Menu
▾
▴
Re: [GMOD-devel] Problems installing gbrowse from CVS
|
From: Lincoln S. <ls...@cs...> - 2005-01-31 16:10:02
|
Hi all, Multiple people are now reporting problems installing or using=20 gbrowse. Most of these problems are related to the system not=20 recognizing directories. I have a feeling that the recent version of perl has broken or changed=20 the behavior of the -d operator. Either that, or there is an=20 incompatibility with recent kernels. Does anyone have more insight? =20 I am going to upgrade my system to 5.8.3 and see if I can reproduce=20 the problem. Lincoln On Sunday 30 January 2005 08:09 pm, Vsevolod (Simon) Ilyushchenko=20 wrote: > Hi, > > I checked out the current version of gbrowse and tried to install > it on a Fedora 1 box with perl 5.8.3. First, I got complaints that > files META.yml and Changes are missing, but it's no big deal. > However, then I ran into problems. If I simply run "perl > Makefile.PL", subsequent "make install" bombs like this: > > make[1]: Entering directory > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > make[1]: Leaving directory > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS > cgi-bin/gbrowse Extracting cgi-bin/gbrowse (with variable > substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" > cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details > Extracting cgi-bin/gbrowse_details (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS > cgi-bin/gbrowse_est > Extracting cgi-bin/gbrowse_est (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS > cgi-bin/gbrowse_img > Extracting cgi-bin/gbrowse_img (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS > cgi-bin/gbrowse_moby > Extracting cgi-bin/gbrowse_moby (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS > cgi-bin/gbrowse_syn > Extracting cgi-bin/gbrowse_syn (with variable substitutions) > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::CAlign.3 >pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser.3pm > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::wormba >se_gene.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado::Type.3pm > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Plugin.3 >pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::ideogram.3 >pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::genscan_tr >anscript.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Realign. >3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::Segment.3p >m Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::wormbase_t >ranscript.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::reftra >nscript.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::PartialSeq >Adaptor.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::GFFhelpe >r.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::BioDatabas >eAdaptor.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::insertion_ >chromosome.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado::Segment::Fe >ature.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::pairwise_p >lot.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::allele_tow >er.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado.3pm > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Util.3pm > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Markup.3 >pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::waba_a >lignment.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::orf.3p >m Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::PadAlign >ment.3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Options. >3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL.3pm > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::DBAdaptor. >3pm Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado::Segment.3pm > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/process_wormbase.pl > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/make_das_conf.pl > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/load_genbank.pl > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/process_sgd.pl > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/register_moby_services.pl > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/process_gadfly.pl > Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/auto/Bio/Graphics/Browser/CAlign >/CAlign.so Installing > INSTALLSITEMAN3DIR=3D/share/man/man1/auto/Bio/Graphics/Browser/CAlign >/CAlign.bs Writing INSTALLSITEMAN1DIR=3D > Can't open file INSTALLSITEMAN1DIR=3D: Is a directory at > /usr/lib/perl5/5.8.3/ExtUtils/Install.pm line 209 > make: *** [pure_site_install] Error 255 > > *** > > This also creates a subdirectory called INSTALLSITEMAN1DIR=3D in the > source directory. > > I tried to specify INSTALLSITEMAN1DIR and INSTALLSITEMAN3DIR as > parameters to Makefile.PL. It bombed in a different way: > > make[1]: Entering directory > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > make[1]: Leaving directory > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS > cgi-bin/gbrowse Extracting cgi-bin/gbrowse (with variable > substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" > cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details > Extracting cgi-bin/gbrowse_details (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS > cgi-bin/gbrowse_est > Extracting cgi-bin/gbrowse_est (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS > cgi-bin/gbrowse_img > Extracting cgi-bin/gbrowse_img (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS > cgi-bin/gbrowse_moby > Extracting cgi-bin/gbrowse_moby (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS > cgi-bin/gbrowse_syn > Extracting cgi-bin/gbrowse_syn (with variable substitutions) > Use of uninitialized value in -d at > /usr/lib/perl5/5.8.3/File/Path.pm line 153. > fileparse(): need a valid pathname at > /usr/lib/perl5/5.8.3/File/Path.pm line 154 > make: *** [pure_site_install] Error 255 > > *** > > Finally, I ran "perl Makefile.PL PREFIX=3D/usr/local/apache" and got > yet another error: > > make[1]: Entering directory > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > make[1]: Leaving directory > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse.PLS > cgi-bin/gbrowse Extracting cgi-bin/gbrowse (with variable > substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" > cgi-bin/gbrowse_details.PLS cgi-bin/gbrowse_details > Extracting cgi-bin/gbrowse_details (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS > cgi-bin/gbrowse_est > Extracting cgi-bin/gbrowse_est (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS > cgi-bin/gbrowse_img > Extracting cgi-bin/gbrowse_img (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS > cgi-bin/gbrowse_moby > Extracting cgi-bin/gbrowse_moby (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS > cgi-bin/gbrowse_syn > Extracting cgi-bin/gbrowse_syn (with variable substitutions) > Files found in blib/arch: installing files in blib/lib into > architecture dependent library tree > Writing /usr/local/apache > Can't open file /usr/local/apache: Is a directory at > /usr/lib/perl5/5.8.3/ExtUtils/Install.pm line 209 > make: *** [pure_site_install] Error 255 > > *** > > Simon =2D-=20 Lincoln D. Stein Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 NOTE: Please copy Sandra Michelsen <mic...@cs...> on all emails regarding scheduling and other time-critical topics. |