Package: sra-toolkit-libs-dev; Maintainer for sra-toolkit-libs-dev is Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>; Source for sra-toolkit-libs-dev is src:sra-sdk (PTS, buildd, popcon).
Reported by: David Steele <dsteele@gmail.com>
Date: Sat, 6 Jul 2013 05:32:19 UTC
Severity: normal
Found in version sra-sdk/2.1.7a-1
Fixed in version sra-sdk/2.3.4-2+dfsg-1
Done: Andreas Tille <tille@debian.org>
Bug is archived. No further changes may be made.
View this report as an mbox folder, status mbox, maintainer mbox
Report forwarded
to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>:
Bug#715133; Package sra-toolkit-libs-dev.
(Sat, 06 Jul 2013 05:32:24 GMT) (full text, mbox, link).
Acknowledgement sent
to David Steele <dsteele@gmail.com>:
New Bug report received and forwarded. Copy sent to Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>.
(Sat, 06 Jul 2013 05:32:24 GMT) (full text, mbox, link).
Message #5 received at maintonly@bugs.debian.org (full text, mbox, reply):
Package: sra-toolkit-libs-dev
Version: 2.1.7a-1
Severity: serious
User: debian-qa@lists.debian.org
Usertags: piuparts, broken-symlink, broken-symlink-shared-library
Hi,
During a test with piuparts, I noticed your package is
responsible for the presence of broken symlinks involving
a shared library. Such failures may indicate a significant
problem with the package.
Usually this is caused by a missing Depends. It may also be
triggered if a Recommended or reverse dependency package
owning the symlink target file is not yet installed. This type
of failure mode needs to be eliminated so that other symlink
problems become more visible. In this case, the problem can be
resolved by creating a trigger for the target file. See the
dpkg triggers documentation[1] and an example on the net[2] for
implementation details.
This is being filed as Serious because it represents a violation
of Policy. Section 8 states "Packages containing shared
libraries must be constructed with a little care to make sure
that the shared library is always available".
A link to the log containing the indicated broken symlinks can
be found on piuparts.debian.org[3]. Search for "Warn: Broken
Symlinks" to see the failure point. A log showing the broken
symlink as an error is appended.
The log contains the following broken symlinks:
/usr/lib/libsrareader.so
-> libsrareader.so.1
/usr/lib/libvdb.so
-> libvdb.so.2
/usr/lib/libkq.so
-> libkq.so.1
/usr/lib/libwvdb.so
-> libwvdb.so.2
/usr/lib/libkxfs.so
-> libkxfs.so.1
/usr/lib/libalign-access.so
-> libalign-access.so.1
/usr/lib/libwsradb.so
-> libwsradb.so.3
/usr/lib/libwsra-schema.so
-> libwsra-schema.so.1
/usr/lib/libwkdb.so
-> libwkdb.so.1
/usr/lib/libkproc.so
-> libkproc.so.1
/usr/lib/libsradb.so
-> libsradb.so.3
/usr/lib/libkfs.so
-> libkfs.so.1
/usr/lib/libkfg.so
-> libkfg.so.1
/usr/lib/libksrch.so
-> libksrch.so.1
/usr/lib/libkxml.so
-> libkxml.so.1
/usr/lib/libksproc.so
-> libksproc.so.1
/usr/lib/libalign-reader.so
-> libalign-reader.so.1
/usr/lib/libklib.so
-> libklib.so.1
/usr/lib/libkdb.so
-> libkdb.so.1
[1] - file:///usr/share/doc/dpkg-dev/triggers.txt.gz
[2] - http://www.seanius.net/blog/2009/09/dpkg-triggers-howto/
[3] - http://piuparts.debian.org/sid/broken_symlinks_issue.html
----------
Start: 2013-07-05 22:14:40 EST
Package: sra-toolkit-libs-dev
Source: sra-sdk
Version: 2.1.7a-1
Installed-Size: 40
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Description: Development files for the NCBI SRA Toolkit's libraries
Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
Description-md5: db6c561e7efde962727ce64ca7bc482d
Section: science
Priority: optional
Filename: pool/main/s/sra-sdk/sra-toolkit-libs-dev_2.1.7a-1_amd64.deb
Size: 6320
MD5sum: c553ab8849494dc77d2b6e1120c8a7cd
SHA1: aa8af248cef9a38dccf26bee24edd47a612c2ab4
SHA256: 3bc66fddaee7a4413a8c1ebe50e345195ea53cdb1bf4f392311d328cb8458f95
Executing: sudo piuparts --scriptsdir /etc/piuparts/scripts --skip-logrotatefiles-test --warn-on-others --fail-on-broken-symlinks --mirror http://127.0.0.1/debian --tmpdir /var/tmp --arch amd64 -b /var/cache/piuparts/basetgz/sid.tar.gz -d sid --no-upgrade-test --apt sra-toolkit-libs-dev=2.1.7a-1
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile.
0m0.0s INFO: FAQ available at http://wiki.debian.org/piuparts/FAQ
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: piuparts version 0.54~201306172307~0.53-14-ge8900a0 starting up.
0m0.0s INFO: Command line arguments: '/usr/sbin/piuparts' '--scriptsdir' '/etc/piuparts/scripts' '--skip-logrotatefiles-test' '--warn-on-others' '--fail-on-broken-symlinks' '--mirror' 'http://127.0.0.1/debian' '--tmpdir' '/var/tmp' '--arch' 'amd64' '-b' '/var/cache/piuparts/basetgz/sid.tar.gz' '-d' 'sid' '--no-upgrade-test' '--apt' 'sra-toolkit-libs-dev=2.1.7a-1'
0m0.0s INFO: Running on: Linux debian-testing 3.9-1-amd64 #1 SMP Debian 3.9.8-1 x86_64
0m0.0s DEBUG: Created temporary directory /var/tmp/tmpc5FTmP
0m0.0s DEBUG: Unpacking /var/cache/piuparts/basetgz/sid.tar.gz into /var/tmp/tmpc5FTmP
0m0.0s DEBUG: Starting command: ['tar', '-C', '/var/tmp/tmpc5FTmP', '-zxf', '/var/cache/piuparts/basetgz/sid.tar.gz']
0m1.2s DEBUG: Command ok: ['tar', '-C', '/var/tmp/tmpc5FTmP', '-zxf', '/var/cache/piuparts/basetgz/sid.tar.gz']
0m1.2s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'mount', '-t', 'proc', 'proc', '/proc']
0m1.2s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'mount', '-t', 'proc', 'proc', '/proc']
0m1.2s DEBUG: sources.list:
deb http://127.0.0.1/debian sid main
deb http://127.0.0.1/debian sid contrib
deb http://127.0.0.1/debian sid non-free
0m1.2s DEBUG: Created policy-rc.d and chmodded it.
0m1.2s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', 'update']
0m5.4s DUMP:
Get:1 http://127.0.0.1 sid InRelease [205 kB]
Get:2 http://127.0.0.1 sid/main amd64 Packages [6398 kB]
Get:3 http://127.0.0.1 sid/contrib amd64 Packages [48.5 kB]
Get:4 http://127.0.0.1 sid/non-free amd64 Packages [84.6 kB]
Get:5 http://127.0.0.1 sid/contrib Translation-en [39.9 kB]
Get:6 http://127.0.0.1 sid/main Translation-en [4246 kB]
Get:7 http://127.0.0.1 sid/non-free Translation-en [72.7 kB]
Fetched 11.1 MB in 3s (3535 kB/s)
Reading package lists...
0m5.4s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', 'update']
0m5.4s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', '-yf', 'dist-upgrade']
0m7.0s DUMP:
Reading package lists...
Building dependency tree...
The following packages will be upgraded:
apt libapt-pkg4.12 libc-bin libc6 multiarch-support
5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 8332 kB of archives.
After this operation, 132 kB of additional disk space will be used.
Get:1 http://127.0.0.1/debian/ sid/main libc-bin amd64 2.17-7 [1298 kB]
Get:2 http://127.0.0.1/debian/ sid/main libc6 amd64 2.17-7 [4624 kB]
Get:3 http://127.0.0.1/debian/ sid/main libapt-pkg4.12 amd64 0.9.9 [926 kB]
Get:4 http://127.0.0.1/debian/ sid/main apt amd64 0.9.9 [1323 kB]
Get:5 http://127.0.0.1/debian/ sid/main multiarch-support amd64 2.17-7 [160 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8332 kB in 0s (45.1 MB/s)
(Reading database ... 6639 files and directories currently installed.)
Preparing to replace libc-bin 2.17-6 (using .../libc-bin_2.17-7_amd64.deb) ...
Unpacking replacement libc-bin ...
Setting up libc-bin (2.17-7) ...
(Reading database ... 6639 files and directories currently installed.)
Preparing to replace libc6:amd64 2.17-6 (using .../libc6_2.17-7_amd64.deb) ...
Unpacking replacement libc6:amd64 ...
Setting up libc6:amd64 (2.17-7) ...
Processing triggers for libc-bin ...
(Reading database ... 6639 files and directories currently installed.)
Preparing to replace libapt-pkg4.12:amd64 0.9.8.2 (using .../libapt-pkg4.12_0.9.9_amd64.deb) ...
Unpacking replacement libapt-pkg4.12:amd64 ...
Setting up libapt-pkg4.12:amd64 (0.9.9) ...
Processing triggers for libc-bin ...
(Reading database ... 6639 files and directories currently installed.)
Preparing to replace apt 0.9.8.2 (using .../archives/apt_0.9.9_amd64.deb) ...
Unpacking replacement apt ...
Setting up apt (0.9.9) ...
gpg: key B98321F9: "Squeeze Stable Release Key <debian-release@lists.debian.org>" not changed
gpg: key 473041FA: "Debian Archive Automatic Signing Key (6.0/squeeze) <ftpmaster@debian.org>" not changed
gpg: key 65FFB764: "Wheezy Stable Release Key <debian-release@lists.debian.org>" not changed
gpg: key 46925553: "Debian Archive Automatic Signing Key (7.0/wheezy) <ftpmaster@debian.org>" not changed
gpg: Total number processed: 4
gpg: unchanged: 4
(Reading database ... 6639 files and directories currently installed.)
Preparing to replace multiarch-support 2.17-6 (using .../multiarch-support_2.17-7_amd64.deb) ...
Unpacking replacement multiarch-support ...
Setting up multiarch-support (2.17-7) ...
0m7.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', '-yf', 'dist-upgrade']
0m7.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /var/tmp/tmpc5FTmP/tmp/scripts/
0m7.0s INFO: Running scripts post_setup
0m7.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/post_setup_experimental']
0m7.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/post_setup_experimental']
0m7.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/post_setup_forbid_home']
0m7.0s DUMP:
Disabling /home
0m7.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/post_setup_forbid_home']
0m7.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/post_setup_squeeze-backports']
0m7.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/post_setup_squeeze-backports']
0m7.0s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', 'clean']
0m7.1s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', 'clean']
0m7.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg', '--get-selections', '*']
0m7.9s DUMP:
apt install
base-files install
base-passwd install
bash install
bsdutils install
coreutils install
dash install
debconf install
debconf-i18n install
debian-archive-keyring install
debianutils install
diffutils install
dpkg install
e2fslibs:amd64 install
e2fsprogs install
eatmydata install
findutils install
gcc-4.7-base:amd64 install
gcc-4.8-base:amd64 install
gnupg install
gpgv install
grep install
gzip install
hostname install
initscripts install
insserv install
libacl1:amd64 install
libapt-pkg4.12:amd64 install
libattr1:amd64 install
libblkid1:amd64 install
libbz2-1.0:amd64 install
libc-bin install
libc6:amd64 install
libcap2:amd64 install
libcomerr2:amd64 install
libdb5.1:amd64 install
libgcc1:amd64 install
liblocale-gettext-perl install
liblzma5:amd64 install
libmount1 install
libncurses5:amd64 install
libpam-modules:amd64 install
libpam-modules-bin install
libpam-runtime install
libpam0g:amd64 install
libpcre3:amd64 install
libreadline6:amd64 install
libselinux1:amd64 install
libsemanage-common install
libsemanage1:amd64 install
libsepol1:amd64 install
libslang2:amd64 install
libss2:amd64 install
libstdc++6:amd64 install
libtext-charwidth-perl install
libtext-iconv-perl install
libtext-wrapi18n-perl install
libtinfo5:amd64 install
libusb-0.1-4:amd64 install
libustr-1.0-1:amd64 install
libuuid1:amd64 install
login install
lsb-base install
mawk install
mount install
multiarch-support install
ncurses-base install
ncurses-bin install
passwd install
perl-base install
readline-common install
sed install
sensible-utils install
sysv-rc install
sysvinit install
sysvinit-utils install
tar install
tzdata install
util-linux install
zlib1g:amd64 install
0m7.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg', '--get-selections', '*']
0m7.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg-divert', '--list']
0m7.9s DUMP:
diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash
diversion of /bin/sh to /bin/sh.distrib by dash
0m7.9s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg-divert', '--list']
0m7.9s INFO: Starting install/purge
0m7.9s INFO: apt-cache does not know about any of the requested packages
0m7.9s INFO: Running scripts pre_test
0m7.9s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_test_root_password']
0m8.0s DUMP:
Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully
0m8.0s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_test_root_password']
0m8.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/var/tmp/tmpc5FTmP']
0m8.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/var/tmp/tmpc5FTmP']
0m9.1s DEBUG: No broken symlinks as far as we can find.
0m9.1s INFO: Running scripts pre_install
0m9.1s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_install_database-server']
0m9.1s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_install_database-server']
0m9.1s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_install_exceptions']
0m9.1s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_install_exceptions']
0m9.1s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m9.1s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m9.1s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-cache', 'show', 'sra-toolkit-libs-dev']
0m10.2s DUMP:
Package: sra-toolkit-libs-dev
Source: sra-sdk
Version: 2.1.7a-1
Installed-Size: 40
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Description-en: Development files for the NCBI SRA Toolkit's libraries
This package provides development support files for the
NCBI SRA Toolkit's libraries.
Description-md5: db6c561e7efde962727ce64ca7bc482d
Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software
Description-md5: db6c561e7efde962727ce64ca7bc482d
Section: science
Priority: optional
Filename: pool/main/s/sra-sdk/sra-toolkit-libs-dev_2.1.7a-1_amd64.deb
Size: 6320
MD5sum: c553ab8849494dc77d2b6e1120c8a7cd
SHA1: aa8af248cef9a38dccf26bee24edd47a612c2ab4
SHA256: 3bc66fddaee7a4413a8c1ebe50e345195ea53cdb1bf4f392311d328cb8458f95
0m10.2s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-cache', 'show', 'sra-toolkit-libs-dev']
0m10.2s DEBUG: Starting command: ['dpkg-deb', '-b', '--nocheck', '/var/tmp/tmpDP7k5_/piuparts-depends-dummy']
0m10.2s DUMP:
dpkg-deb: warning: not checking contents of control area
dpkg-deb: building an unknown package in '/var/tmp/tmpDP7k5_/piuparts-depends-dummy.deb'.
0m10.2s DEBUG: Command ok: ['dpkg-deb', '-b', '--nocheck', '/var/tmp/tmpDP7k5_/piuparts-depends-dummy']
0m10.2s DEBUG: Copying /var/tmp/tmpDP7k5_/piuparts-depends-dummy.deb to /var/tmp/tmpc5FTmP/tmp
0m10.2s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb']
0m10.2s DUMP:
Selecting previously unselected package piuparts-depends-dummy.
(Reading database ... 6639 files and directories currently installed.)
Unpacking piuparts-depends-dummy (from tmp/piuparts-depends-dummy.deb) ...
Setting up piuparts-depends-dummy (0.invalid.0) ...
0m10.2s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg', '-i', 'tmp/piuparts-depends-dummy.deb']
0m10.2s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', '-yf', 'install']
0m10.5s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m10.5s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', '-yf', 'install']
0m10.5s INFO: Installation of ['tmp/piuparts-depends-dummy.deb'] ok
0m10.5s DEBUG: Removing /var/tmp/tmpc5FTmP/tmp/piuparts-depends-dummy.deb
0m10.5s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg', '--purge', 'piuparts-depends-dummy']
0m10.5s DUMP:
(Reading database ... 6639 files and directories currently installed.)
Removing piuparts-depends-dummy ...
0m10.5s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'dpkg', '--purge', 'piuparts-depends-dummy']
0m10.5s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', 'clean']
0m10.6s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', 'clean']
0m11.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/var/tmp/tmpc5FTmP']
0m11.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/var/tmp/tmpc5FTmP']
0m12.5s DEBUG: No broken symlinks as far as we can find.
0m12.5s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-cache', 'policy']
0m13.7s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://127.0.0.1/debian/ sid/non-free Translation-en
500 http://127.0.0.1/debian/ sid/main Translation-en
500 http://127.0.0.1/debian/ sid/contrib Translation-en
500 http://127.0.0.1/debian/ sid/non-free amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=non-free
origin 127.0.0.1
500 http://127.0.0.1/debian/ sid/contrib amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=contrib
origin 127.0.0.1
500 http://127.0.0.1/debian/ sid/main amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=main
origin 127.0.0.1
Pinned packages:
0m13.7s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-cache', 'policy']
0m13.7s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-cache', 'policy', 'sra-toolkit-libs-dev']
0m13.7s DUMP:
sra-toolkit-libs-dev:
Installed: (none)
Candidate: 2.1.7a-1
Version table:
2.1.7a-1 0
500 http://127.0.0.1/debian/ sid/main amd64 Packages
0m13.7s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-cache', 'policy', 'sra-toolkit-libs-dev']
0m13.7s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', '-y', 'install', 'sra-toolkit-libs-dev=2.1.7a-1']
0m14.2s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sra-toolkit-libs-dev
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 6320 B of archives.
After this operation, 41.0 kB of additional disk space will be used.
Get:1 http://127.0.0.1/debian/ sid/main sra-toolkit-libs-dev amd64 2.1.7a-1 [6320 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 6320 B in 0s (147 kB/s)
Selecting previously unselected package sra-toolkit-libs-dev.
(Reading database ... 6639 files and directories currently installed.)
Unpacking sra-toolkit-libs-dev (from .../sra-toolkit-libs-dev_2.1.7a-1_amd64.deb) ...
Setting up sra-toolkit-libs-dev (2.1.7a-1) ...
0m14.2s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'apt-get', '-y', 'install', 'sra-toolkit-libs-dev=2.1.7a-1']
0m14.2s INFO: Running scripts post_install
0m14.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/var/tmp/tmpc5FTmP']
0m14.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/var/tmp/tmpc5FTmP']
0m15.3s ERROR: FAIL: Broken symlinks:
/usr/lib/libsrareader.so -> libsrareader.so.1
/usr/lib/libvdb.so -> libvdb.so.2
/usr/lib/libkq.so -> libkq.so.1
/usr/lib/libwvdb.so -> libwvdb.so.2
/usr/lib/libkxfs.so -> libkxfs.so.1
/usr/lib/libalign-access.so -> libalign-access.so.1
/usr/lib/libwsradb.so -> libwsradb.so.3
/usr/lib/libwsra-schema.so -> libwsra-schema.so.1
/usr/lib/libwkdb.so -> libwkdb.so.1
/usr/lib/libkproc.so -> libkproc.so.1
/usr/lib/libsradb.so -> libsradb.so.3
/usr/lib/libkfs.so -> libkfs.so.1
/usr/lib/libkfg.so -> libkfg.so.1
/usr/lib/libksrch.so -> libksrch.so.1
/usr/lib/libkxml.so -> libkxml.so.1
/usr/lib/libksproc.so -> libksproc.so.1
/usr/lib/libalign-reader.so -> libalign-reader.so.1
/usr/lib/libklib.so -> libklib.so.1
/usr/lib/libkdb.so -> libkdb.so.1
0m15.8s DEBUG: Starting command: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'umount', '/proc']
0m15.8s DEBUG: Command ok: ['chroot', '/var/tmp/tmpc5FTmP', 'eatmydata', 'umount', '/proc']
0m15.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/var/tmp/tmpc5FTmP']
0m15.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/var/tmp/tmpc5FTmP']
0m15.8s DEBUG: Removed directory tree at /var/tmp/tmpc5FTmP
0m15.8s ERROR: piuparts run ends.
ret=1
End: 2013-07-05 22:14:57 EST
Severity set to 'normal' from 'serious'
Request was from Dave Steele <dsteele@gmail.com>
to control@bugs.debian.org.
(Sat, 06 Jul 2013 21:57:57 GMT) (full text, mbox, link).
Reply sent
to Andreas Tille <tille@debian.org>:
You have taken responsibility.
(Tue, 24 Dec 2013 09:24:10 GMT) (full text, mbox, link).
Notification sent
to David Steele <dsteele@gmail.com>:
Bug acknowledged by developer.
(Tue, 24 Dec 2013 09:24:10 GMT) (full text, mbox, link).
Message #12 received at 715133-close@bugs.debian.org (full text, mbox, reply):
Source: sra-sdk
Source-Version: 2.3.4-2+dfsg-1
We believe that the bug you reported is fixed in the latest version of
sra-sdk, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 715133@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated sra-sdk package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Mon, 23 Dec 2013 22:27:00 +0100
Source: sra-sdk
Binary: sra-toolkit sra-toolkit-libs0 sra-toolkit-libs-dev
Architecture: source amd64
Version: 2.3.4-2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
sra-toolkit - utilities for the NCBI Sequence Read Archive
sra-toolkit-libs-dev - Development files for the NCBI SRA Toolkit's libraries
sra-toolkit-libs0 - Libraries for the SRA Toolkit
Closes: 715133
Changes:
sra-sdk (2.3.4-2+dfsg-1) unstable; urgency=medium
.
* New upstream version
* debian/control:
- Add missing Depends: sra-toolkit-libs0 to sra-toolkit-libs-dev
Closes: #715133
- Standards-Version: 3.9.5 (no changes needed)
* debian/sra-toolkit-libs0.symbols: Adapted to new upstream version
Checksums-Sha1:
8cb99f2f41e4d44457f161ea115a00cfc108e79b 1558 sra-sdk_2.3.4-2+dfsg-1.dsc
5a959f75ca3677a31b73624984b88f2fae989799 2213588 sra-sdk_2.3.4-2+dfsg.orig.tar.xz
ca87a49dd72ee7c3be5dfc0bcddb8444edff74c0 40246 sra-sdk_2.3.4-2+dfsg-1.debian.tar.gz
031bdba04de8ea63e09d8299576fb052da685f30 878946 sra-toolkit_2.3.4-2+dfsg-1_amd64.deb
45e0d18d2b4cde6d26912326bd8155481a019c52 1114540 sra-toolkit-libs0_2.3.4-2+dfsg-1_amd64.deb
78f7a8ca9d25f8b064a5f6c912262ef3b6df0d22 5616 sra-toolkit-libs-dev_2.3.4-2+dfsg-1_amd64.deb
Checksums-Sha256:
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0b589b5b02b7c1fb238da128cb5af88291dc7f4051ae31b3537e9c82dbf319a3 2213588 sra-sdk_2.3.4-2+dfsg.orig.tar.xz
f225989adcc94fec739744491565ab1dc6bd8f9cd7a67642d81844b422ed7a18 40246 sra-sdk_2.3.4-2+dfsg-1.debian.tar.gz
656ae7e29b7a6ea1041f8f566a049030a4642ab31369baa51cbc23923c8eed0f 878946 sra-toolkit_2.3.4-2+dfsg-1_amd64.deb
6161ab7fd745249cd44522d6154e1e8cd5c7303f213391e4354c2d8366239f26 1114540 sra-toolkit-libs0_2.3.4-2+dfsg-1_amd64.deb
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Files:
f809b727a2e0100583b70b1b673e78a6 1558 science optional sra-sdk_2.3.4-2+dfsg-1.dsc
bbf4f9edc6b680d7768e8673c224d813 2213588 science optional sra-sdk_2.3.4-2+dfsg.orig.tar.xz
92c5377f5407a65c2c815af38fdfe69e 40246 science optional sra-sdk_2.3.4-2+dfsg-1.debian.tar.gz
49e22c2e15107d86dbdc339f1ed012f9 878946 science optional sra-toolkit_2.3.4-2+dfsg-1_amd64.deb
eb0c8f1f747f760f2e55e4ac00d0360c 1114540 science optional sra-toolkit-libs0_2.3.4-2+dfsg-1_amd64.deb
7248f061e76a873cee13e8a08b686058 5616 science optional sra-toolkit-libs-dev_2.3.4-2+dfsg-1_amd64.deb
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Bug archived.
Request was from Debbugs Internal Request <owner@bugs.debian.org>
to internal_control@bugs.debian.org.
(Wed, 29 Jan 2014 07:29:23 GMT) (full text, mbox, link).
Send a report that this bug log contains spam.
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