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AUR (en) - openms

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Package Details: openms 2.0.0-2

Git Clone URL: https://aur-dev.archlinux.org/openms.git (read-only)
Package Base: openms
Description: C++ library and tools for LC/MS data management and analyses
Upstream URL: http://open-ms.sourceforge.net/
Licenses: BSD
Submitter: saxonbeta
Maintainer: saxonbeta
Last Packager: saxonbeta
Votes: 1
Popularity: 0.000000
First Submitted: 2014-04-24 21:42
Last Updated: 2015-06-26 00:30

Dependencies (12)

Required by (0)

Sources (3)

Latest Comments

levitsky commented on 2015-06-03 13:53

Great, thanks!

saxonbeta commented on 2015-06-01 22:26

Sorry, my bad there was a missing dependency. Try now with this new PKGBUILD

levitsky commented on 2015-06-01 21:33

Thanks for looking into this! Now I get the following error:

CMake Error at /usr/share/cmake-3.2/Modules/FindPackageHandleStandardArgs.cmake:138 (message):
Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
(Required is at least version "3.1.0")
Call Stack (most recent call first):
/usr/share/cmake-3.2/Modules/FindPackageHandleStandardArgs.cmake:374 (_FPHSA_FAILURE_MESSAGE)
cmake/modules/FindEigen3.cmake:76 (find_package_handle_standard_args)
src/openms/cmake_findExternalLibs.cmake:116 (find_package)
src/openms/CMakeLists.txt:63 (include)

Let me know if you need the full log.

saxonbeta commented on 2015-06-01 18:31

I have updated to version 2.0. At the moment it is incompatible with SeqAn 2.0, so I have modified the script to compile SeqAn using the provided sources within openms. It is recommended to uninstall the SeqAn package installed from AUR.

saxonbeta commented on 2015-06-01 12:48

Indeed, it's a problem with seqan 2.0. The developers made some changes to I/O modules and others. Currently I an working in a patch, stay tuned.

levitsky commented on 2015-05-29 14:50

I get the following error in build():

[ 20%] Building CXX object CMakeFiles/OpenMS.dir/source/FORMAT/FASTAFile.C.o
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C: In member function ‘void OpenMS::FASTAFile::load(const OpenMS::String&, std::vector<OpenMS::FASTAFile::FASTAEntry>&)’:
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:78:5: error: ‘RecordReader’ is not a member of ‘seqan’
seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:78:37: error: expected primary-expression before ‘,’ token
seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:78:39: error: ‘SinglePass’ is not a member of ‘seqan’
seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:78:57: error: expected primary-expression before ‘>’ token
seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:78:59: error: expected primary-expression before ‘>’ token
seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:78:70: error: ‘reader’ was not declared in this scope
seqan::RecordReader<std::fstream, seqan::SinglePass<> > reader(in);
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:82:25: error: ‘atEnd’ was not declared in this scope
while (!atEnd(reader))
^
/home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:82:25: note: suggested alternative:
In file included from /usr/include/seqan/store.h:61:0,
from /usr/include/seqan/seq_io/fai_index.h:41,
from /usr/include/seqan/seq_io.h:72,
from /home/lev/openms/src/OpenMS-1.11.1/source/FORMAT/FASTAFile.C:41:
/usr/include/seqan/store/store_annotation.h:628:1: note: ‘seqan::atEnd’
atEnd(Iter<TFragmentStore, AnnotationTree<TSpec> > & it)
^
CMakeFiles/OpenMS.dir/build.make:4781: recipe for target 'CMakeFiles/OpenMS.dir/source/FORMAT/FASTAFile.C.o' failed
make[2]: *** [CMakeFiles/OpenMS.dir/source/FORMAT/FASTAFile.C.o] Error 1
CMakeFiles/Makefile2:3919: recipe for target 'CMakeFiles/OpenMS.dir/all' failed
make[1]: *** [CMakeFiles/OpenMS.dir/all] Error 2
Makefile:126: recipe for target 'all' failed
make: *** [all] Error 2
==> ERROR: A failure occurred in build().
Aborting...

Can it be a compatibility problem with seqan or ...?
I have seqan 2.0.0-1.