[MINC-users] compiling the minc bundle

[Pierre Bellec]

Dear Minc users,

I am using the big Makefile Vladimir Vonof wrote to compile a full minc
bundle on a server where I do not have access to sudo. I followed the
instructions from the Minc wikibook:
http://en.wikibooks.org/wiki/MINC/Tutorials/SourceInstall#Step_5:_Run_your_build.28s.29

After downloading the make file, I ran the following line:
make minc-full BUILD_DIR=$HOME/tmp/build_minc
INSTALL_DIR=$HOME/progs/minc-2011-12

Everything went well for a while but it crashed when
compiling mni_perllib-0.08

mkdir
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/auto/mni_perllib:
Permission denied at /usr/lib/perl5/5.8.8/ExtUtils/Install.pm line 207
make[1]: *** [pure_site_install] Error 13
make[1]: Leaving directory
`/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08'
make: *** [/home/pbellec/progs/minc-2011-12/perl/MNI.pm] Error 2

Any suggestion on how to fix this problem will be very much appreciated.

Pierre

PS: Here's the whole compilation message just in case:

mkdir -p /home/pbellec/tmp/build_minc/src
mkdir -p /home/pbellec/progs/minc-2011-12/bin
mkdir -p /home/pbellec/progs/minc-2011-12/lib
mkdir -p /home/pbellec/progs/minc-2011-12/include
mkdir -p /home/pbellec/progs/minc-2011-12/share/mni-models
mkdir -p /home/pbellec/progs/minc-2011-12/share/mni_autoreg
mkdir -p /home/pbellec/progs/minc-2011-12/share/man/man1
mkdir -p /home/pbellec/progs/minc-2011-12/share/man/man3
ls -l
total 512
-rw-r--r-- 1 pbellec gsf-624-02    36 Jan  1 21:08 1
drwxr-xr-x 2 pbellec gsf-624-02 32768 Jan  1 20:59 bin
-rw-r--r-- 1 pbellec gsf-624-02   423 Jan  1 21:08 compilation_error.txt
drwxr-xr-x 3 pbellec gsf-624-02 32768 Dec 31 00:46 etc
drwxr-xr-x 5 pbellec gsf-624-02 32768 Jan  1 20:59 include
drwxr-xr-x 3 pbellec gsf-624-02 32768 Jan  1 20:59 lib
-rw-r--r-- 1 pbellec gsf-624-02 40111 Dec 31 00:33 Makefile
drwxr-xr-x 4 pbellec gsf-624-02 32768 Dec 31 00:40 man
drwxr-xr-x 4 pbellec gsf-624-02 32768 Dec 31 00:46 perl
drwxr-xr-x 9 pbellec gsf-624-02 32768 Dec 31 00:43 share
cd /home/pbellec/tmp/build_minc/src/mni_perllib-0.08 && \
echo -e /home/pbellec/progs/minc-2011-12 \\n\\n\\n > dummy_response_file &&
\
echo perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 \
                   INSTALLDIRS=site \
                   INSTALLSITELIB=/home/pbellec/progs/minc-2011-12/perl \
                   INSTALLSITEBIN=/home/pbellec/progs/minc-2011-12/bin \

INSTALLSITEMAN1DIR=/home/pbellec/progs/minc-2011-12/share/man/man1 \

INSTALLSITEMAN3DIR=/home/pbellec/progs/minc-2011-12/share/man/man3 <
dummy_response_file  && \
perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12 \
                   INSTALLDIRS=site \
                   INSTALLSITELIB=/home/pbellec/progs/minc-2011-12/perl \
                   INSTALLSITEBIN=/home/pbellec/progs/minc-2011-12/bin \

INSTALLSITEMAN1DIR=/home/pbellec/progs/minc-2011-12/share/man/man1 \

INSTALLSITEMAN3DIR=/home/pbellec/progs/minc-2011-12/share/man/man3 <
dummy_response_file  && \
make && \
make install && \
touch /home/pbellec/progs/minc-2011-12/perl/MNI.pm
perl ./Makefile.PL SITEPREFIX=/home/pbellec/progs/minc-2011-12
INSTALLDIRS=site INSTALLSITELIB=/home/pbellec/progs/minc-2011-12/perl
INSTALLSITEBIN=/home/pbellec/progs/minc-2011-12/bin
INSTALLSITEMAN1DIR=/home/pbellec/progs/minc-2011-12/share/man/man1
INSTALLSITEMAN3DIR=/home/pbellec/progs/minc-2011-12/share/man/man3
I need to know the default directory for static, per-package data (eg.,
models).  This is used so that packages distributed from the MNI have a
consistent, uniform way of searching for such data.  Whatever directory
you specify, you can change your mind later by redoing the
configure/build/install cycle for the MNI Perl Library; or, you can just
put symbolic links in the directory you specify here, pointing to the
real location of the data for whatever MNI packages you use at your
site.  And users can always override this default directory using the
MNI_DATAPATH environment variable.

Default directory for model data [/usr/local/mni/data]? Default directory
for model data [/usr/local/mni/data]? Writing Makefile for mni_perllib
make[1]: Entering directory
`/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08'
rm -f MNI/DataDir.pm
sed 's|@DEFAULT_DATA_DIR@|/usr/local/mni/data|' MNI/DataDir.pm.in >
MNI/DataDir.pm
chmod 444 MNI/DataDir.pm
Skip blib/lib/MNI/TagPoint.pm (unchanged)
Skip blib/lib/MNI/Spawn.pm (unchanged)
Skip blib/lib/MNI/Startup.pm (unchanged)
Skip blib/lib/MNI.pm (unchanged)
Skip blib/lib/mni_perllib.pod (unchanged)
Skip blib/lib/MNI/MiscUtilities.pm (unchanged)
Skip blib/lib/MNI/FileUtilities.pm (unchanged)
Skip blib/lib/MNI/Spawn.pod (unchanged)
Skip blib/lib/MNI/PathUtilities.pm (unchanged)
Skip blib/lib/MNI/TagSet.pm (unchanged)
Skip blib/lib/MNI/NumericUtilities.pm (unchanged)
Skip blib/lib/MNI/MincUtilities.pm (unchanged)
Skip blib/lib/MNI/DataDir.pm (unchanged)
Skip blib/lib/MNI/Batch.pm (unchanged)
Manifying blib/man3/MNI::TagPoint.3pm
Manifying blib/man3/MNI::Startup.3pm
Manifying blib/man3/MNI::MiscUtilities.3pm
Manifying blib/man3/mni_perllib.3pm
Manifying blib/man3/MNI::FileUtilities.3pm
Manifying blib/man3/MNI::Spawn.3pm
Manifying blib/man3/MNI::PathUtilities.3pm
Manifying blib/man3/MNI::NumericUtilities.3pm
Manifying blib/man3/MNI::TagSet.3pm
Manifying blib/man3/MNI::DataDir.3pm
Manifying blib/man3/MNI::MincUtilities.3pm
Manifying blib/man3/MNI::Batch.3pm
make[1]: Leaving directory
`/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08'
make[1]: Entering directory
`/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08'
Skip blib/lib/MNI/TagPoint.pm (unchanged)
Skip blib/lib/MNI/Spawn.pm (unchanged)
Skip blib/lib/MNI/Startup.pm (unchanged)
Skip blib/lib/MNI.pm (unchanged)
Skip blib/lib/mni_perllib.pod (unchanged)
Skip blib/lib/MNI/MiscUtilities.pm (unchanged)
Skip blib/lib/MNI/FileUtilities.pm (unchanged)
Skip blib/lib/MNI/Spawn.pod (unchanged)
Skip blib/lib/MNI/PathUtilities.pm (unchanged)
Skip blib/lib/MNI/TagSet.pm (unchanged)
Skip blib/lib/MNI/NumericUtilities.pm (unchanged)
Skip blib/lib/MNI/MincUtilities.pm (unchanged)
Skip blib/lib/MNI/DataDir.pm (unchanged)
Skip blib/lib/MNI/Batch.pm (unchanged)
Manifying blib/man3/MNI::DataDir.3pm
Installing /home/pbellec/progs/minc-2011-12/share/man/man3/MNI::DataDir.3pm
make[1]: Leaving directory
`/sb/home/pbellec/tmp/build_minc/src/mni_perllib-0.08'