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[GMOD-devel] RE: Gmod-devel digest, Vol 1 #448 - 5 msgs
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From: Axelrod, N. <NAx...@ve...> - 2005-02-01 22:19:31
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If this is of any help, I've noticed that in our attempt to install the latest release of Gbrowse the gbrowse.conf directory was recursively generated resulting in links like the following for the Volvox demo - http://www.venterinstitute.org/cgi-bin/gbrowse/gbrowse/gbrowse/gbrowse/g browse/gbrowse/?source=3Dvolvox;name=3DctgA Nelson -----Original Message----- From: gmo...@li... [mailto:gmo...@li...] On Behalf Of gmo...@li... Sent: Monday, January 31, 2005 11:08 PM To: gmo...@li... Subject: Gmod-devel digest, Vol 1 #448 - 5 msgs Send Gmod-devel mailing list submissions to gmo...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/gmod-devel or, via email, send a message with subject or body 'help' to gmo...@li... You can reach the person managing the list at gmo...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of Gmod-devel digest..." Today's Topics: 1. Re: [Bioperl-l] Re: RPMs for Bioperl and GMOD (Hilmar Lapp) 2. Re: Problems installing gbrowse from CVS (Allen Day) 3. Re: Problems installing gbrowse from CVS (Zhiliang Hu) 4. Re: Problems installing gbrowse from CVS (Scott Cain) 5. Re: Problems installing gbrowse from CVS (Allen Day) --__--__-- Message: 1 Cc: Allen Day <all...@uc...>, Lincoln Stein <ls...@cs...>, Bioperl <bio...@bi...>, gmo...@li... From: Hilmar Lapp <hl...@gn...> Date: Mon, 31 Jan 2005 13:28:25 -0800 To: Lincoln Stein <ls...@cs...> Subject: [GMOD-devel] Re: [Bioperl-l] Re: RPMs for Bioperl and GMOD On Jan 31, 2005, at 7:35 AM, Lincoln Stein wrote: > Perhaps we should split the modules into bioperl-db and > bioperl-db-oracle. > > And so forth. Sure you could ... but where do you draw the line? E.g.,=20 gbrowse-pgsql-png-no-gif-SVG-no-staden-Ace-berkeleyDB.rpm ... I mean,=20 applying this to all dependencies will lead to permutations of several=20 dependencies - which I'm not sure will further the goal of making it=20 easier on the end user's end ... Just my two cents ... -hilmar --=20 ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- --__--__-- Message: 2 Date: Mon, 31 Jan 2005 13:57:51 -0800 (PST) From: Allen Day <all...@uc...> To: "Vsevolod (Simon) Ilyushchenko" <si...@cs...> cc: gmo...@li... Subject: Re: [GMOD-devel] Problems installing gbrowse from CVS this is my doing, i'm making modifications to Makefile.PL to try to get the official ExtUtils::MakeMaker arguments, when passed in, to do the right thing. as you can see it isn't working yet :). please use the=20 stable tag/branch unless you want to help fix these problems. -allen On Sun, 30 Jan 2005, Vsevolod (Simon) Ilyushchenko wrote: > Hi, >=20 > I checked out the current version of gbrowse and tried to install it on=20 > a Fedora 1 box with perl 5.8.3. First, I got complaints that files=20 > META.yml and Changes are missing, but it's no big deal. However, then I=20 > ran into problems. If I simply run "perl Makefile.PL", subsequent "make=20 > install" bombs like this: >=20 > make[1]: Entering directory=20 > `/home/simonf/gbrowse/cvs-gbrowse/Generic-Genome-Browser/libalign' > make[1]: Leaving directory=20 > `/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=20 > cgi-bin/gbrowse_details > Extracting cgi-bin/gbrowse_details (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_est.PLS=20 > cgi-bin/gbrowse_est > Extracting cgi-bin/gbrowse_est (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_img.PLS=20 > cgi-bin/gbrowse_img > Extracting cgi-bin/gbrowse_img (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_moby.PLS=20 > cgi-bin/gbrowse_moby > Extracting cgi-bin/gbrowse_moby (with variable substitutions) > /usr/bin/perl "-Iblib/arch" "-Iblib/lib" cgi-bin/gbrowse_syn.PLS=20 > cgi-bin/gbrowse_syn > Extracting cgi-bin/gbrowse_syn (with variable substitutions) > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::CAlign.3pm > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::wormbase_g= e ne.3pm > Installing INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado::Type.3pm > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Plugin.3pm > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::ideogram.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::genscan_transc= r ipt.3pm > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Realign.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::Segment.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::wormbase_trans= c ript.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::reftranscr= i pt.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::PartialSeqAdap= t or.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::GFFhelper.3p= m > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::BioDatabaseAda= p tor.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::insertion_chro= m osome.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado::Segment::Featur= e .3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::pairwise_plot.= 3 pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Glyph::allele_tower.3= p m > Installing = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::Chado.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Util.3pm > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Markup.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::waba_align= m ent.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::GFF::Aggregator::orf.3pm > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::PadAlignment= . 3pm > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::Graphics::Browser::Options.3pm > Installing = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL.3pm > Installing=20 > = INSTALLSITEMAN3DIR=3D/share/man/man1/Bio::DB::Das::BioSQL::DBAdaptor.3pm > Installing=20 > 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=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/auto/Bio/Graphics/Browser/CAlign/CAl= i gn.so > Installing=20 > INSTALLSITEMAN3DIR=3D/share/man/man1/auto/Bio/Graphics/Browser/CAlign/CAl= i gn.bs > Writing INSTALLSITEMAN1DIR=3D > Can't open file INSTALLSITEMAN1DIR=3D: Is a directory at=20 > /usr/lib/perl5/5.8.3/ExtUtils/Install.pm line 209 > make: *** [pure_site_install] Error 255 >=20 > *** >=20 > This also creates a subdirectory called INSTALLSITEMAN1DIR=3D in the=20 > source directory. >=20 > I tried to specify INSTALLSITEMAN1DIR and INSTALLSITEMAN3DIR as=20 > parameters to Makefile.PL. It bombed in a different way: >=20 > 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 >=20 > *** >=20 > Finally, I ran "perl Makefile.PL PREFIX=3D/usr/local/apache" and got = yet > another error: >=20 > 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 >=20 > *** >=20 > Simon >=20 --__--__-- Message: 3 Date: Mon, 31 Jan 2005 16:03:09 -0600 (CST) From: Zhiliang Hu <hu...@db...> To: gmo...@li... Subject: Re: [GMOD-devel] Problems installing gbrowse from CVS On Mon, 31 Jan 2005, Lincoln Stein wrote: > Hi all, >=20 > Multiple people are now reporting problems installing or using=3D20 > gbrowse. Most of these problems are related to the system not=3D20 > recognizing directories. >=20 > I have a feeling that the recent version of perl has broken or changed=3D20 > the behavior of the -d operator. Either that, or there is an=3D20 > incompatibility with recent kernels. Does anyone have more insight? =3D20 > I am going to upgrade my system to 5.8.3 and see if I can = reproduce=3D20 > the problem. >=20 > Lincoln Good you are on top of it... hope my error from installing GBrowse 1.62 may provide more 'evidence' for you to diagnose - 'make test' or 'make install' complained it cannot locate "IO.pm" while I do find it in one of the paths: # make test ........(deleted lines).......... t/01yeast....Can't locate Bio/Root/IO.pm in @INC (@INC contains: /usr/local/lib/perl5/5.8.5/i686-linux /usr/local/lib/perl5/5.8.5/i686-linux /usr/local/lib/perl5/5.8.5 /usr/local/lib/perl5/site_perl/5.8.5/i686-linux /usr/local/lib/perl5/site_perl/5.8.5/i686-linux /usr/local/lib/perl5/site_perl/5.8.5 /usr/local/lib/perl5/site_perl/5.8.5/i686-linux /usr/local/lib/perl5/site_perl/5.8.5 /usr/local/lib/perl5/site_perl /usr/share/ . /usr/local/lib/perl5/5.8.5/i686-linux /usr/local/lib/perl5/5.8.5 /usr/local/lib/perl5/site_perl/5.8.5/i686-linux /usr/local/lib/perl5/site_perl/5.8.5 /usr/local/lib/perl5/site_perl /usr/share/ .) at t/01yeast.t line 9. BEGIN failed--compilation aborted at t/01yeast.t line 9. t/01yeast....dubious Test returned status 2 (wstat 512, 0x200) FAILED--1 test script could be run, alas--no output ever seen make: *** [test_dynamic] Error 2 # find / -name IO.pm /usr/lib/perl5/5.8.0/i386-linux-thread-multi/IO.pm /usr/local/lib/perl5/5.8.5/i686-linux/IO.pm /usr/local/lib/perl5/site_perl/5.8.5/SOAP/Transport/IO.pm --__--__-- Message: 4 Date: Mon, 31 Jan 2005 17:35:40 -0500 (EST) From: Scott Cain <ca...@cs...> To: Zhiliang Hu <hu...@ge...> cc: gmo...@li... Subject: Re: [GMOD-devel] Problems installing gbrowse from CVS Zhiliang, Do you have a recent build of BioPerl installed, if so you should see something like=20 /usr/local/lib/perl5/site_perl/5.8.4/Bio/Root/IO.pm (note the Bio/Root/ before the IO.pm). It isn't in your output below. Scott ---------------------------------------------------------------------- Scott Cain, Ph. D. ca...@cs... GMOD Coordinator, http://www.gmod.org/ (216)392-3087 ---------------------------------------------------------------------- On Mon, 31 Jan 2005, Zhiliang Hu wrote: >=20 > On Mon, 31 Jan 2005, Lincoln Stein wrote: >=20 > > Hi all, > >=20 > > Multiple people are now reporting problems installing or using=3D20 > > gbrowse. Most of these problems are related to the system not=3D20 > > recognizing directories. > >=20 > > I have a feeling that the recent version of perl has broken or changed=3D20 > > the behavior of the -d operator. Either that, or there is an=3D20 > > incompatibility with recent kernels. Does anyone have more insight? =3D20 > > I am going to upgrade my system to 5.8.3 and see if I can reproduce=3D20 > > the problem. > >=20 > > Lincoln >=20 > Good you are on top of it... hope my error from installing GBrowse > 1.62 may provide more 'evidence' for you to diagnose - 'make test' or > 'make install' complained it cannot locate "IO.pm" while I do find it > in one of the paths: >=20 > # make test > ........(deleted lines).......... > t/01yeast....Can't locate Bio/Root/IO.pm in @INC (@INC contains: > /usr/local/lib/perl5/5.8.5/i686-linux > /usr/local/lib/perl5/5.8.5/i686-linux /usr/local/lib/perl5/5.8.5 > /usr/local/lib/perl5/site_perl/5.8.5/i686-linux > /usr/local/lib/perl5/site_perl/5.8.5/i686-linux > /usr/local/lib/perl5/site_perl/5.8.5 > /usr/local/lib/perl5/site_perl/5.8.5/i686-linux > /usr/local/lib/perl5/site_perl/5.8.5 /usr/local/lib/perl5/site_perl > /usr/share/ . /usr/local/lib/perl5/5.8.5/i686-linux > /usr/local/lib/perl5/5.8.5 > /usr/local/lib/perl5/site_perl/5.8.5/i686-linux > /usr/local/lib/perl5/site_perl/5.8.5 /usr/local/lib/perl5/site_perl > /usr/share/ .) at t/01yeast.t line 9. > BEGIN failed--compilation aborted at t/01yeast.t line 9. > t/01yeast....dubious > Test returned status 2 (wstat 512, 0x200) > FAILED--1 test script could be run, alas--no output ever seen > make: *** [test_dynamic] Error 2 >=20 >=20 > # find / -name IO.pm > /usr/lib/perl5/5.8.0/i386-linux-thread-multi/IO.pm > /usr/local/lib/perl5/5.8.5/i686-linux/IO.pm > /usr/local/lib/perl5/site_perl/5.8.5/SOAP/Transport/IO.pm >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------- > This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting > Tool for open source databases. Create drag-&-drop reports. Save time > by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. > Download a FREE copy at http://www.intelliview.com/go/osdn_nl > _______________________________________________ > Gmod-devel mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-devel >=20 --__--__-- Message: 5 Date: Mon, 31 Jan 2005 16:46:45 -0800 (PST) From: Allen Day <all...@uc...> To: Lincoln Stein <ls...@cs...> cc: gmo...@li..., "Vsevolod (Simon) Ilyushchenko" <si...@cs...>, Scott Cain <ca...@cs...> Subject: Re: [GMOD-devel] Problems installing gbrowse from CVS HEAD should manage to get through the "Makefile.PL && make && make test && make install" process again. There is still a lot of missing=20 functionality though, so I wouldn't recommend updating to HEAD unless=20 you're willing to deal with this. For those of you who are interested in helping to get everything working on HEAD again, update Generic-Genome-Browser/TODO . I've put a list of functionality in there, and compare how v1.64 tag compares to the HEAD tag. It shows what works in both, what is new in HEAD, and what works in 1.64 but is not working on HEAD yet and why. Scott, can you please forward this to the appropriate gbrowse lists,=20 thanks. -Allen On Mon, 31 Jan 2005, Lincoln Stein wrote: > Hi all, >=20 > Multiple people are now reporting problems installing or using=20 > gbrowse. Most of these problems are related to the system not=20 > recognizing directories. >=20 > I have a feeling that the recent version of perl has broken or changed > 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. >=20 > Lincoln >=20 > 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 >=20 >=20 --__--__-- _______________________________________________ Gmod-devel mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-devel End of Gmod-devel Digest |