Hello,
I beleive the .travis.yml does work but it is still under active development.
The Ubuntu instructions in the linux developers page have been tested on a clean install and should work (https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page).
However I have not yet tested a build on a Debian system. I will make an attempt to build today on a clean debian "jessie" install. But I have one question, what branch are you attempting to build, because their is no "stable5_branch-5622-gf3d0bcd" branch in the git repo?
-Zeke
On 02/18/2016 09:59 AM, Yaroslav Halchenko wrote:
Hi Z K et al,
What would be the recommended/tested debian/ubuntu release to approach the build with some guarantee of success? Is the .travis.yml "exercised" (failed to quickly find a sign of it on travis-ci.org)?
I have tried on debian jessie to build stable5_branch-5622-gf3d0bcd of the git/annex repo, using following command:
{ ./setup_configure && ./configure --prefix=/usr/local/freesurfer/dev --with-pkgs-dir=${PWD}/../freesurfer-packages/centos6-x86_64-packages --disable-Werror --with-petsc-dir=/usr/lib/x86_64-linux-gnu && make -j3; } 2>&1 | tee ../freesurfer-upstream.buildlog1.txtand before that installing various build depends and helpers through
apt-get install libtool automake gfortran libglu1-mesa-dev libfreetype6-dev uuid-dev libxmu-dev libxmu-headers libxi-dev libx11-dev libxt-dev libxaw7-dev liblapack-dev tcsh curl git libmpich-dev git git-annex petsc-dev makebut the build fails with
mv -f .deps/xmlToHtml.Tpo .deps/xmlToHtml.Po /bin/bash ../libtool --tag=CC --mode=link g++ -L/usr/lib64 -L/usr/X11R6/lib64 -fopenmp -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/mni/current/lib -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/vxl/current/lib -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/itk/current/lib/InsightToolkit -o xmlToHtml xmlToHtml.o ../xml2/libxml2.a -lz mv -f .deps/fsPrintHelp-fsPrintHelp.Tpo .deps/fsPrintHelp-fsPrintHelp.Po ../libtool: line 469: CDPATH: command not found /bin/bash ../libtool --tag=CC --mode=link g++ -DBUILD_MAIN -L/usr/lib64 -L/usr/X11R6/lib64 -fopenmp -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/mni/current/lib -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/vxl/current/lib -L/home/yoh/deb/gits/pkg-exppsy/freesurfer-upstream/../freesurfer-packages/centos6-x86_64-packages/itk/current/lib/InsightToolkit -o fsPrintHelp fsPrintHelp-fsPrintHelp.o ../xml2/libxml2.a -lz ../libtool: line 469: CDPATH: command not found libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.11, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.11 libtool: and run autoconf again. Makefile:1674: recipe for target 'xmlToHtml' failed make[3]: *** [xmlToHtml] Error 63 make[3]: *** Waiting for unfinished jobs.... libtool: Version mismatch error. This is libtool 2.4.2 Debian-2.4.2-1.11, but the libtool: definition of this LT_INIT comes from an older release. libtool: You should recreate aclocal.m4 with macros from libtool 2.4.2 Debian-2.4.2-1.11 libtool: and run autoconf again. Makefile:1658: recipe for target 'fsPrintHelp' failed make[3]: *** [fsPrintHelp] Error 63
suggesting that not full auto/libtool'ification was carried out by ./setup_configure, but I didn't check detail yet.
full log available at http://www.onerussian.com/tmp/freesurfer-upstream.buildlog1.txt
Thanks in advance for the hints
On Tue, 02 Feb 2016, Z K wrote:
Hello Alle,
The naming of "configure.in" vs. "configure.ac" is not the issue. The script is erroring out because file 'm4/autotroll.m4' does not exist. Do you have that file (it should have been included in the checkout)?
I would recommend using our git repo which mirrors our CVS repo. Please see the following page:
https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page
Hope this helps,
-Zeke
On 02/02/2016 04:11 AM, Alle Meije Wink wrote:
I'm trying to build FreeSurfer from source on my Debian 8 (jessie) system. (64 bit, using g++ 4.9 for compilation)
After $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot login $ cvs -d :pserver:anonymous@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P dev $ cd dev $ cvs update -d # just to make sure $ ./setup_configure
I get these messages:
rm -rf autom4te.cache libtoolize --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `config'. libtoolize: linking file `config/ltmain.sh' libtoolize: putting macros in `m4'. libtoolize: linking file `m4/libtool.m4' libtoolize: linking file `m4/ltoptions.m4' libtoolize: linking file `m4/ltsugar.m4' libtoolize: linking file `m4/ltversion.m4' libtoolize: linking file `m4/lt~obsolete.m4' libtoolize: Consider adding `AC_CONFIG_MACRO_DIR([m4])' to configure.in and libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree. aclocal aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: error: configure.in:2045: file 'm4/autotroll.m4' does not exist
Which looks like a not-(anymore)supported use of autoconf? I found one previous message on the list about autotroll https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/021854.h... that provided another version of configure.in which might solve the issue.
And it did in the original case but sadly not for me. I get the same error message also with the new configure.in -- there should probably be a configure.ac?
If anyone knows how to make this work (e.g. by modifying the configure script) that would be fantastic. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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