>> It isn't the case, I have noticed that Makefile.config.incl is not getting picked up.
Not surprising since SRC_ROOT is goofed up: -include $(SRC_ROOT)Makefile.config.incl # -include means if it doesn't exist just don't use it I think you're to the point where you need to locate someone onsite who can help you resolve these issues. I've just done a build on Ubuntu 9.10 without any trouble around $PWD or SRC_ROOT, there's something odd with your system in particular, I'm afraid. You might want to have a look at \trunk\trans_proteomic_pipeline\installer_linux\install-prerequisites-ubuntu -9_04.sh (it works for 9.10 too). Brian -----Original Message----- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza Sent: Tuesday, August 18, 2009 4:16 AM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make It isn't the case, I have noticed that Makefile.config.incl is not getting picked up. That latest suggestion didn't work I am still not getting any further with the same error message: make: *** /opt/trans_proteomic_pipeline/ src/: Is a directory. Stop. On Aug 17, 9:53 pm, "Brian Pratt" <brian.pr...@insilicos.com> wrote: > No change needed - if the Makefile.config.incl file is there it gets used, > if it's not that's OK too. > > Let's try another workaround for the PWD strangeness - try this command > (with a clean, unmodified Makefile) > > export PWD=/opt/trans_proteomic_pipeline/src ; make all install > > -----Original Message----- > From: spctools-discuss@googlegroups.com > > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza > Sent: Sunday, August 16, 2009 11:17 PM > To: spctools-discuss > Subject: [spctools-discuss] Re: Failure with make > > Firstly I want to clarify a section in the README file. I am not > familiar with compiling applications from source but I assume if I > want to use a modified configuration file I need to edit the original > Makefile to point to Makefile.config.incl? The installation > instructions say to create the Makefile.config.incl file but I didn't > see any instructions in regards to modifying the original Makefile. > > Secondly, when setting the SRC_ROOT as suggested I get the following > error: > > make: *** /opt/trans_proteomic_pipeline/src/: Is a directory. Stop. > > Eliza. > > On Aug 14, 12:06 am, "Brian Pratt" <brian.pr...@insilicos.com> wrote: > > Eh, so it goes in the wild and wooly world of linux distros. > > > Of those alternate methods, only > > SRC_ROOT= $(shell pwd)/ > > seems to work well with mingw. Eliza, can you please verify that this > works > > well for your linux? > > > Brian > > > -----Original Message----- > > From: spctools-discuss@googlegroups.com > > > [mailto:spctools-disc...@googlegroups.com] On Behalf Of Natalie Tasman > > Sent: Thursday, August 13, 2009 1:24 PM > > To: spctools-discuss@googlegroups.com > > Subject: [spctools-discuss] Re: Failure with make > > > Hi Mike, > > > That's a strange report about Ubuntu. I'm routinely building on 8.04 > > and 9.04. Did something change in 9.10? > > > -Natalie > > > On Aug 13, 2009, at 1:09 PM, Mike Coleman wrote: > > > > [sorry about the previous half-finished post] > > > > I can speak to that, having just bumped into it. SRC_ROOT is defined > > > as $(PWD)/ in the Makefile, but $PWD may not exist in the environment, > > > leading to a definition of "SRC_ROOT=/". > > > > In particular, on the latest version of Ubuntu, 'sudo printenv' shows > > > no definition of PWD. I'm not that crazy about them having left it > > > out, but there it is, and there's really no standard that says it has > > > to be defined. > > > > For GNU make, you could use one of > > > > $(realpath .) > > > $(abspath .) > > > $(shell pwd) > > > > The best solution, though, would be to get rid of SRC_ROOT altogether > > > and use relative paths, if possible. > > > > Mike > > > > On Aug 13, 11:51 am, "Brian Pratt" <brian.pr...@insilicos.com> wrote: > > >> Natalie is correct, the issue is around SRC_ROOT="/" . > > > >> As she says, your current working directory needs to be the one that > > >> contains the main TPP makefile (and the Makefile.pwiz.incl file). > > > >> -----Original Message----- > > >> From: spctools-discuss@googlegroups.com > > > >> [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza > > >> Sent: Thursday, August 13, 2009 7:46 AM > > >> To: spctools-discuss > > >> Subject: [spctools-discuss] Re: Failure with make > > > >> I got the latest version of TPP (4.3.0) and this time when trying to > > >> make I am getting the following error: > > > >> Makefile.incl:431: /Makefile.pwiz.incl: No such file or directory > > >> make: *** No rule to make target `/Makefile.pwiz.incl'. Stop. > > > >> On Aug 5, 10:25 pm, Natalie Tasman <natalie.tas...@insilicos.com> > > >> wrote: > > >>> Hi Eliza, > > > >>> It sounds like something strange is going on. Maybe you should re- > > >>> load the sourcecode. Also, I've never seen "SRC_ROOT="/"" come up > > >>> before. Are you starting the build from /, rather than the actual > > >>> TPP/ > > >>> src directory? You want to cd there first. > > > >>> It does sound like a corrupted checkout (missing files, etc), too, > > >>> possibly. > > > >>> Natalie > > > >>> On Aug 5, 2009, at 1:29 AM, Eliza wrote: > > > >>>> Hi Natalie, > > > >>>> I have tried your suggestion and 'make distclean; make" fails at: > > > >>>> make -C ../extern/xtandem/src SRC_ROOT="/" ARCH=linux > > >>>> BUILD_DIR=/../ > > >>>> build/linux clean > > >>>> make[1]: Entering directory `/usr/local/src/tpp-4.2.1/extern/ > > >>>> xtandem/ > > >>>> src' > > >>>> make[1]: *** No rule to make target `clean'. Stop. > > > >>>> Thanks, > > >>>> Eliza. > > > >>>> On Jul 31, 8:19 pm, Natalie Tasman <natalie.tas...@insilicos.com> > > >>>> wrote: > > >>>>> Hi Eliza, > > > >>>>> I haven't run into this before, but you may want to try a "make > > >>>>> distclean; make" sequence. I would also look at the compiler > > >>>>> output > > >>>>> earlier in the stream and see if there were any uncaught errors > > >>>>> building the "AminoAcid" that might provide a clue. > > > >>>>> Please let us know how it goes, and good luck, > > > >>>>> Natalie > > > >>>>> On Jul 31, 2009, at 4:25 AM, Eliza wrote: > > > >>>>>> Hi, > > > >>>>>> I am receiving the following error when trying to issue 'make' in > > >>>>>> the > > >>>>>> src directory: > > > >>>>>> make[1]: *** No rule to make target `/../build/linux/ > > >>>>>> AminoAcid.o', > > >>>>>> needed by `/../build/linux/libpwiz.a'. Stop. > > >>>>>> make[1]: Leaving directory `/usr/local/src/tpp-4.2.1/src' > > >>>>>> make: *** [default] Error 2 > > > >>>>>> TPP version 4.2.1 > > >>>>>> Debian Etch kernel 2.6.15.4 > > >>>>>> Compiler version 4.3.2 > > > >>>>>> Thanks, > > >>>>>> Eliza. --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
