compiling summon on centos 5 x86_64
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I downloaded tpp 4.1.1 and got that to compile. I then pointed RAMPROOT in Makefile to trans_proteomic_pipeline/src/Parsers/ramp . It looks like it requires the older .c version of RAMP, but the newer version has a newer api and uses .cpp code. First thing it tries to do is look for RAMPROOT/ramp.h (which it finds), RAMPROOT/ramp.o, and RAMPROOT/base64.o . It can't find the .o object files since the summon makefile tries to compile the older .c files. So I went into RAMPROOT and made symlinks to ramp.o and ramp_base64.o (base64.o) under RAMPROOT from trans_proteomic_pipeline/build/linux/ . It then complains that it can't find ramp.o in the summon directory:
g++ -o summon InOut.o quantitation.o PeaksUtils.o IonGenerator.o Modifier.o SumoAnalysis.o Digestion.o Masses.o base64.o ramp.o main.o -L/usr/lib64 -L/usr/.libs -L/usr/cblas/.libs -lgsl -lgslcblas -lz -lm
g++: ramp.o: No such file or directory
So I also made a symlink to the same ramp.o from the tpp/build/linux/ directory in the summon build directory and then it blows up with this during linking :
g++ -o summon InOut.o quantitation.o PeaksUtils.o IonGenerator.o Modifier.o SumoAnalysis.o Digestion.o Masses.o base64.o ramp.o main.o -L/usr/lib64 -L/usr/.libs -L/usr/cblas/.libs -lgsl -lgslcblas -lz -lm
ramp.o: In function `ramp_nextTag(char*, int, RAMPFILE*)':
ramp.cpp:(.text+0x50b): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x574): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.o: In function `getIndexOffset(RAMPFILE*)':
ramp.cpp:(.text+0x706): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x716): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.cpp:(.text+0x74f): undefined reference to `random_access_gztell(random_access_gzFile*)'
ramp.cpp:(.text+0x779): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.cpp:(.text+0x7a9): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x7b9): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.o: In function `rampCloseFile(RAMPFILE*)':
ramp.cpp:(.text+0x95d): undefined reference to `random_access_gzclose(random_access_gzFile*)'
ramp.o: In function `getInstrumentStruct(RAMPFILE*)':
ramp.cpp:(.text+0xab4): undefined reference to `pwiz::msdata::RAMPAdapter::getInstrument(InstrumentStruct&) const'
ramp.cpp:(.text+0xade): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0xaef): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0xb36): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.cpp:(.text+0xb4b): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0xb9d): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0xbe3): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.o: In function `readEndMz(RAMPFILE*, long)':
ramp.cpp:(.text+0xed8): undefined reference to `pwiz::msdata::RAMPAdapter::getScanHeader(unsigned long, ScanHeaderStruct&) const'
ramp.cpp:(.text+0xf2b): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0xf3c): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.o: In function `readStartMz(RAMPFILE*, long)':
ramp.cpp:(.text+0x108a): undefined reference to `pwiz::msdata::RAMPAdapter::getScanHeader(unsigned long, ScanHeaderStruct&) const'
ramp.cpp:(.text+0x10db): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x10ec): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.o: In function `readMSRun(RAMPFILE*, RunHeaderStruct*)':
ramp.cpp:(.text+0x13ab): undefined reference to `pwiz::msdata::RAMPAdapter::getRunHeader(RunHeaderStruct&) const'
ramp.cpp:(.text+0x13c3): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x13d4): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.cpp:(.text+0x13ec): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x14f6): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x14fe): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.o: In function `readPeaksCount(RAMPFILE*, long)':
ramp.cpp:(.text+0x15bd): undefined reference to `pwiz::msdata::RAMPAdapter::getScanHeader(unsigned long, ScanHeaderStruct&) const'
ramp.cpp:(.text+0x163a): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x1655): undefined reference to `random_access_gztell(random_access_gzFile*)'
ramp.cpp:(.text+0x16ae): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x16e1): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.o: In function `readMsLevel(RAMPFILE*, long)':
ramp.cpp:(.text+0x1792): undefined reference to `pwiz::msdata::RAMPAdapter::getScanHeader(unsigned long, ScanHeaderStruct&) const'
ramp.cpp:(.text+0x17c3): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x17d3): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x17ec): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.o: In function `readHeader(RAMPFILE*, long, ScanHeaderStruct*)':
ramp.cpp:(.text+0x1938): undefined reference to `pwiz::msdata::RAMPAdapter::getScanHeader(unsigned long, ScanHeaderStruct&) const'
ramp.cpp:(.text+0x1969): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x1bc1): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x1c82): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x1d11): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.o: In function `readIndex(RAMPFILE*, long, int*)':
ramp.cpp:(.text+0x287f): undefined reference to `pwiz::msdata::RAMPAdapter::scanCount() const'
ramp.cpp:(.text+0x28a1): undefined reference to `pwiz::msdata::RAMPAdapter::getScanHeader(unsigned long, ScanHeaderStruct&) const'
ramp.cpp:(.text+0x29d2): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x2a0a): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.cpp:(.text+0x2a95): undefined reference to `random_access_gztell(random_access_gzFile*)'
ramp.cpp:(.text+0x2b43): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.cpp:(.text+0x2b65): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x2b77): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.cpp:(.text+0x2b96): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x2c68): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x2c81): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x2ca5): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x2dac): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x2e17): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x2e38): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.o: In function `readPeaks(RAMPFILE*, long)':
ramp.cpp:(.text+0x3057): undefined reference to `pwiz::msdata::RAMPAdapter::getScanPeaks(unsigned long, std::vector<double, std::allocator<double> >&) const'
ramp.cpp:(.text+0x314d): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.cpp:(.text+0x33cb): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.cpp:(.text+0x3414): undefined reference to `b64_decode(char*, char const*, int)'
ramp.cpp:(.text+0x354e): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x3572): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x3643): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x38c5): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.cpp:(.text+0x3905): undefined reference to `b64_decode(char*, char const*, int)'
ramp.cpp:(.text+0x3a82): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.cpp:(.text+0x3c37): undefined reference to `random_access_gzread(random_access_gzFile*, char*, unsigned int)'
ramp.o: In function `rampOpenFile(char const*)':
ramp.cpp:(.text+0x40b5): undefined reference to `random_access_gzopen(char const*)'
ramp.cpp:(.text+0x40d6): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.cpp:(.text+0x40ef): undefined reference to `random_access_gzgets(random_access_gzFile*, char*, int)'
ramp.cpp:(.text+0x418b): undefined reference to `random_access_gzeof(random_access_gzFile*)'
ramp.cpp:(.text+0x41d0): undefined reference to `random_access_gzclose(random_access_gzFile*)'
ramp.cpp:(.text+0x4203): undefined reference to `pwiz::msdata::RAMPAdapter::RAMPAdapter(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
ramp.cpp:(.text+0x424f): undefined reference to `random_access_gzseek(random_access_gzFile*, long, int)'
ramp.o: In function `rampConstructInputPath(char*, int, char const*, char const*)':
ramp.cpp:(.text+0x4a04): undefined reference to `isPathSeperator(char)'
ramp.cpp:(.text+0x4a54): undefined reference to `findRightmostPathSeperator(char*)'
ramp.cpp:(.text+0x4a75): undefined reference to `findRightmostPathSeperator_const(char const*)'
ramp.o: In function `rampValidateOrDeriveInputFilename(char*, int, char*)':
ramp.cpp:(.text+0x4ed7): undefined reference to `fixPath(char*, int)'
ramp.cpp:(.text+0x4edf): undefined reference to `findRightmostPathSeperator(char*)'
collect2: ld returned 1 exit status
make: *** Error 1
If you could provide the older version of RAMP that this is supposed to compile against it would help. We also wouldn't have to download the gigantic TPP package as well probably.