Cannot compile latest SVN release under Fedora 7 64-bit

[GATTACA]

Hello.

I've just downloaded the latest source code from SVN.
I've tried compiling TPP and it fails at PepXMLViewer.

Here is the stderr I'm getting when it fails:
---------------------------------------------------------------------------------------------
cd Visualization/PepXMLViewer; make
make[1]: Entering directory `/data/tpp.data/trans_proteomic_pipeline/
src/Visualization/PepXMLViewer'
g++ -O2 Field.o Filter.o HeaderMRSSQ.o HeaderOnly.o IndexFile.o
main.o MRSOffsetOnly.o Options.o PepXNodeVecBuilder.o
PepXNodeVecSorter.o PepXParser.o PepXViewer.o PipelineAnalysis.o
SAXHandler.o SQOffsetOnly.o utility.o XMLNode.o XMLTree.o ../../
TPPVersionInfo.o libexpat.a /usr/lib/libboost_regex.a /usr/lib/
libboost_filesystem.a /usr/lib/libboost_serialization.a -o
PepXMLViewer.cgi
g++: /usr/lib/libboost_regex.a: No such file or directory
g++: /usr/lib/libboost_filesystem.a: No such file or directory
g++: /usr/lib/libboost_serialization.a: No such file or directory
make[1]: *** [PepXMLViewer.cgi] Error 1
make[1]: Leaving directory `/data/tpp.data/trans_proteomic_pipeline/
src/Visualization/PepXMLViewer'
make: *** [PepXMLViewer.cgi] Error 2
---------------------------------------------------------------------------------------------

Seems like it's looking for libboost_regex.a.

The Makefile looks for libboost_regex-gcc-mt.a in /lib/ but it's not
there under Fedora 7 64-bit. It is not in /lib64 or /usr/lib64 or /usr/
lib for that matter. As far as I can tell, this file is not installed.

A quick search of the fedora repositories indicates i have
boost-1.33.1-13 installed both 64-bit and 32-bit.

Suggestions?

Thanks

Damian

[Brian Pratt]

Looks like you may need to set up a symlink for /usr/lib/libboost_regex.a

I'm in the midst of a linux build too (on Mandrake, so no boost RPMs,
bleah), hitting similar problems...

- Brian

[Greg Bowersock]

I just tried in on 64bit CentOS 4.5 and had a similar error, but only with libboost_regex.a. All it took to fix it for me was to go into /usr/lib and run the following:

ln -s /usr/lib64/libboost_regex.a libboost_regex.a
 

Greg

 

[Greg Bowersock]

Actually I spoke too soon, and had all three of the same come up eventually. The same softlink command works for each file though.

[GATTACA]

Greg,

Are you saying that running these three commands fixed the problem:
ln -s /usr/lib64/libboost_regex.a /usr/lib/libboost_regex.a
ln -s /usr/lib64/libboost_regex.a /usr/lib/libboost_filesystem.a
ln -s /usr/lib64/libboost_regex.a /usr/lib/libboost_serialization.a

?

On Aug 23, 1:51 pm, "Greg Bowersock" <bowers...@gmail.com> wrote:
> Actually I spoke too soon, and had all three of the same come up eventually.
> The same softlink command works for each file though.
>

> On 8/23/07, Greg Bowersock <bowers...@gmail.com> wrote:
>
>
>
> > I just tried in on 64bit CentOS 4.5 and had a similar error, but only with
> > libboost_regex.a. All it took to fix it for me was to go into /usr/lib and
> > run the following:
> > ln -s /usr/lib64/libboost_regex.a libboost_regex.a
>
> > Greg
>

[Greg Bowersock]

No, I meant linking the files of the same name:

ln -s /usr/lib64/libboost_regex.a /usr/lib/libboost_regex.a
ln -s /usr/lib64/libboost_filesystem.a /usr/lib/libboost_filesystem.a
ln -s /usr/lib64/libboost_serialization.a  /usr/lib/libboost_serialization.a

Sorry for the confusion.

 

Greg
 

[GATTACA]

Thanks Greg, got it to work using your links.

For anyone else who might have this problem these are the boost
libraries you need:
boost-1.33.1-13.fc7
boost-devel-static-1.33.1-13.fc7
boost-devel-1.33.1-13.fc7

Damian

On Aug 24, 9:36 am, "Greg Bowersock" <bowers...@gmail.com> wrote:
> No, I meant linking the files of the same name:
> ln -s /usr/lib64/libboost_regex.a /usr/lib/libboost_regex.a
> ln -s /usr/lib64/libboost_filesystem.a /usr/lib/libboost_filesystem.a
> ln -s /usr/lib64/libboost_serialization.a /usr/lib/libboost_serialization.a
>
> Sorry for the confusion.
>
> Greg
>

[Greg Bowersock]

Just curious, but did anyone else get the following error (even though everything compiles correctly now) with the latest svn code:

./bin/Mascot2XML: error while loading shared libraries: libarchive.so.1: cannot open shared object file: No such file or directory
 

I'm just starting to try to troubleshoot the error, as libarchive.so.1 is in my library path, unless the location was hardcoded into the source somewhere with a recent change.

 

Greg

 

On 8/24/07, GATTACA <dfe...@umich.edu> wrote:

[Greg Bowersock]

Ok, I found the problem. Apparently the libarchive is automatically installed now when tpp is compiled and installed, and I haven't closed any of my windows in quite a while, so I needed to rerun ldconfig to update my linked libraries.

 

Greg

 

[Brian Pratt]

Yes, the libarchive thing is new, and is admittedly a bit of a pain - it leads to dependencies on some other libs, so it can become an RPM-fest - but it makes Mascot2XML run a lot faster since it allows Mascot2XML to write all those little .dta and .out files directly into the .tgz file instead of beating the heck out of the disk. 

 

Brian

---

From: spctools...@googlegroups.com [mailto:spctools...@googlegroups.com] On Behalf Of Greg Bowersock
Sent: Monday, August 27, 2007 11:53 AM
To: spctools...@googlegroups.com
Subject: Re: Cannot compile latest SVN release under Fedora 7 64-bit