Ah ok thanks! That explains the problem. I'll make sure we have a fix in the upcoming release.
On Mon, Mar 18, 2013 at 10:59 AM, Damian <[email protected]> wrote: > > On 03/18/2013 01:06 PM, Joseph Slagel wrote: > > Thanks for running the script. That is odd. Where are you running the > make command from, are you in the directory trans_proteomic_pipeline/src? > > Yes. > > > If not then the Makefile might not be able to find the find_arch.sh > script and therefore would output an error but then continue. If that > isn't the case then do you have a file on your system named > /etc/lsb-release and does it have any contents? > > Yes I have this file. > Here is the contents of it: > > LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch > > > HTH, > Damian > > > -Joe > > On Mon, Mar 18, 2013 at 9:33 AM, GATTACA <[email protected]> wrote: > >> 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]: >> >>> 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. >> >> >> > > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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