gff2aplot →
2.0-9+b2 →
armhf → 2018-10-11 16:52:03
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| gff2aplot 2.0-9+b2 (armhf) Thu, 11 Oct 2018 16:45:28 +0000 |
+==============================================================================+
Package: gff2aplot
Version: 2.0-9+b2
Source Version: 2.0-9
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-dc0b48c3-1ab4-4ad3-ba05-0e2291bb38d6' 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 [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 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://anonscm.debian.org/git/debian-med/gff2aplot.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/gff2aplot.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 341 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main gff2aplot 2.0-9 (dsc) [2014 B]
Get:2 http://172.17.0.1/private buster-staging/main gff2aplot 2.0-9 (tar) [328 kB]
Get:3 http://172.17.0.1/private buster-staging/main gff2aplot 2.0-9 (diff) [10.4 kB]
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I: NOTICE: Log filtering will replace 'build/gff2aplot-PhdHYO/gff2aplot-2.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gff2aplot-PhdHYO' with '<<BUILDDIR>>'
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| Install build-essential |
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Setup apt archive
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dpkg-scanpackages: warning: Packages in archive but missing from override file:
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gpg: keybox '/<<BUILDDIR>>/resolver-PYcGN7/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-PYcGN7/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 libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
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sbuild-build-depends-core-dummy
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Arch check ok (armhf included in any)
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| Install package build dependencies |
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Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10)
Filtered Build-Depends: debhelper (>= 10)
dpkg-deb: building package 'sbuild-build-depends-gff2aplot-dummy' in '/<<BUILDDIR>>/resolver-PYcGN7/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)
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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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules 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 libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtool 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 libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtool libxml2 m4 man-db po-debconf
sbuild-build-depends-gff2aplot-dummy
0 upgraded, 35 newly installed, 0 to remove and 82 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:15 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
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Get:32 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
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+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+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_8.1.0-12+rpi1 gcc-8-base_8.1.0-12+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 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_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 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 Tue Nov 14 10:22:05 2017 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_2.0-9.dsc
dpkg-source: info: extracting gff2aplot in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gff2aplot_2.0.orig.tar.gz
dpkg-source: info: unpacking gff2aplot_2.0-9.debian.tar.xz
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
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.0-9+b2
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-dc0b48c3-1ab4-4ad3-ba05-0e2291bb38d6
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 2.0-9+b2
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build gff2aplot-2.0
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
make[1]: Entering directory '/<<PKGBUILDDIR>>'
###
### RUNNING MAKEFILE
###
### Finishing PERL script from "src/gff2aplot.pl" -> "bin/gff2aplot.pl"
### Thu Oct 11 16:51:30 UTC 2018 -- 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]
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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 25 and 4063 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4027) 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 25 and 4063 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output 25 or more bytes (assuming 4027) 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:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: 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:282:76: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
if ((sscanf(scores,"%[^:]:%s",waste,waste2)) == 2) sprintf(scores,"%s:%s",waste2,waste);
^~ ~~~~~
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 2 and 2000 bytes 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:722:23: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",xName,yName,xb,yb,xe,ye,frames,xName,yName,xb,yb,xe,ye,frames);
^~ ~~~~~
ali2gff.c:722:19: note: using the range [0, 4294967295] for directive argument
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",xName,yName,xb,yb,xe,ye,frames,xName,yName,xb,yb,xe,ye,frames);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:722:19: note: using the range [0, 4294967295] for directive argument
ali2gff.c:722:19: note: using the range [0, 4294967295] for directive argument
ali2gff.c:722:19: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 82 and 4156 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:939:27: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
sprintf(nextGAP,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t",xName,yName,fxb,fyb,fxe,fye);
^~ ~~~~~
ali2gff.c:939:23: note: using the range [0, 4294967295] for directive argument
sprintf(nextGAP,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t",xName,yName,fxb,fyb,fxe,fye);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:939:23: note: using the range [0, 4294967295] for directive argument
ali2gff.c:939:23: note: using the range [0, 4294967295] for directive argument
ali2gff.c:939:23: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 28 and 2062 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:946:26: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",xName,yName,xb,yb,xe,ye,frames,xName,yName,xb,yb,xe,ye,frames);
^~ ~~~~~
ali2gff.c:946:22: note: using the range [0, 4294967295] for directive argument
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",xName,yName,xb,yb,xe,ye,frames,xName,yName,xb,yb,xe,ye,frames);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:946:22: note: using the range [0, 4294967295] for directive argument
ali2gff.c:946:22: note: using the range [0, 4294967295] for directive argument
ali2gff.c:946:22: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 82 and 4156 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:481:23: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",yName,xName,yb,xb,ye,xe,frames,yName,xName,yb,xb,ye,xe,frames);
^~ ~~~~~
ali2gff.c:481:19: note: using the range [0, 4294967295] for directive argument
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",yName,xName,yb,xb,ye,xe,frames,yName,xName,yb,xb,ye,xe,frames);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:481:19: note: using the range [0, 4294967295] for directive argument
ali2gff.c:481:19: note: using the range [0, 4294967295] for directive argument
ali2gff.c:481:19: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 82 and 4156 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:698:27: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
sprintf(nextGAP,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t",yName,xName,fyb,fxb,fye,fxe);
^~ ~~~~~
ali2gff.c:698:23: note: using the range [0, 4294967295] for directive argument
sprintf(nextGAP,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t",yName,xName,fyb,fxb,fye,fxe);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:698:23: note: using the range [0, 4294967295] for directive argument
ali2gff.c:698:23: note: using the range [0, 4294967295] for directive argument
ali2gff.c:698:23: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 28 and 2062 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:705:26: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",yName,xName,yb,xb,ye,xe,frames,yName,xName,yb,xb,ye,xe,frames);
^~ ~~~~~
ali2gff.c:705:22: note: using the range [0, 4294967295] for directive argument
sprintf(nextMUM,"%s:%s\tMUMmer\talignment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\t# MUM\n%s:%s\tMUMmer\tfragment\t%lu:%lu\t%lu:%lu\t1.000\t+:+\t%s\n",yName,xName,yb,xb,ye,xe,frames,yName,xName,yb,xb,ye,xe,frames);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:705:22: note: using the range [0, 4294967295] for directive argument
ali2gff.c:705:22: note: using the range [0, 4294967295] for directive argument
ali2gff.c:705:22: note: using the range [0, 4294967295] for directive argument
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 82 and 4156 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:1093:44: 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%5.3f\t%c:%c\t%c:%c\n",xName,yName,source,xb,yb,xe,ye,score,strand1,strand2,frameChar,frameChar);
^~ ~~~~~
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 36 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:1092:44: warning: '%s' directive writing up to 999 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
if (opt_r) sprintf (aliPrintString,"%s:%s\t%s\talignment\t%lu:%lu\t%lu:%lu\t%5.3f\t%c:%c\t%c:%c\n",yName,xName,source,yb,xb,ye,xe,score,strand2,strand1,frameChar,frameChar);
^~ ~~~~~
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 36 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:1053:43: warning: ' seqbounds ' directive writing 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
else sprintf (seqboundsline,"\t%s\tseqbounds\t%lu:%lu\t%lu:%lu\t.\t.\t.\n",source,xb,yb,xe,ye);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 27 and 1062 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ali2gff.c:1052:43: warning: ' seqbounds ' directive writing 11 bytes into a region of size between 0 and 999 [-Wformat-overflow=]
if (opt_r) sprintf (seqboundsline,"\t%s\tseqbounds\t%lu:%lu\t%lu:%lu\t.\t.\t.\n",source,yb,xb,ye,xe);
^~~~~~~~~~~~~
In file included from /usr/include/stdio.h:862,
from ali2gff.h:20,
from ali2gff.c:64:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:33:10: note: '__builtin___sprintf_chk' output between 27 and 1062 bytes into a destination of size 1000
return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__bos (__s), __fmt, __va_arg_pack ());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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'
'./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
dh_installexamples -a
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' in '../gff2aplot_2.0-9+b2_armhf.deb'.
dpkg-deb: building package 'gff2aplot-dbgsym' in '../gff2aplot-dbgsym_2.0-9+b2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../gff2aplot_2.0-9+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build gff2aplot-2.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-10-11T16:51:57Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
gff2aplot_2.0-9+b2_armhf.changes:
---------------------------------
Format: 1.8
Date: Tue, 14 Nov 2017 11:15:53 +0100
Source: gff2aplot (2.0-9)
Binary: gff2aplot
Binary-Only: yes
Architecture: armhf
Version: 2.0-9+b2
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
gff2aplot - pair-wise alignment-plots for genomic sequences in PostScript
Changes:
gff2aplot (2.0-9+b2) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Checksums-Sha256:
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Files:
a0a86e3c8caeb2c4b1cb47fa63ec215e 25356 debug optional gff2aplot-dbgsym_2.0-9+b2_armhf.deb
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bfb046a41d874e27e63aa6005bca4aed 307924 science optional gff2aplot_2.0-9+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
gff2aplot-dbgsym_2.0-9+b2_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 25356 bytes: control archive=540 bytes.
387 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: gff2aplot-dbgsym
Source: gff2aplot (2.0-9)
Version: 2.0-9+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 39
Depends: gff2aplot (= 2.0-9+b2)
Section: debug
Priority: optional
Description: debug symbols for gff2aplot
Build-Ids: 92f4b4e1fcbebb3e7ecb165ffdcfef6af975015c
drwxr-xr-x root/root 0 2017-11-14 10:15 ./
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/lib/debug/.build-id/92/
-rw-r--r-- root/root 28992 2017-11-14 10:15 ./usr/lib/debug/.build-id/92/f4b4e1fcbebb3e7ecb165ffdcfef6af975015c.debug
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-11-14 10:15 ./usr/share/doc/gff2aplot-dbgsym -> gff2aplot
gff2aplot_2.0-9+b2_armhf.deb
----------------------------
new Debian package, version 2.0.
size 307924 bytes: control archive=3188 bytes.
2815 bytes, 49 lines control
5093 bytes, 59 lines md5sums
Package: gff2aplot
Source: gff2aplot (2.0-9)
Version: 2.0-9+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 615
Depends: libc6 (>= 2.7), perl:any
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.
drwxr-xr-x root/root 0 2017-11-14 10:15 ./
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/bin/
-rwxr-xr-x root/root 24108 2017-11-14 10:15 ./usr/bin/ali2gff
-rwxr-xr-x root/root 5381 2017-11-14 10:15 ./usr/bin/blat2gff
-rwxr-xr-x root/root 201809 2017-11-14 10:15 ./usr/bin/gff2aplot
-rwxr-xr-x root/root 36734 2017-11-14 10:15 ./usr/bin/parseblast
-rwxr-xr-x root/root 10232 2017-11-14 10:15 ./usr/bin/sim2gff
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/doc/gff2aplot/
-rw-r--r-- root/root 66824 2017-11-14 10:15 ./usr/share/doc/gff2aplot/GFF2APLOT_MANUAL.ps.gz
-rw-r--r-- root/root 2211 2003-06-05 15:45 ./usr/share/doc/gff2aplot/README.gz
-rw-r--r-- root/root 221 2017-11-14 10:15 ./usr/share/doc/gff2aplot/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1167 2017-11-14 10:15 ./usr/share/doc/gff2aplot/changelog.Debian.gz
-rw-r--r-- root/root 1422 2017-11-14 10:15 ./usr/share/doc/gff2aplot/copyright
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/doc/gff2aplot/examples/
drwxr-xr-x root/root 0 2017-11-14 10:15 ./usr/share/doc/gff2aplot/examples/mhcregion/
-rw-r--r-- root/root 2984 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/README.gz
-rw-r--r-- root/root 12273 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff.gz
-rw-r--r-- root/root 3807 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sgp1.gff
-rw-r--r-- root/root 12211 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff.gz
-rw-r--r-- root/root 9392 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gz
-rw-r--r-- root/root 4496 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.tblastx.gff.gz
-rw-r--r-- root/root 10206 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs.fa.gz
-rw-r--r-- root/root 2033 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/hs.gff
-rw-r--r-- root/root 19866 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/index.html
-rw-r--r-- root/root 12293 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/kk.sim.gz
-rw-r--r-- root/root 885 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mhc2+sgp1.rc
-rw-r--r-- root/root 797 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mhc2.rc
-rw-r--r-- root/root 55 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mhc2labels.rc
-rw-r--r-- root/root 65 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mhc2spc.rc
-rw-r--r-- root/root 10893 2003-06-05 15:45 ./usr/share/doc/gff2aplot/examples/mhcregion/mm.fa.gz
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 3352
Build-Time: 34
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 308
Job: gff2aplot_2.0-9
Machine Architecture: armhf
Package: gff2aplot
Package-Time: 389
Source-Version: 2.0-9
Space: 3352
Status: successful
Version: 2.0-9+b2
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Finished at 2018-10-11T16:51:57Z
Build needed 00:06:29, 3352k disc space