Ulrich, Yes did I try running them as the same user, but I'm not sure if you're suggesting a lack of permissions or a change in environment variables depending on the user?
On Sep 25, 8:45 pm, Ulrich auf dem Keller <ukel...@interchange.ubc.ca> wrote: > I just saw these e-mails. Did you try to run 'make install' as the > same user you ran 'make all'? At least on Mac OS X you have to create > the directory (e.g. /usr/local/tpp/) first manually, change > permissions e.g. to 777, run 'make install' as the same user who ran > 'make all' and then change the permissions back to whatever is more > appropriate. I guess 'make install' needs environment variables set > during 'make all'. > > Maybe, that helps. > > Ulrich > > On Sep 25, 2009, at 7:30 PM, Natalie Tasman wrote: > > > 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 -~----------~----~----~----~------~----~------~--~---
