot →
2.0-11 →
armhf → 2019-02-01 05:40:03
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| gff2aplot 2.0-11 (armhf) Fri, 01 Feb 2019 05:33:35 +0000 |
+==============================================================================+
Package: gff2aplot
Version: 2.0-11
Source Version: 2.0-11
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-1681f20c-ad71-4248-a856-cf04e24325d2' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
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Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 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 350 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main gff2aplot 2.0-11 (dsc) [2082 B]
Get:2 http://172.17.0.1/private buster-staging/main gff2aplot 2.0-11 (tar) [328 kB]
Get:3 http://172.17.0.1/private buster-staging/main gff2aplot 2.0-11 (diff) [19.9 kB]
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I: NOTICE: Log filtering will replace 'build/gff2aplot-73VF5v/gff2aplot-2.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gff2aplot-73VF5v' with '<<BUILDDIR>>'
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| Install build-essential |
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Merged Build-Depends: build-essential, fakeroot
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gpg: keybox '/<<BUILDDIR>>/resolver-Q08mKr/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Q08mKr/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
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
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+------------------------------------------------------------------------------+
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~)
Filtered Build-Depends: debhelper (>= 11~)
dpkg-deb: building package 'sbuild-build-depends-gff2aplot-dummy' in '/<<BUILDDIR>>/resolver-Q08mKr/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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Install gff2aplot build dependencies (apt-based resolver)
---------------------------------------------------------
Installing build dependencies
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Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libuchardet0 libxml2 m4 man-db
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation 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 bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libglib2.0-0 libicu63 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-gff2aplot-dummy
0 upgraded, 32 newly installed, 0 to remove and 16 not upgraded.
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Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
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Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
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Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-14+rpi1 gcc-8_8.2.0-14+rpi1 libc6-dev_2.28-5+rpi1 libstdc++-8-dev_8.2.0-14+rpi1 libstdc++6_8.2.0-14+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~beta1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-14+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-14+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-14+rpi1 gcc-8-base_8.2.0-14+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.4-15+rpi1 kmod_25-2 krb5-locales_1.17-1 libacl1_2.2.52-3 libapparmor1_2.13.2-3 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-14+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-14+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-5+rpi1 libc-dev-bin_2.28-5+rpi1 libc6_2.28-5+rpi1 libc6-dev_2.28-5+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_8.2.0-14+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.155-1 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-14+rpi1 libgcc1_1:8.2.0-14+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-14+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1~rc1-1 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.17-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-15+rpi1 libkmod2_25-2 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-2 libldap-common_2.4.47+dfsg-2 liblz4-1_1.8.3-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnpth0_1.6-1 libnss-systemd_240-4+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-4+rpi1 libpam0g_1.1.8-4 libpcre3_2:8.39-11+rpi1 libperl5.24_5.24.1-4 libperl5.28_5.28.1-3 libpipeline1_1.5.1-1 libplymouth4_0.9.4-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-14+rpi1 libstdc++6_8.2.0-14+rpi1 libsystemd0_240-4+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-8 libubsan1_8.2.0-14+rpi1 libuchardet0_0.0.6-3 libudev1_240-4+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-1 mawk_1.3.3-17 mount_2.33.1-0.1 multiarch-support_2.28-5+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 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 systemd_240-4+rpi1 systemd-sysv_240-4+rpi1 sysvinit-utils_2.93-5 tar_1.30+dfsg-4 tzdata_2018i-1 udev_240-4+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jan 30 13:15:32 2019 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_2.0-11.dsc
dpkg-source: info: extracting gff2aplot in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz
dpkg-source: info: unpacking gff2aplot_2.0-11.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
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-1681f20c-ad71-4248-a856-cf04e24325d2
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gff2aplot
dpkg-buildpackage: info: source version 2.0-11
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot 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 build-arch
dh build-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
###
### Fri Feb 1 05:39:28 UTC 2019 -- buildd
### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl"
###
### 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]
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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__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=]
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:873,
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
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c: In function 'processMumfile':
ali2gff.c:421:30: warning: 'fyb' may be used uninitialized in this function [-Wmaybe-uninitialized]
unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps
^~~
ali2gff.c:732:12: warning: 'score' may be used uninitialized in this function [-Wmaybe-uninitialized]
score = (score - errCount)/score; // match percentage
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:421:20: warning: 'fxb' may be used uninitialized in this function [-Wmaybe-uninitialized]
unsigned long int fxb, fxe, fyb, fye; // start and end positions of gaps resp. fragments of gaps
^~~
ali2gff.c: In function 'processSimfile':
ali2gff.c:1073:15: warning: 'yrev' may be used uninitialized in this function [-Wmaybe-uninitialized]
ye = yrev-ye;
~~~~^~~
ali2gff.c:1064:41: warning: 'yseqLen_4' may be used uninitialized in this function [-Wmaybe-uninitialized]
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]
if (!opt_i || ((xe - xb < xseqLen_4) && (ye - yb < yseqLen_4))) {
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src/ali2gff'
mkdir -p ./bin
cp ./src/ali2gff/ali2gff \
./bin/ali2gff
mode of 'bin/gff2aplot.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x)
mode of 'bin/parseblast.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x)
mode of 'bin/blat2gff.pl' changed from 0664 (rw-rw-r--) to 0755 (rwxr-xr-x)
mode of 'bin/sim2gff.pl' changed from 0664 (rw-rw-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
fakeroot debian/rules binary-arch
dh binary-arch
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_strip -a
dh_makeshlibs -a
dh_shlibdeps -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_2.0-11_armhf.deb'.
dpkg-deb: building package 'gff2aplot' in '../gff2aplot_2.0-11_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../gff2aplot_2.0-11_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)
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Build finished at 2019-02-01T05:39:56Z
Finished
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I: Built successfully
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| Changes |
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gff2aplot_2.0-11_armhf.changes:
-------------------------------
Format: 1.8
Date: Wed, 30 Jan 2019 14:12:34 +0100
Source: gff2aplot
Binary: gff2aplot
Architecture: armhf
Version: 2.0-11
Distribution: buster-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
Closes: 890789 909714
Changes:
gff2aplot (2.0-11) unstable; urgency=medium
.
* README files in examples are actually scripts - fix PATH to gff2aplot
* Add autopkgtest
Closes: #890789, #909714
* Fix issue with Perl 5.28
* Fix definition of CP in upstream makefile
* Try hard to make sprint buffers have proper size
* Recommends: graphicsmagick | imagemagick, ghostscript (+ Test-Depends)
* Fix README used as shell script for testing
* hardening=+all
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| Package contents |
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gff2aplot-dbgsym_2.0-11_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 25468 bytes: control archive=536 bytes.
375 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gff2aplot-dbgsym
Source: gff2aplot
Version: 2.0-11
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 39
Depends: gff2aplot (= 2.0-11)
Section: debug
Priority: optional
Description: debug symbols for gff2aplot
Build-Ids: 87e2fb69273550065ed79b36f16a51e30b0038f3
drwxr-xr-x root/root 0 2019-01-30 13:12 ./
drwxr-xr-x root/root 0 2019-01-30 13:12 ./usr/
drwxr-xr-x root/root 0 2019-01-30 13:12 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-30 13:12 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-01-30 13:12 ./usr/lib/debug/.build-id/
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drwxr-xr-x root/root 0 2019-01-30 13:12 ./usr/share/
drwxr-xr-x root/root 0 2019-01-30 13:12 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-01-30 13:12 ./usr/share/doc/gff2aplot-dbgsym -> gff2aplot
gff2aplot_2.0-11_armhf.deb
--------------------------
new Debian package, version 2.0.
size 312964 bytes: control archive=3412 bytes.
2841 bytes, 49 lines control
5686 bytes, 66 lines md5sums
Package: gff2aplot
Version: 2.0-11
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 635
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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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 3992
Build-Time: 35
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 289
Job: gff2aplot_2.0-11
Machine Architecture: armhf
Package: gff2aplot
Package-Time: 381
Source-Version: 2.0-11
Space: 3992
Status: successful
Version: 2.0-11
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Finished at 2019-02-01T05:39:56Z
Build needed 00:06:21, 3992k disc space