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Package Details: openms 2.7.0-1

Package Actions

Git Clone URL:	https://aur.archlinux.org/openms.git (read-only, click to copy)
Package Base:	openms
Description:	C++ library and tools for LC/MS data management and analyses
Upstream URL:	http://www.openms.de
Licenses:	BSD
Submitter:	saxonbeta
Maintainer:	lukaszimmermann
Last Packager:	lukaszimmermann
Votes:	6
Popularity:	0.000000
First Submitted:	2014-04-24 21:42 (UTC)
Last Updated:	2021-10-06 12:07 (UTC)

Dependencies (16)

boost (boost-git^AUR)
coin-or-mp
eigen (eigen-git^AUR)
glpk (glpk-git^AUR, glpk-cut-log^AUR)
hdf5 (hdf5-git^AUR, hdf5-openmpi)
qt5-base (qt5-base-git^AUR, qt5-base-headless^AUR)
qt5-svg (qt5-svg-git^AUR)
sqlite (sqlite-fossil^AUR)
xerces-c
autoconf (autoconf-git^AUR) (make)
automake (automake-git^AUR) (make)
cmake (cmake-git^AUR) (make)
fakeroot (fakeroot-git^AUR, fakeroot-tcp^AUR) (make)
gcc (gcc11^AUR, gcc-git^AUR, gccrs-git^AUR, gcc-snapshot^AUR) (make)
make (make-git^AUR) (make)
patch (patch-git^AUR) (make)

Required by (0)

Sources (5)

Pinned Comments

levitsky commented on 2023-08-31 23:24 (UTC)

Since this package is outdated and I wanted a way to install openms, I made openms-bin that uses the deb package from the Github release. I put the maintainers and contributors of this package as contributors over there because I borrowed some stuff from here. I'm not really an AUR guru so please feel free to comment. Thank you guys for this package.

Latest Comments

« First ‹ Previous 1 2 3

lukaszimmermann commented on 2017-08-08 09:27 (UTC)

Is this going to be updated? I'd volunteer to take care of this package if not.

levitsky commented on 2015-06-03 13:53 (UTC)

Great, thanks!

saxonbeta commented on 2015-06-01 22:26 (UTC)

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

levitsky commented on 2015-06-01 21:33 (UTC)

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 (UTC)

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 (UTC)

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 (UTC)

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.