I successfully installed the standalone version of SpectraST on an Ubuntu machine, but I had to make the two following changes. Perhaps these changes could be made to the prerequisites script and the source, respectively. Details below.
1. install libgsl0-dev from apt-get 2. modify SpectraST_util.cpp to include unistd.h As for the first, I understand that the prerequisites scripts don't include Ubuntu 13.04. Perhaps the second issue is also specific to later ubuntu versions. ~Jeff * * * * *Ubuntu 13.04, 64-bit* *TPP 4.6.3* *1. gsl dependency* *Reproduce: * $ cd TPP-4.6.3/trans_proteomic_pipeline/src/Search/SpectraST $ make -f Makefile_STANDALONE_LINUX ... g++ -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DSTANDALONE_LINUX -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraSTDenoiser.cpp -o linux_standalone/SpectraSTDenoiser.o SpectraSTDenoiser.cpp:8:28: fatal error: gsl/gsl_vector.h: No such file or directory compilation terminated. make: *** [linux_standalone/SpectraSTDenoiser.o] Error 1 *Fix:* $ sudo apt-get install libgsl0-dev *2. unistd.h (getcwd)* * * *Reproduce:* $ make -f Makefile_STANDALONE_LINUX ... g++ -I/usr/include -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DSTANDALONE_LINUX -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -Werror -Wformat -Wstrict-aliasing -Wno-deprecated -Wno-char-subscripts -O2 -c SpectraST_util.cpp -o linux_standalone/SpectraST_util.o SpectraST_util.cpp: In function ‘char* safepath_getcwd(char*, int)’: SpectraST_util.cpp:587:30: error: ‘getcwd’ was not declared in this scope make: *** [linux_standalone/SpectraST_util.o] Error 1 *Fix:* Change the relevant lines in SpectraST_util.cpp: #ifdef _MSC_VER // if under Visual Studio #include <direct.h> // for getcwd #else #include <unistd.h> #endif -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
