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 -~----------~----~----~----~------~----~------~--~---
