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