Hi Joe, I ran the find_arch.sh script and it returned a blank line which is really weird since I'm running RHEL 6.3
I manually forced the script to set the DISTRIB_ID to be "RedHat" and things compiled now. Thanks for the help! Damian On Wednesday, March 13, 2013 1:45:07 PM UTC-4, [email protected] wrote: > > 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] <javascript:>> 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] >> <javascript:>>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] <javascript:>. >>> To post to this group, send email to >>> [email protected]<javascript:> >>> . >>> 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] <javascript:>. >> To post to this group, send email to >> [email protected]<javascript:> >> . >> 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.
