Hi Ulrich,

I am new to Linux.  My system is Ubuntu 8.04.  I met the same problem when 
I tried to install TPP.  I followed your suggestion.  However, after "make 
all" command, I got following message.
tranche@tranche-server:/usr/local/src/TPP-4.6.3/trans_proteomic_pipeline/src$make
 all
tar: htmldoc/png/.svn/text-base/libpng.3.svn-base: Cannot open: No such 
file or directory
tar: htmldoc/png/.svn/text-base/pngwtran.c.svn-base: Cannot open: No such 
file or directory
....
....
tar: htmldoc/doc/htmldoc-fig51.png: Cannot open: No such file or directory
tar: htmldoc/doc/htmldoc-fig56.png: Cannot open: No such file or directory
tar: htmldoc/COPYING.txt: Cannot open: No such file or directory
tar: Error exit delayed from previous errors

Then I tried to go ahead to "make install' follow the suggestion. 
tranche@tranche-server:/usr/local/src/TPP-4.6.3/trans_proteomic_pipeline/src$make
 install
# Create Directories
mkdir -p /usr/local/tpp/
mkdir -p /usr/local/tpp/bin/
mkdir -p /usr/local/tpp/cgi-bin/
mkdir -p /usr/local/tpp/schema/
mkdir -p /usr/local/tpp/html/js
# Copy all source executables and configuration files to their location
cp -f 
/usr/local/src/TPP-4.6.3/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/ASAPRatioPeptideParser
 
/usr/local/tpp/bin/
cp: cannot stat 
`/usr/local/src/TPP-4.6.3/trans_proteomic_pipeline/src/../build/Ubuntu-x86_64/ASAPRatioPeptideParser':
 
No such file or directory
make: *** [install-linux-xml] Error 1

Any suggestion?

Thanks,

Zhongping


On Tuesday, September 29, 2009 2:58:01 AM UTC-4, Ulrich auf dem Keller 
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...@googlegroups.com <javascript:> 
> >> 
> >>>>>>>>>>>> [mailto:spctools...@googlegroups.com <javascript:>] 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...@googlegroups.com <javascript:> 
> >> 
> >>>>>>>>>>>>> [mailto:spctools...@googlegroups.com <javascript:>] 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 
> > 
> > > 
>
>
>

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