That's another good suggestion. I didn't see Brian's message when I replied today :)
On Sep 25, 2009, at 8:00 AM, Brian Pratt wrote: > I'd say next step is try to perform a build on a different computer > and transfer the binaries to the computer you want to use. There's > something very peculiar about that system, but hopefully it won't > affect TPPs ability to run once it has been built elsewhere. > > On Thu, Sep 24, 2009 at 10:41 PM, Eliza <blond...@googlemail.com> > wrote: > > Any more suggestions? There is quite a lot of interest in getting TPP > running in the lab and at this point I am not sure how to proceed. > > On Sep 18, 8:15 pm, Brian Pratt <brian.pr...@insilicos.com> wrote: > > (FWIW, Ubuntu is a flavor of Debian) > > > > That's interesting - does "make clean all" work after your first > "make > > all"? It sounds like the build is somehow changing the > environment, or > > maybe even its own makefiles... > > > > On Thu, Sep 17, 2009 at 11:45 PM, Eliza <blond...@googlemail.com> > wrote: > > > > > I haven't tried your suggestion of running it on another distro > yet > > > Natalie, but I did get the latest version when that was > announced and > > > I got a little bit further. I was able to run 'make all' > without any > > > errors, but when I run try to run 'make install' I'm back with the > > > error message "Makefile.incl:431: /Makefile.pwiz.incl: No such > file or > > > directory > > > make: *** No rule to make target `/Makefile.pwiz.incl'. Stop." > > > > > I am not using Ubuntu, but Debian. > > > > > On Sep 4, 8:40 pm, Natalie Tasman <natalie.tas...@insilicos.com> > > > wrote: > > > > Hi Eliza, > > > > > > At this point, it might be worthwhile trying to compile the > TPP on > > > > another linux distribution that works well. For example, Ubuntu > > > > 8.04. Then, I'd be sure to run the correct "install > prerequisites" > > > > file from tpp/installer_linux to make sure all the required > system > > > > packages are installed. > > > > > > Then again, it wouldn't hurt to run the correct "install > > > > prerequisites" for your own system. Currently, the Ubuntu > 9.04 script > > > > seems to work for 9.10 also, if you're using that. > > > > > > Good luck, > > > > > > Natalie > > > > > > On Sep 4, 2009, at 1:05 AM, Eliza wrote: > > > > > > > Mike - having an empty Makefile.config.incl didn't fix > anything. I am > > > > > still getting the error: make: *** No rule to make target `/ > > > > > Makefile.pwiz.incl'. Stop. > > > > > > > On Sep 1, 10:21 pm, Mike Coleman <tutu...@gmail.com> wrote: > > > > >> Okay, this turned out to be useful. It appears that the > contents of > > > > >> your file 'Makefile.config.incl' is including itself (it > appears to > > > > >> be > > > > >> a copy of 'Makefile.incl'). This recurses about 1000 > times, at which > > > > >> point you hit the file handle limit. The resulting error is > > > > >> apparently ignored due to the '-include'. > > > > > > >> So, either make 'Makefile.config.incl' an empty file, or > otherwise I > > > > >> think it should be just a short file including a few variable > > > > >> definitions. Also, verify that neither of these files is a > symbolic > > > > >> or hard link to the other. > > > > > > >> Probably this will fix things, or at least move things > forward. > > > > > > >> Mike > > > > > > >> On Aug 31, 2:34 am, Eliza <blond...@googlemail.com> wrote: > > > > > > >>> OK I have added make.strace.gz to the file uploads. > > > > > > >>> On Aug 28, 6:34 pm, Mike Coleman <tutu...@gmail.com> wrote: > > > > > > >>>> Okay, if you really want to bring out the big guns, do > something > > > > >>>> like > > > > >>>> this > > > > > > >>>> $ strace -f -s 1024 -v -o make.strace make > > > > > > >>>> and put the resulting 'make.strace' log somewhere where > we can > > > > >>>> look at > > > > >>>> it. I think this is erroring out pretty quickly, so > hopefully that > > > > >>>> log won't be too huge. No promises, but this may very > well clarify > > > > >>>> what's going wrong. > > > > > > >>>> You'll have to install the strace package if it's not > already > > > > >>>> present. > > > > > > >>>> Mike > > > > > > >>>> On Aug 28, 4:59 am, Eliza <blond...@googlemail.com> wrote: > > > > > > >>>>> That doesn't make any difference. > > > > > > >>>>> On Aug 27, 8:12 pm, "Brian Pratt" > <brian.pr...@insilicos.com> > > > > >>>>> wrote: > > > > > > >>>>>> Yeah, that's what we use here too. Perhaps you could > try it as > > > > >>>>>> a different, > > > > >>>>>> newly created user? It sounds like there is something > peculiar > > > > >>>>>> about your > > > > >>>>>> shell setup. > > > > > > >>>>>> -----Original Message----- > > > > >>>>>> From: spctools-discuss@googlegroups.com > > > > > > >>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf Of > Eliza > > > > >>>>>> Sent: Thursday, August 27, 2009 12:13 AM > > > > >>>>>> To: spctools-discuss > > > > >>>>>> Subject: [spctools-discuss] Re: Failure with make > > > > > > >>>>>> Bash > > > > > > >>>>>> On Aug 20, 11:55 pm, "Brian Pratt" > <brian.pr...@insilicos.com> > > > > >>>>>> wrote: > > > > >>>>>>> We basically tried that already: Eliza says the > suggested > > > > > > >>>>>>> export PWD=/opt/trans_proteomic_pipeline/src ; make > all install > > > > > > >>>>>>> did not work. She also tried the "SRC_ROOT= $(shell > pwd)" > > > > >>>>>>> change to the > > > > >>>>>>> makefile. There's something deeper going on. > > > > > > >>>>>>> Eliza, what shell do you use? I do see from googling > that > > > > >>>>>>> $PWD might be > > > > >>>>>>> bash-specific, possibly there are other unintended bash > > > > >>>>>>> dependencies. > > > > > > >>>>>>> Brian > > > > > > >>>>>>> -----Original Message----- > > > > >>>>>>> From: spctools-discuss@googlegroups.com > > > > > > >>>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf > Of Mike > > > > >>>>>>> Coleman > > > > >>>>>>> Sent: Thursday, August 20, 2009 1:26 PM > > > > >>>>>>> To: spctools-discuss > > > > >>>>>>> Subject: [spctools-discuss] Re: Failure with make > > > > > > >>>>>>> Eliza, > > > > > > >>>>>>> I'mstill suspicious about the $PWD thing. If you're > running > > > > >>>>>>> 'make' > > > > >>>>>>> normally, you might try something like > > > > > > >>>>>>> $ PWD=$(pwd) make ... > > > > > > >>>>>>> instead of just > > > > > > >>>>>>> $ make ... > > > > > > >>>>>>> to see whether that improves your situation. > Alternatively, > > > > >>>>>>> for the > > > > >>>>>>> 'root' steps, you could do something like > > > > > > >>>>>>> $ sudo PWD=$(pwd) make ... > > > > > > >>>>>>> Mike > > > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
