Hello, i've got problems installing the bioperl-ext package... I've tried http://www.bioperl.org/Core/Latest/INSTALL and other ways but there's always a problem. I really need the package to work in one of the following days. Besides, this seems to be a common problem - and I never saw a working answer... I hope this can help you understanding my problem. wouter@wout:~/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext$ perl Makefile.PL Writing Makefile for Bio::Ext::Align Writing Makefile for Bio::Ext wouter@wout:~/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext$ make make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt binnengegaan cc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC "-I/usr/lib/perl/5.10/CORE" -DPOSIX -DNOERROR Align.c Running Mkbootstrap for Bio::Ext::Align () chmod 644 Align.bs rm -f ../blib/arch/auto/Bio/Ext/Align/Align.so cc -shared -O2 -g -L/usr/local/lib Align.o -o ../blib/arch/auto/Bio/Ext/Align/Align.so libs/libsw.a \ -lm \ chmod 755 ../blib/arch/auto/Bio/Ext/Align/Align.so cp Align.bs ../blib/arch/auto/Bio/Ext/Align/Align.bs chmod 644 ../blib/arch/auto/Bio/Ext/Align/Align.bs make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt verlaten wouter@wout:~/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext$ make test make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt binnengegaan make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt verlaten make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt binnengegaan PERL_DL_NONLAZY=1 /usr/bin/perl "-I../blib/lib" "-I../blib/arch" test.pl 1..2 ok 1 2..2 Testing bp_sw with a protein alignment... ProteinSW Matrix calculation: [ 0] Cells 0% one 1 WLGQRNLVSSTGGNLLNVWLKDW W+G RN+V NLLNVW +DW two 1 WMGNRNVV-----NLLNVWFRDW ok 2 make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt verlaten wouter@wout:~/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext$ make install make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt binnengegaan make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt verlaten Files found in blib/arch: installing files in blib/lib into architecture dependent library tree !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!! ERROR: Can't create '/usr/local/lib/perl/5.10.0/Bio/Ext' Do not have write permissions on '/usr/local/lib/perl/5.10.0/Bio/Ext' !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!! at -e line 1 make: *** [pure_site_install] Fout 255 wouter@wout:~/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext$ sudo make install [sudo] password for wouter: make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt binnengegaan make[1]: Map '/home/wouter/Documenten/SCHOOL/Perl/bioperl-ext-1.4/Bio/Ext/Align' wordt verlaten Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Writing /usr/local/lib/perl/5.10.0/auto/Bio/Ext/.packlist Appending installation info to /usr/local/lib/perl/5.10.0/perllocal.pod and than when i run my script: wouter@wout:~/Documenten/SCHOOL/Perl$ perl HMMtest.pl The C-compiled engine for Hidden Markov Model (HMM) has not been installed. Please read the install the bioperl-ext package BEGIN failed--compilation aborted at /usr/share/perl5/Bio/Tools/HMM.pm line 140. Compilation failed in require at HMMtest.pl line 3. many thanks W