Finally managed to get TPP 4.5.0 installed on Ubuntu 10.04, thanks to much help from Damian
svn co https://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-5-0/trans_proteomic_pipeline/ "Checked out revision 5627" cd trans_proteomic_pipeline/src/ make clean make ERRORS: In file included from Parsers/mzParser/saxhandler.cpp:133: Parsers/mzParser/mzParser.h:3538: error: ‘uint32_t’ has not been declared Parsers/mzParser/mzParser.h:3539: error: ‘uint64_t’ does not name a type Parsers/mzParser/mzParser.h:3617: error: ‘uint32_t’ has not been declared Parsers/mzParser/mzParser.h:3618: error: ‘uint64_t’ does not name a type make: *** [/usr/local/src/trans_proteomic_pipeline/src/../build/Ubuntu- x86_64/saxhandler.o] Error 1 root@blackburn2:/usr/local/src/trans_proteomic_pipeline/src# I then made that changes suggested online If Make reports an error in saxhandler.h, add "#include <stdint.h>" (Without the quotation marks) to the top of the saxhandler.h file. src/Parsers/Algorithm2XML/saxhandler.h extern/xtandem/src/saxhandler.h This has not effect, the result being the same error as above, I changed these files back to the way they originally were and then I edited Parsers/mzParser/mzParser.h, add "#include <stdint.h>" (Without the quotation marks) to the top of the saxhandler.h file make clean make ERROR: cc1plus: warnings being treated as errors Parsers/mzParser/saxmzxmlhandler.cpp: In member function ‘f_off SAXMzxmlHandler::readIndexOffset()’: Parsers/mzParser/saxmzxmlhandler.cpp:550: error: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result make: *** [/usr/local/src/trans_proteomic_pipeline/src/../build/Ubuntu- x86_64/saxmzxmlhandler.o] Error 1 editied line 550 of Parsers/mzParser/saxmzxmlhandler.cpp to "size_t dummy=fread(buffer,1,200,f);" make clean make ERROR cc1plus: warnings being treated as errors Parsers/mzParser/saxmzmlhandler.cpp: In member function ‘f_off SAXMzmlHandler::readIndexOffset()’: Parsers/mzParser/saxmzmlhandler.cpp:668: error: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result make: *** [/home/sgarnett/Downloads/trans_proteomic_pipeline/src/../ build/Ubuntu-x86_64/saxmzmlhandler.o] Error 1 edited line 668 of Parsers/mzParser/saxmzmlhandler.cpp to 'size_t dummy=fread(buffer,1,200,f);' make clean make ERROR: cc1plus: warnings being treated as errors pep_dbcount.cpp: In function ‘int main(int, char**)’: pep_dbcount.cpp:111: error: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result pep_dbcount.cpp:163: error: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result make[1]: *** [Ubuntu-x86_64/pep_dbcount.o] Error 1 make[1]: Leaving directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/src/util' cp: cannot stat `Ubuntu-x86_64/pep_dbcount': No such file or directory make: *** [/home/sgarnett/Downloads/trans_proteomic_pipeline/src/../ build/Ubuntu-x86_64/pep_dbcount] Error 1 edited line 111 of util/pep_dbcount.cpp to 'char* dummy = fgets(szBuf, SIZE_BUF, fp);' edited line 163 of util/pep_dbcount.cpp to 'char* dummy = fgets(szBuf, SIZE_BUF, fp);' make clean make ERROR: cc1plus: warnings being treated as errors translateDNA2AA-FASTA.cpp: In function ‘int main(int, char**)’: translateDNA2AA-FASTA.cpp:127: error: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result translateDNA2AA-FASTA.cpp: In function ‘void LOAD_DBASE(char*, FILE*)’: translateDNA2AA-FASTA.cpp:269: error: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result make[1]: *** [Ubuntu-x86_64/translateDNA2AA-FASTA.o] Error 1 make[1]: Leaving directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/src/util' cp: cannot stat `Ubuntu-x86_64/translateDNA2AA-FASTA': No such file or directory make: *** [/home/sgarnett/Downloads/trans_proteomic_pipeline/src/../ build/Ubuntu-x86_64/translateDNA2AA-FASTA] Error 1 edited line 127 of util/translateDNA2AA-FASTA.cpp to 'char* dummy = fgets(szBuf, SIZE_DESCR, fpIn);' edited line 269 of util/translateDNA2AA-FASTA.cpp to 'char* dummy = fgets(szBuf, SIZE_DESCR, fpIn);' make clean make ERROR: cc1plus: warnings being treated as errors calculate_pi.cpp: In function ‘void ADD_PI(char*)’: calculate_pi.cpp:158: error: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result make[1]: *** [Ubuntu-x86_64/calculate_pi.o] Error 1 make[1]: Leaving directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/src/util' cp: cannot stat `Ubuntu-x86_64/calculate_pi': No such file or directory make: *** [/home/sgarnett/Downloads/trans_proteomic_pipeline/src/../ build/Ubuntu-x86_64/calculate_pi] Error 1 edited line 158 of util/calculate_pi.cpp "int dummy = system(szTmp);" make clean make ERROR: cd Search/SpectraST; make all make[1]: Entering directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/src/Search/SpectraST' make[1]: Nothing to be done for `all'. make[1]: Leaving directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/src/Search/SpectraST' echo "JAVA_HOME not defined, skipping Java targets" JAVA_HOME not defined, skipping Java targets make -C ../COVERAGE/ make[1]: Entering directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/COVERAGE' mkdir -p Ubuntu-x86_64 g++ -Wno-deprecated -I/usr/include -O3 -c main.cxx -o Ubuntu- x86_64/main.o g++ -Wno-deprecated -I/usr/include -O3 -c Coverage.cxx -o Ubuntu- x86_64/Coverage.o g++ -O3 -o ../src/../build/Ubuntu-x86_64/batchcoverage Ubuntu-x86_64/ main.o Ubuntu-x86_64/Coverage.o -lm -lz -lbz2 -lpthread make[1]: Leaving directory `/home/sgarnett/Downloads/ trans_proteomic_pipeline/COVERAGE' make install All files are in the correct place and it seems to be working. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
