Hi I haven't had issues up till after make install, however on downloading perl libraries as specified here: http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS
and checking for installation of all with, cd /usr/local/tpp/bin export PERL5LIB=/usr/local/tpp/lib/perl ./test_tpi.pl I get the warning that the following three libraries (TPP, TPP::StatUtilities and tpplib_perl) are missing. I am not sure how to download them since cpan can't find them by name and ".pm" files are in the folder "/home/tpp/svn/trans_proteomic_pipeline/perl/lib" Thanks Shagun On Tuesday, August 13, 2019 at 8:14:58 PM UTC-4, smdb wrote: > > 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 <[email protected]> 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]. >>>> 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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