Damian, The reason for the funny error is because the build destination is a directory named <operating system>-<architecture>. In your case the operating system wasn't filled in hence the " -x86_64".
Buried deep in the Makefile(s) for TPP is OBJ_ARCH, the destination used for the build directory. Its value is derived from the variable ARCH, and how this gets assigned is, well, convoluted. I think on your system it will run a shell script called find_arch.sh which should be at the very least be assigning it to "unknown". So the quick and dirty fix is to just override its value at the time you run make using the line: % make ARCH=redhat-x86_64 If you have a chance though, could you run the find_arch.sh script and send along the output? I'd like to see if we can get the actual problem fixed. Thanks, Joe On Wed, Mar 13, 2013 at 10:24 AM, David Shteynberg < [email protected]> wrote: > Hey Damian, > > You can try a sed command to replace the directory containing '-' which > makes it break at the mkdir. > > Try: sed -i 's/-x86_64/x86_64/g' Makefile* > > -David > > > On Wed, Mar 13, 2013 at 9:06 AM, GATTACA <[email protected]> wrote: > >> Hi guys, >> >> I'm trying to update our version of TPP to the latest-n-greatest stable >> release. >> I've downloaded TPP-4.6.2.tgz from sourceforge and gone through the usual >> make command. >> >> I get this error when I hit the X!Tandem build step: >> >> mkdir -p >> /usr/local/apps/tpp/trans_proteomic_pipeline/src/../build/-x86_64 >> make -C ../extern/xtandem/src_tpp >> TANDEM_PARAMETERS_INSTALL_DIR="/usr/local/apps/tpp/bin/" >> SRC_ROOT="/usr/local/apps/tpp/trans_proteomic_pipeline/src/" ARCH=-x86_64 >> BUILD_DIR=/usr/local/apps/tpp/trans_proteomic_pipeline/src/../build/-x86_64 >> EXPAT_LIB=/usr/local/apps/tpp/trans_proteomic_pipeline/src/../extern/expat-2.0.1/.libs/libexpat.a >> ZLIB_INCL="" ZLIB_LIB="-lz " >> HDF5_INCL="/usr/local/apps/tpp/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6/hdf5/include" >> HDF5_LIB="/usr/local/apps/tpp/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6/hdf5/lib/libhdf5_cpp.a >> /usr/local/apps/tpp/trans_proteomic_pipeline/src/../extern/hdf5-1.8.6/hdf5/lib/libhdf5.a" >> MZPARSER_LIB="/usr/local/apps/tpp/trans_proteomic_pipeline/src/../build/-x86_64/libmzparser.a >> " >> MZPARSER_INCL="/usr/local/apps/tpp/trans_proteomic_pipeline/src/Parsers/mzParser" >> USER_OBJS="/usr/local/apps/tpp/trans_proteomic_pipeline/src/../build/-x86_64/TPPVersionInfo.o" >> make[1]: Entering directory >> `/usr/local/apps/tpp/trans_proteomic_pipeline.v462/extern/xtandem/src_tpp' >> mkdir -p -x86_64 >> mkdir: invalid option -- 'x' >> Try `mkdir --help' for more information. >> make[1]: *** No rule to make target `-x86_64/base64.d', needed by >> `/usr/local/apps/tpp/trans_proteomic_pipeline/src/../build/-x86_64/tandem'. >> Stop. >> make[1]: Leaving directory >> `/usr/local/apps/tpp/trans_proteomic_pipeline.v462/extern/xtandem/src_tpp' >> make: *** [xtandem] Error 2 >> >> I think there is a typo in the make file at the mkdir -p -x86_64 command? >> Any suggestions on what I could do to remedy this would be greatly >> appreciated. >> >> In case it helps, I'm running RHEL 6.3. 64-bit, fully patched, gcc >> version 4.4.7 20120313 (Red Hat 4.4.7-3) >> >> Thanks in advance for any and all help. >> >> Damian >> >> -- >> 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?hl=en >> . >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > > -- > 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?hl=en. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- 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?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
