A bit more detail, maybe - logs etc - "does not work" covers a lot of ground...
On Fri, Sep 4, 2009 at 11:52 AM, Eileen Yue <y...@ohsu.edu> wrote: > Thank you! > > I just tried to change the database into nonindexed in sequest.params and > keep all the results same. It does not work either though I have both > nonindexed and indexed database in the folder. > > > > > > *From:* spctools-discuss@googlegroups.com [mailto: > spctools-disc...@googlegroups.com] *On Behalf Of *Brian Pratt > *Sent:* 04 September 2009 11:37 > *To:* spctools-discuss@googlegroups.com > *Subject:* [spctools-discuss] Re: problem for the tpp ananlysis with > indexed database > > > > That's right, the indexed database format is nonstandard and TPP doesn't > know how to read it. I think, though, that if you provide the nonindexed > version then you can probably have it both ways. > > On Fri, Sep 4, 2009 at 11:05 AM, Eileen Yue <y...@ohsu.edu> wrote: > > > May I check with one question? > > I use bioworker to run the database search. I noticed that if I use the > indexed database search, after I load on the TPP to do the protein > probability analysis. TPP will not work. > > I can not use indexed database to run the search in order to load on TPP > for protein probability analysis,is this right? > > Thanks > Eileen > > -----Original Message----- > From: spctools-discuss@googlegroups.com [mailto: > spctools-disc...@googlegroups.com] On Behalf Of Natalie Tasman > Sent: 04 September 2009 10:41 > To: spctools-discuss@googlegroups.com > Subject: [spctools-discuss] Re: Failure with make > > > 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'm still 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 -~----------~----~----~----~------~----~------~--~---
