Thank you Ulrich, I followed your suggestions and have managed to get TPP running.
Thanks to everybody else too who has tried to assist me :-) On Sep 29, 9:58 am, Ulrich auf dem Keller <ukel...@interchange.ubc.ca> wrote: > Hi Eliza, > > I think it's an environment problem. This is exactly what I get when > building as non-root user with the source in his home directory and > then trying to install to e.g. '/usr/local/tpp/' as default in > Makefile.incl by 'sudo make install'. It also doesn't work when > building and installing as root. You may try building and installing > as the user who got the TPP source. I would try to go to 'src' within > TPP source directory as a normal user, then build it by running 'make > all' (don't use sudo here). Next create the desired installation > directory as specified in 'Makefile.incl' with e.g. 'sudo mkdir /usr/ > local/tpp', change permissions of this directory with e.g. 'sudo chmod > -R 777 /usr/local/tpp', then run 'make install' from within TPP 'src'. > This should install correctly to '/usr/local/tpp'. Finally, change > permissions of '/usr/local/tpp' to e.g. root::wheel or whatever is the > default for those directories on your system. > > It's just an idea, maybe you already tried it... > > Cheers, > > Ulrich > > On Sep 28, 2009, at 7:26 PM, Eliza wrote: > > > > > Brian/Natalie > > > I tried building on x64 Ubuntu 9.04 desktop (including running the > > pre- > > requisites script) and got the same error: > > > Makefile.incl:431: /Makefile.pwiz.incl: No such file or directory > > make: *** No rule to make target `/Makefile.pwiz.incl'. Stop. > > > When I asked the advice of a 'linux expert' they said that the problem > > is most likely a poorly written make file and something I should > > report rather than fix myself. > > > On Sep 25, 6:00 pm, Brian Pratt <brian.pr...@insilicos.com> 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 -~----------~----~----~----~------~----~------~--~---
