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 <[email protected] <javascript:>> > 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 [email protected] <javascript:>. >> 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. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/78e71e08-75e3-4606-a169-94a786b1b2be%40googlegroups.com.
