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Re: [Open-ms-general] Building pyOpenMS
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From: Hannes R. <han...@gm...> - 2014-11-02 12:45:01
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Hi Kristina thanks for the output, unfortunately I missed part of the command that is needed, can you add a "-V" to the test so that the whole test output will be in the file? Personally, I think if the tests of the tools that you want to use are working I think OpenMS will work fine for you. @all is somebody else building on 14.04 and running into the same issues? Hannes On 1 November 2014 18:08, Kristina Plate <pl...@un...> wrote: > Dear Hannes, > > thanks for your answer! I ran the commands and stored the output in the > attached file. > For 'File_test' I used the command > > ctest -R ^File_test > > instead, because there are 39 other tests with this expression as well. By > the way these 39 tests passed. > Please tell me if you need some specific information about software (e.g. > versions) or the system! > > Thanks! > Kristina > ____________________ > Kristina Plate > Master of Science, Biomathematics > > Institute for Microbiology > Ernst-Moritz-Arndt-University Greifswald > Friedrich-Ludwig-Jahn-Straße 15 > 17489 Greifswald > > > *On 31 October 2014 16:31, Hannes Röst <han...@gm... > <https://groupware.uni-greifswald.de/han...@gm...>> wrote:* > Dear Kristina > > You can always check cdash for the status of compilation and testing of > OpenMS where our nightly tests are published: > http://cdaseitherh.openms.de/index.php?project=OpenMS > <http://cdash.openms.de/index.php?project=OpenMS> > > currently it seems that all tests run through on Unix platforms. > > can you run the following commands and report the output? > > ctest -R File_test > ctest -R LPWrapper_test > ctest -R Param_test > > in general, failing tests are not a good sign and in this case, it seems > to be some sub-part of OpenMS that does not work as expected. It is likely > that you linked against a library version that we have not tested yet or on > a system we have not yet tested where a few things are not as expected. > > Hannes > > > On 28 October 2014 19:24, Kristina Plate <pl...@un...> > wrote: >> >> Hi, >> >> sorry for the late answer. Only yesterday I could try to rebuild pyOpenMS >> so it took some time. >> >> The building went without any errors, but when I run >> >> ~Development/OpenMS-build$ make test >> >> 3 of the tests failed: >> >> Running tests... >> Test project /home/kristina/Development/OpenMS-build >> Start 1: test_pyopenms_unittests >> 1/1666 Test #1: test_pyopenms_unittests >> ............................................... Passed 18.86 sec >> Start 2: pyopenms_unittest_test000.py >> 2/1666 Test #2: pyopenms_unittest_test000.py >> .......................................... Passed 1.70 sec >> [...] >> Start 1666: Tutorial_PeakIntensityPredictor >> 1666/1666 Test #1666: Tutorial_PeakIntensityPredictor >> ....................................... Passed 0.03 sec >> >> 99% tests passed, 3 tests failed out of 1666 >> >> Total Test time (real) = 351.93 sec >> >> The following tests FAILED: >> 43 - File_test (Failed) >> 72 - LPWrapper_test (Failed) >> 76 - Param_test (SEGFAULT) >> Errors while running CTest >> make: *** [test] Fehler 8 >> >> When I follow the user tutorial of OpenMS, Knime and pyOpenMS I didn't >> notice any problems. Does anybody know whether the failures have any effect >> on the functionality of OpenMS or pyOpenMS or how to fix them? >> Sorry for the additional trouble! >> >> Thanks in advance! >> Kristina >> ____________________ >> Kristina Plate >> Master of Science, Biomathematics >> >> Institute for Microbiology >> Ernst-Moritz-Arndt-University Greifswald >> Friedrich-Ludwig-Jahn-Straße 15 >> 17489 Greifswald >> >> >> On 14 October 2014 13:32, Hannes Röst <han...@gm...> wrote: >> The fix is now pushed into develop, so by updating that branch you >> should get a working copy of pyOpenMS (works on my machine) >> >> Hannes >> >> On 14 October 2014 11:30, Hannes Röst <han...@gm...> wrote: >> > There is still an issue with pyOpenMS, which I just fixed here: >> > >> > https://github.com/OpenMS/OpenMS/pull/1046 >> > >> > this means that the develop branch will currently not compile. However >> > the branch described in the ticket does compile, so you could use that >> > or wait till we merge and then use the develop branch >> > >> > Sorry for the mess >> > >> > Hannes >> > >> > >> > >> > On 13 October 2014 20:51, Aiche, Stephan <Ste...@fu...> >> wrote: >> >> He Kristina, >> >> >> >> the problem you describe was fixed today [1]. Could you update your >> clone >> >> and check if you are now able to build pyOpenMS. >> >> >> >> Cheers >> >> Stephan >> >> >> >> [1] >> >> >> https://github.com/OpenMS/OpenMS/commit/8e62874f90148d26b7b0e889db9552087ddc6719 >> >> >> >> On 13 Oct 2014, at 14:32, Kristina Plate <pl...@un...> >> wrote: >> >> >> >> Hi, >> >> >> >> I opened this thread even before the user meeting in september and >> thought >> >> after that I could help myself. By now I changed my system to 64bit, >> >> downloaded the developer version of OpenMS and built it on my computer. >> >> Knime and OpenMS itself are working perfect, but if I run "make >> pypopenms" I >> >> still get the same error (in a modified form). >> >> >> >> This time I will try to describe my problem as precise as possible. >> First >> >> some information about my system: >> >> >> >> OS: Ubuntu 14.04 LTS 64bit >> >> Cython version: 0.19rc1 >> >> Python version: 2.7.6 >> >> OpenMS is already installed. >> >> >> >> The CMake command with the option -DPYOPENMS=ON runs without any >> exceptions >> >> but after some time when running "make pyopenms" the following error >> >> occures: >> >> >> >> kristina@mh-ws4:~/Development/OpenMS-build$ make pyopenms >> >> [ 0%] Built target OpenSwathAlgo >> >> [ 97%] Built target OpenMS >> >> [100%] Built target SuperHirn >> >> INFO:root:parse >> >> /home/kristina/Development/OpenMS/src/pyOpenMS/pxds/DeNovoAlgorithm.pxd >> >> [...] >> >> INFO:root:create wrapper for free function removeOutliersRANSAC >> >> INFO:root:create wrapper for free function writable >> >> Autwrap has wrapped 437 classes, 4468 methods and 68 enums >> >> >> >> Error compiling Cython file: >> >> ------------------------------------------------------------ >> >> ... >> >> assert len(mzs) == len(intensities), "Input vectors for set_peaks >> >> need to have the same length (mz and intensity vecgtor)" >> >> >> >> cdef _MSSpectrum[_Peak1D] * spec_ = self.inst.get() >> >> >> >> spec_.clear(0) # empty vector , keep meta data >> >> chrom_.reserve(<int>len(mzs)) # allocate space for incoming data >> >> ^ >> >> ------------------------------------------------------------ >> >> >> >> pyopenms/pyopenms.pyx:39424:14: undeclared name not builtin: chrom_ >> >> >> >> Error compiling Cython file: >> >> ------------------------------------------------------------ >> >> ... >> >> assert len(rts) == len(intensities), "Input vectors for set_peaks >> >> need to have the same length (rt and intensity vecgtor)" >> >> >> >> cdef _MSChromatogram[_ChromatogramPeak] * chrom_ = self.inst.get() >> >> >> >> chrom_.clear(0) # empty vector, keep meta data >> >> chrom_.reserve(<int>len(rts)) # allocate space for incoming data >> >> ^ >> >> ------------------------------------------------------------ >> >> >> >> pyopenms/pyopenms.pyx:40109:14: Object of type >> >> 'MSChromatogram[ChromatogramPeak]' has no attribute 'reserve' >> >> created pyopenms.cpp >> >> copied files needed for distribution to pyopenms/ >> >> >> >> >> >> [100%] Built target pyopenms_create_cpp >> >> running build_ext >> >> building 'pyopenms' extension >> >> x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv >> -O2 >> >> -Wall -Wstrict-prototypes -fPIC -Iextra_includes >> >> -I/usr/lib/python2.7/dist-packages/numpy/core/include >> >> -I/home/kristina/Development/OpenMS/src/openswathalgo/include >> >> -I/home/kristina/Development/OpenMS-build/src/openswathalgo/include >> >> -I/usr/include -I/home/kristina/Development/OpenMS/src/openms/include >> >> -I/home/kristina/Development/OpenMS-build/src/openms/include >> >> -I/usr/include/qt4/QtDesigner -I/usr/include/qt4/QtDeclarative >> >> -I/usr/include/qt4/QtScriptTools -I/usr/include/qt4/QtDBus >> >> -I/usr/include/qt4/QtDesigner -I/usr/include/qt4/QtXml >> >> -I/usr/include/qt4/QtSql -I/usr/include/qt4/QtOpenGL >> >> -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtXmlPatterns >> >> -I/usr/include/qt4/QtWebKit -I/usr/include/qt4/QtHelp >> >> -I/usr/include/qt4/QtUiTools -I/usr/include/qt4/QtTest >> >> -I/usr/include/qt4/QtScript -I/usr/include/qt4/QtSvg >> >> -I/usr/include/qt4/Qt3Support -I/usr/include/qt4/QtGui >> >> -I/usr/include/qt4/QtCore -I/usr/share/qt4/mkspecs/default >> >> -I/usr/include/qt4 -I/usr/include/qt4/QtCore -I/usr/include >> >> -I/home/kristina/Development/contrib-build/include >> -I/usr/include/libsvm >> >> -I/usr/include -I/usr/include >> >> -I/home/kristina/Development/contrib-build/include >> >> -I/home/kristina/Development/contrib-build/include/eigen3 >> >> -I/home/kristina/Development/contrib-build/include/WildMagic >> >> -I/home/kristina/Development/OpenMS/src/openswathalgo/include >> >> -I/home/kristina/Development/OpenMS-build/src/openswathalgo/include >> >> -I/usr/include -I/usr/include >> >> -I/home/kristina/Development/OpenMS/src/superhirn/include >> >> -I/home/kristina/Development/OpenMS-build/src/superhirn/include >> >> -I/usr/include -I/home/kristina/Development/OpenMS/src/openms/include >> >> -I/home/kristina/Development/OpenMS-build/src/openms/include >> >> -I/usr/include/qt4/QtDesigner -I/usr/include/qt4/QtDeclarative >> >> -I/usr/include/qt4/QtScriptTools -I/usr/include/qt4/QtDBus >> >> -I/usr/include/qt4/QtDesigner -I/usr/include/qt4/QtXml >> >> -I/usr/include/qt4/QtSql -I/usr/include/qt4/QtOpenGL >> >> -I/usr/include/qt4/QtNetwork -I/usr/include/qt4/QtXmlPatterns >> >> -I/usr/include/qt4/QtWebKit -I/usr/include/qt4/QtHelp >> >> -I/usr/include/qt4/QtUiTools -I/usr/include/qt4/QtTest >> >> -I/usr/include/qt4/QtScript -I/usr/include/qt4/QtSvg >> >> -I/usr/include/qt4/Qt3Support -I/usr/include/qt4/QtGui >> >> -I/usr/include/qt4/QtCore -I/usr/share/qt4/mkspecs/default >> >> -I/usr/include/qt4 -I/usr/include/qt4/QtCore -I/usr/include >> >> -I/home/kristina/Development/contrib-build/include >> -I/usr/include/libsvm >> >> -I/usr/include -I/usr/include >> >> -I/home/kristina/Development/contrib-build/include >> >> -I/home/kristina/Development/contrib-build/include/eigen3 >> >> -I/home/kristina/Development/contrib-build/include/WildMagic >> >> -I/home/kristina/Development/OpenMS/src/openswathalgo/include >> >> -I/home/kristina/Development/OpenMS-build/src/openswathalgo/include >> >> -I/usr/include -I/usr/include >> >> -I/usr/local/lib/python2.7/dist-packages/autowrap/data_files/boost >> >> -I/usr/local/lib/python2.7/dist-packages/autowrap/data_files >> >> -I/home/kristina/Development/OpenMS/src/pyOpenMS/pxds >> >> -I/usr/include/python2.7 -c pyopenms/pyopenms.cpp -o >> >> build/temp.linux-x86_64-2.7/pyopenms/pyopenms.o >> >> cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid >> for >> >> C/ObjC but not for C++ [enabled by default] >> >> pyopenms/pyopenms.cpp:1:2: error: #error Do not use this file, it is >> the >> >> result of a failed Cython compilation. >> >> #error Do not use this file, it is the result of a failed Cython >> >> compilation. >> >> ^ >> >> error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 >> >> make[3]: *** [src/pyOpenMS/CMakeFiles/pyopenms] Fehler 1 >> >> make[2]: *** [src/pyOpenMS/CMakeFiles/pyopenms.dir/all] Fehler 2 >> >> make[1]: *** [src/pyOpenMS/CMakeFiles/pyopenms.dir/rule] Fehler 2 >> >> make: *** [pyopenms] Fehler 2 >> >> >> >> I already tried some hints Hannes told me: I deleted all pyopenms.* >> befor a >> >> new compiling run and I tried either Cython version 0.20 or 0.19 but >> there >> >> was not any difference in the output message. >> >> >> >> I would be very thankful if someone could help me with this problem. >> Please >> >> ask for more information if I forgot something important. >> >> >> >> Thanks in advance! >> >> Kristina >> >> ____________________ >> >> Kristina Plate >> >> Master of Science, Biomathematics >> >> >> >> Institute for Microbiology >> >> Ernst-Moritz-Arndt-University Greifswald >> >> Friedrich-Ludwig-Jahn-Straße 15 >> >> 17489 Greifswald >> >> >> >> >> ------------------------------------------------------------------------------ >> >> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS >> Reports >> >> Are you Audit-Ready for PCI DSS 3.0 Compliance? 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