Your message dated Sat, 18 Aug 2018 07:49:55 +0000
with message-id <e1fqvzf-000bvg...@fasolo.debian.org>
and subject line Bug#906510: fixed in tophat 2.1.1+dfsg1-2
has caused the Debian Bug report #906510,
regarding tophat: FTBFS in buster/sid (No rule to make target
'../src/libtophat.a')
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
906510: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=906510
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:tophat
Version: 2.1.1+dfsg1-1
Severity: serious
Tags: ftbfs
Dear maintainer:
I tried to build this package in buster but it failed:
--------------------------------------------------------------------------------
[...]
debian/rules build-arch
dh build-arch --no-parallel
dh_update_autotools_config -a
dh_autoreconf -a
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
sh: 1: git: not found
configure.ac:20: installing './compile'
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_configure -- --with-boost-libdir=/usr/lib/x86_64-linux-gnu
./configure --build=x86_64-linux-gnu --prefix=/usr
--includedir=\${prefix}/include --mandir=\${prefix}/share/man
--infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var
--disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu
--libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode
--disable-dependency-tracking --with-boost-libdir=/usr/lib/x86_64-linux-gnu
[... snipped ...]
checking for strdup... yes
checking for strrchr... yes
checking for strtol... yes
checking for strsep... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) none
checking dependency style of g++... (cached) none
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
-- tophat 2.1.1 Configuration Results --
C++ compiler: g++ -std=gnu++98 -Wall -Wno-strict-aliasing -g -gdwarf-2
-Wuninitialized -O3 -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong
-Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include
Linker flags: -L/usr/lib/x86_64-linux-gnu -Wl,-z,relro -Wl,-z,now
BOOST libraries: -lboost_thread -lboost_system
GCC version: gcc (Debian 8.2.0-3) 8.2.0
Host System type: x86_64-pc-linux-gnu
Install prefix: /usr
Install eprefix: ${prefix}
See config.h for further configuration information.
Email bug reports to <tophat.cuffli...@gmail.com>.
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_build -a
make -j1
make[1]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -std=gnu++98
-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -g -O2
-fdebug-prefix-map=/<<BUILDDIR>>/tophat-2.1.1+dfsg1=. -fstack-protector-strong
-Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o
prep_reads.o prep_reads.cpp
make[3]: *** No rule to make target '../src/libtophat.a', needed by
'prep_reads'. Stop.
make[3]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1/src'
make[2]: *** [Makefile:384: all-recursive] Error 1
make[2]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
make[1]: *** [Makefile:325: all] Error 2
make[1]: Leaving directory '/<<BUILDDIR>>/tophat-2.1.1+dfsg1'
dh_auto_build: make -j1 returned exit code 2
make: *** [debian/rules:14: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit
status 2
--------------------------------------------------------------------------------
The build was made with "dpkg-buildpackage -B" in my autobuilder.
Most probably, it also fails here in reproducible builds:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/tophat.html
where you can get a full build log if you need it.
If this is really a bug in one of the build-depends, please use reassign and
affects,
so that this is still visible in the BTS web page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: tophat
Source-Version: 2.1.1+dfsg1-2
We believe that the bug you reported is fixed in the latest version of
tophat, 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 906...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated tophat 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sat, 18 Aug 2018 09:28:30 +0200
Source: tophat
Binary: tophat
Architecture: source
Version: 2.1.1+dfsg1-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
tophat - fast splice junction mapper for RNA-Seq reads
Closes: 906510
Changes:
tophat (2.1.1+dfsg1-2) unstable; urgency=medium
.
* Fix Makefile.am
Closes: #906510
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.0
* Remove unneeded get-orig-source target
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--- End Message ---
