Re: Flexbar 2.5 release
Hi Johannes,
for very confusing reasons when I wrote my first mail only the first
test failed. I now fixed the PATH for the tests and all went fine.
(I have no idea why not all tests failed before when the PATH was
wrong.)
In short: I have dealt with the issue and uploaded the last version.
Sorry for the confusion
Andreas.
On Thu, Aug 21, 2014 at 01:32:19PM +0200, Röhr, Johannes wrote:
> Hi Andreas,
>
> to check if the zlib library is available I use a cmake find package command. If it is successful zlib include directories as well as link libraries are set using cmake variables and additionally -DSEQAN_HAS_ZLIB=1 is specified. The error message you listed for the decompression test is shown by Flexbar if SEQAN_HAS_ZLIB was not set for the build.
>
> It seems like it is not set, even though -DSEQAN_HAS_ZLIB=1 is specified. I would not think that something has to be fixed in seqan, as I had no problems to build Flexbar with zlib support so far and the test completes successfully when I try it. I'm not exactly sure what is going on. Could it be the case that include directories or link libraries for zlib are not specified or available for the build? Perhaps that is why SEQAN_HAS_ZLIB does not get set in the end.
>
> Kind regards,
> Johannes
>
>
> On 07 Aug 2014, at 14:14, Andreas Tille <andreas@an3as.eu> wrote:
>
> > Hi Johannes,
> >
> > somehow this update went out of my focus. I now catched up and updated
> > the packaging to also include running the test suite. My test endet up
> > in
> >
> > make[1]: Entering directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > /usr/bin/cmake -H/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src -B/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
> > /usr/bin/cmake -E cmake_progress_start /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu/CMakeFiles /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gn
> > make -f CMakeFiles/Makefile2 all
> > make[2]: Entering directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > make -f src/CMakeFiles/flexbar.dir/build.make src/CMakeFiles/flexbar.dir/depend
> > make[3]: Entering directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > cd /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src /home/tillea/d
> > Scanning dependencies of target flexbar
> > make[3]: Leaving directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > make -f src/CMakeFiles/flexbar.dir/build.make src/CMakeFiles/flexbar.dir/build
> > make[3]: Entering directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > /usr/bin/cmake -E cmake_progress_report /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu/CMakeFiles 1
> > [100%] Building CXX object src/CMakeFiles/flexbar.dir/Flexbar.cpp.o
> > cd /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu/src && /usr/bin/c++ -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1 -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werro
> > Linking CXX executable ../flexbar
> > cd /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/flexbar.dir/link.txt --verbose=1
> > /usr/bin/c++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wl,-z,relro CMakeFiles/flexbar.dir/Flexbar.cpp.o -o ../flexbar -rdynamic -ltbb -lz -lbz2
> > make[3]: Leaving directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > /usr/bin/cmake -E cmake_progress_report /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu/CMakeFiles 1
> > [100%] Built target flexbar
> > make[2]: Leaving directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > /usr/bin/cmake -E cmake_progress_start /home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu/CMakeFiles 0
> > make[1]: Leaving directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src/obj-x86_64-linux-gnu'
> > debian/rules override_dh_auto_test
> > make[1]: Entering directory '/home/tillea/debian-maintain/repack/flexbar/flexbar_v2.5_src'
> > cd test; PATH="../obj-*;$PATH" ./flexbar_validate.sh
> >
> > Testing fasta:
> > Test 1 OK
> > Test 2 OK
> > Test 3 OK
> > Test 4 OK
> > Test 5 OK
> >
> > Testing csfasta:
> > Test 1 OK
> > Test 2 OK
> > Test 3 OK
> > Test 4 OK
> > Test 5 OK
> >
> > Testing fastq:
> > Test 1 OK
> > Test 2 OK
> > Test 3 OK
> > Test 4 OK
> > Test 5 OK
> >
> > Testing csfastq:
> > Test 1 OK
> > Test 2 OK
> > Test 3 OK
> > Test 4 OK
> > Test 5 OK
> >
> > Testing decompression:
> > Input file decompression canceled.
> > This build does not support zlib!
> >
> > debian/rules:9: recipe for target 'override_dh_auto_test' failed
> >
> >
> >
> > ...
> >
> > Do I need some other options to cmake to enable zlib? The Build
> > says:
> > -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_ZLIB=1
> >
> > Or is this some issue that needs to be fixed in seqan library?
> >
> > Kind regards
> >
> > Andreas.
> >
> >
> > On Tue, Jul 01, 2014 at 10:03:40PM +0200, Röhr, Johannes wrote:
> >> Hey Tony and Andreas,
> >>
> >> yesterday, I released Flexbar version 2.5 on sourceforge. A source download is provided and the release is tagged in the svn repo, so the new version would be ready for packaging. By the way, I also included some tests to check compression support.
> >>
> >> Kind regards,
> >> Johannes
> >
> > --
> > http://fam-tille.de
>
>
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