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 <[email protected]> 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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