problem installing TPP 5.2 on CentOS Linux release 7.3.1611

[smdb]

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. However I still have the same problem.

Could you please help me?

Thanks in advance!

Salva.

[David Shteynberg]

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

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[smdb]

update:

I updated some packages :

 libstdc++-static.x86_64
 glibc-static

and that problem is gone.

Salva.

[smdb]

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.

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[smdb]

Ok sorry. Problem solved installing 

• yum install perl-devel

[Shagun Gupta]

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