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. 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/CAGJJY%3D_He6B1J9ExHT1MEysFuE%2B96QDkh6Av_cT%3D54HjzvBqjQ%40mail.gmail.com.
