TPP 5.2 compile error Ubuntu 18.04

[Alejandro]

Hello all,

Im trying to install TPP 5.2 on a computer running Ubuntu 18.04. I'm following the guide but so far I have been unsuccessful. I just changed the username and kept the tpp group. The install location is as is in the guide, and the /dat would be different. After running

make all

As per the guide I tried to run again (make all) but always throws the same error.

I get the following error:;

~/svn/trans_proteomic_pipeline$ make all

g++  -g  -std=c++11 -Wno-deprecated -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE   -DTPPLIB -I/home/laptop/svn/trans_proteomic_pipeline/src -I/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/include -D__LINUX__ -fPIC -MMD -c -o /home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/artifacts/Parsers/mzParser/saxmzmlhandler.o /home/laptop/svn/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp 

/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp:571:58: error: no ‘bool mzpSAXMzmlHandler::readHeaderFromOffset(f_off)’ member function declared in class ‘mzpSAXMzmlHandler’

 bool mzpSAXMzmlHandler::readHeaderFromOffset(f_off offset){

                                                                                                    ^

/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/mzParser/saxmzmlhandler.cpp:633:60: error: no ‘bool mzpSAXMzmlHandler::readSpectrumFromOffset(f_off)’ member function declared in class ‘mzpSAXMzmlHandler’

 bool mzpSAXMzmlHandler::readSpectrumFromOffset(f_off offset){

                                                                                                        ^

/home/laptop/svn/trans_proteomic_pipeline/src/Parsers/Makefile:87: recipe for target '/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/artifacts/Parsers/mzParser/saxmzmlhandler.o' failed

make: *** [/home/laptop/svn/trans_proteomic_pipeline/build/gnu-x86_64/artifacts/Parsers/mzParser/saxmzmlhandler.o] Error 1

The "^" sign is bellow the closing parenthesis on (f_off offset) and on my terminal is highlighted in red

I really don't know how to troubleshoot this.

Any help would be appreciated.

Alejandro

[Eric Deutsch]

Hi Alejandro, which checkout did you do? Was it this?

 

svn checkout -r 7909 http://svn.code.sf.net/p/sashimi/code/trunk/trans_proteomic_pipeline

 

Or a little different?

 

Thanks,

Eric

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[Alejandro]

HI Eric,

I think it was the 7909, but I'm not 100% sure. I could try again using the 7909.

Alejandro

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[Alejandro]

HI Eric,

I went ahead and checked which version were available and used the 7922, it now compiled and installed successfully. After some permissions troubleshooting with apache I have it running! I followed the "testing ". The only thing that is not working is to check for the ions in the pepxml file. I get the following error:

Error - scan 10000 is an MS1 scan in the mzXML file /home/laptop/Documents/TPP_data/tests/QuickYeastUPS1/UPS1_50000amol_R1.mzML

I can click on the Spectrum and see the peptide table but whenever I click on the ions I see that error.

Otherwise the rest of the test goes fine.

Alejandro