Ok sorry. Problem solved installing - yum install perl-devel
On Tuesday, August 13, 2019 at 5:12:47 PM UTC-7, smdb wrote: > > Thanks David: > That problem was solved, but after some minutes with the compilation > running I got the following error and I still didn't find any solution > around: > [tpp@sealion trans_proteomic_pipeline]$ make all > cp /home/tpp/svn/trans_proteomic_pipeline/perl/bin/compareProts3.pl > /home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/bin > perl -MExtUtils::MY -e 'MY->fixin(shift)' -- > /home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/bin/compareProts3.pl > Can't locate ExtUtils/MY.pm in @INC (@INC contains: /usr/local/lib64/perl5 > /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .). > BEGIN failed--compilation aborted. > make: *** > [/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/bin/compareProts3.pl] > > Error 2 > > I would appreciate your help with this. > Thanks! > Salva. > > > On Tuesday, August 13, 2019 at 12:30:56 PM UTC-7, David Shteynberg wrote: >> >> Hi Salva, >> >> It seems some libraries are missing on your linux setup. Can you install >> these C++ dependencies and try again? >> >> /usr/bin/ld: cannot find -lpthread >> /usr/bin/ld: cannot find -lstdc++ >> /usr/bin/ld: cannot find -lm >> /usr/bin/ld: cannot find -lc >> >> Thanks, >> -David >> >> On Tue, Aug 13, 2019 at 12:22 PM smdb <smd...@msn.com> wrote: >> >>> Following instructions to install TPP, I do make all command and I get: >>> >>> [tpp@sealion trans_proteomic_pipeline]$ make all >>> cd >>> /home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014; >>> >>> make >>> make[1]: Entering directory >>> `/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014' >>> cd MSToolkit ; make lite ; cd ../CometSearch ; make >>> make[2]: Entering directory >>> `/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014/MSToolkit' >>> ar rcs libmstoolkitlite.a adler32.o compress.o crc32.o deflate.o >>> inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o >>> xmlparse.o xmlrole.o xmltok.o mzp.MSNumpress.o mzp.mzp_base64_lite.o >>> mzp.BasicSpectrum_lite.o mzp.mzParser_lite.o mzp.RAMPface_lite.o >>> mzp.saxhandler_lite.o mzp.saxmzmlhandler_lite.o mzp.saxmzxmlhandler_lite.o >>> mzp.Czran_lite.o mzp.mz5handler_lite.o mzp.mzpMz5Config_lite.o >>> mzp.mzpMz5Structs_lite.o mzp.BasicChromatogram_lite.o mzp.PWIZface_lite.o >>> Spectrum.o MSObject.o mzMLWriter.o MSReaderLite.o >>> make[2]: Leaving directory >>> `/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014/MSToolkit' >>> make[2]: Entering directory >>> `/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014/CometSearch' >>> g++ -O3 -Wall -fpermissive -Wextra -Wno-write-strings -static >>> -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC -I. -I../MSToolkit/include >>> CometPreprocess.cpp -c >>> ar rcs libcometsearch.a Threading.o CometInterfaces.o CometSearch.o >>> CometPreprocess.o CometPostAnalysis.o CometMassSpecUtils.o CometWriteOut.o >>> CometWriteSqt.o CometWritePepXML.o CometWritePercolator.o CometWriteTxt.o >>> CometSearchManager.o CometCheckForUpdates.o >>> make[2]: Leaving directory >>> `/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014/CometSearch' >>> g++ -O3 -Wall -Wextra -static -Wno-char-subscripts -D_LARGEFILE_SOURCE >>> -D_FILE_OFFSET_BITS=64 -D__LINUX__ -IMSToolkit/include -ICometSearch >>> Comet.o -LMSToolkit -LCometSearch -lcometsearch -lmstoolkitlite -lm >>> -lpthread -o comet.exe >>> /usr/bin/ld: cannot find -lpthread >>> /usr/bin/ld: cannot find -lstdc++ >>> /usr/bin/ld: cannot find -lm >>> /usr/bin/ld: cannot find -lc >>> collect2: error: ld returned 1 exit status >>> make[1]: *** [comet.exe] Error 1 >>> make[1]: Leaving directory >>> `/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014' >>> make: *** >>> [/home/tpp/svn/trans_proteomic_pipeline/build/linux-x86_64/artifacts/comet_source_2018014/comet] >>> >>> Error 2 >>> >>> Then, I saw post at: >>> https://groups.google.com/d/msg/spctools-discuss/6_rYJ_9aefE/FdO0LdbjBgAJ >>> and I update the comet_source_2018014.zip >>> <https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/extern/comet_source_2018014.zip>. >>> >>> However I still have the same problem. >>> >>> Could you please help me? >>> >>> Thanks in advance! >>> >>> Salva. >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to spctools...@googlegroups.com. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/spctools-discuss/bbd47ec6-5d03-4f1f-8835-6a6b0104dd92%40googlegroups.com >>> >>> <https://groups.google.com/d/msgid/spctools-discuss/bbd47ec6-5d03-4f1f-8835-6a6b0104dd92%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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