[Bioperl-l] upgrading GBrowse from 2.08 to 2.38, problems with BioPerl 1.6.901 upgrade
Matthew Conte
mconte at umd.edu
Fri Jun 17 18:17:49 UTC 2011
Hello,
I've emailed both the GBrowse and BioPerl mailing lists since I'm trying to
upgrade GBrowse from 2.08 to 2.38, but I'm running into some problems due to
the BioPerl 1.6.901 installation that is required. I'm long overdue for the
upgrade and I'd especially like to take advantage of the newer user accounts
feature.
I'm installing this on OS X 10.6.7 server with Perl 5.10.0.
I've run "sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'" and the
relevant output is:
*...*
*CPAN.pm: Going to build L/LD/LDS/GBrowse-2.38.tar.gz*
*
*
*Checking prerequisites...*
* requires:*
* ! Bio::Root::Version (1.006001) is installed, but we need version >=
1.0069*
* recommends:*
* * Bio::DB::Sam (1.19) is installed, but we prefer to have 1.2*
* * Bio::Das is not installed*
* * DBD::Pg is not installed*
* * Net::OpenID::Consumer is not installed*
*
*
*...*
*
*
*---- Unsatisfied dependencies detected during ----*
*---- LDS/GBrowse-2.38.tar.gz ----*
* Bio::Root::Version [requires]*
*Shall I follow them and prepend them to the queue*
*of modules we are processing right now? [yes] *
*Running Build test*
* Delayed until after prerequisites*
*Running Build install*
* Delayed until after prerequisites*
*Running install for module 'Bio::Root::Version'*
*
*
*...*
*
*
*Building BioPerl*
* CJFIELDS/BioPerl-1.6.901.tar.gz*
* ./Build -- OK*
*Warning (usually harmless): 'YAML' not installed, will not store persistent
state*
*Running Build test*
*t/Align/AlignStats.t ......................... ok *
*t/Align/AlignUtil.t .......................... ok *
*t/Align/Graphics.t ........................... Bareword found where
operator expected at (eval 14) line 2, near "'The optional module GD
generated the following error: *
*Can't"*
* (Might be a runaway multi-line '' string starting on line 1)*
* (Missing operator before t?)*
*Bareword found where operator expected at (eval 14) line 2, near "'boot_GD'
symbol"*
* (Missing operator before symbol?)*
*Bareword found where operator expected at (eval 14) line 2, near "2level"*
* (Missing operator before level?)*
*Bareword found where operator expected at (eval 14) line 3, near ") line"*
* (Missing operator before line?)*
*Number found where operator expected at (eval 14) line 3, near "line 1"*
* (Do you need to predeclare line?)*
*Bareword found where operator expected at (eval 14) line 4, near "1*
*Compilation"*
* (Missing operator before Compilation?)*
*Bareword found where operator expected at (eval 14) line 4, near ") line"*
* (Missing operator before line?)*
*Number found where operator expected at (eval 14) line 4, near "line 1."*
* (Do you need to predeclare line?)*
*String found where operator expected at (eval 14) line 5, at end of line*
* (Missing operator before ?)*
*t/Align/Graphics.t ........................... 1/? *
*# Failed test 'use Bio::Align::Graphics;'*
*# at t/Align/Graphics.t line 9.*
*# Tried to use 'Bio::Align::Graphics'.*
*# Error: Attempt to reload GD.pm aborted.*
*# Compilation failed in require at
/Users/Matt/.cpan/build/BioPerl-1.6.901-blYCfR/blib/lib/Bio/Align/Graphics.pm
line 41.*
*# BEGIN failed--compilation aborted at
/Users/Matt/.cpan/build/BioPerl-1.6.901-blYCfR/blib/lib/Bio/Align/Graphics.pm
line 41.*
*# Compilation failed in require at (eval 15) line 2.*
*# BEGIN failed--compilation aborted at (eval 15) line 2.*
*
*
*# Failed test 'require Bio::Align::Graphics;'*
*# at t/Align/Graphics.t line 10.*
*# Tried to require 'Bio::Align::Graphics'.*
*# Error: Attempt to reload Bio/Align/Graphics.pm aborted.*
*# Compilation failed in require at (eval 16) line 2.*
*
*
*# Failed test 'Bio::Align::Graphics->can(...)'*
*# at t/Align/Graphics.t line 11.*
*# Bio::Align::Graphics->can('new') failed*
*# Bio::Align::Graphics->can('draw') failed*
*# Bio::Align::Graphics->can('height') failed*
*# Bio::Align::Graphics->can('width') failed*
*# Bio::Align::Graphics->can('aln_length') failed*
*# Bio::Align::Graphics->can('aln_format') failed*
*# Bio::Align::Graphics->can('no_sequences') failed*
*Can't locate object method "catfile" via package "Bio::Root::IO" (perhaps
you forgot to load "Bio::Root::IO"?) at t/Align/Graphics.t line 15.*
*# Tests were run but no plan was declared and done_testing() was not seen.*
*t/Align/Graphics.t ........................... Dubious, test returned 2
(wstat 512, 0x200)*
*Failed 3/3 subtests *
*t/Align/SimpleAlign.t ........................ ok *
*t/Align/TreeBuild.t .......................... ok *
*
*
*...*
*
*
*t/Assembly/ContigSpectrum.t .................. ok *
*t/Assembly/IO/bowtie.t ....................... skipped: The optional module
Bio::Tools::Run::Samtools (or dependencies thereof) was not installed*
*t/Assembly/IO/sam.t .......................... Bareword found where
operator expected at (eval 41) line 2, near "'The optional module
Bio::DB::Sam generated the following error: *
*Can't"*
* (Might be a runaway multi-line '' string starting on line 1)*
* (Missing operator before t?)*
*Bareword found where operator expected at (eval 41) line 2, near "2level"*
* (Missing operator before level?)*
*Bareword found where operator expected at (eval 41) line 3, near "2level"*
* (Missing operator before level?)*
*Bareword found where operator expected at (eval 41) line 5, near "2level"*
* (Missing operator before level?)*
*Bareword found where operator expected at (eval 41) line 5, near "2level"*
* (Missing operator before level?)*
*Bareword found where operator expected at (eval 41) line 6, near "207.*
* at"*
* (Missing operator before at?)*
*Bareword found where operator expected at (eval 41) line 6, near ") line"*
* (Missing operator before line?)*
*Number found where operator expected at (eval 41) line 6, near "line 1"*
* (Do you need to predeclare line?)*
*Bareword found where operator expected at (eval 41) line 7, near "1*
*Compilation"*
* (Missing operator before Compilation?)*
*Bareword found where operator expected at (eval 41) line 7, near ") line"*
* (Missing operator before line?)*
*Number found where operator expected at (eval 41) line 7, near "line 1."*
* (Do you need to predeclare line?)*
*String found where operator expected at (eval 41) line 8, at end of line*
* (Missing operator before ?)*
*t/Assembly/IO/sam.t .......................... 1/? Bio::Assembly::IO: could
not load sam - for more details on supported formats please see the
Assembly::IO docs*
*Exception *
*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: Failed to load module Bio::Assembly::IO::sam. *
*------------- EXCEPTION: Bio::Root::Exception -------------*
*MSG: __PACKAGE__ requires installation of samtools (libbam) and
Bio::DB::Sam (available on CPAN; not part of BioPerl)*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472*
*STACK: Bio::Assembly::IO::sam::BEGIN Bio/Assembly/IO/sam.pm:189*
*STACK: Bio::Root::Root::_load_module Bio/Assembly/IO/sam.pm:195*
*STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:296*
*STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138*
*STACK: t/Assembly/IO/sam.t:29*
*-----------------------------------------------------------*
*BEGIN failed--compilation aborted at Bio/Assembly/IO/sam.pm line 195.*
*Compilation failed in require at Bio/Root/Root.pm line 543.*
*
*
*STACK: Error::throw*
*STACK: Bio::Root::Root::throw Bio/Root/Root.pm:472*
*STACK: Bio::Root::Root::_load_module Bio/Root/Root.pm:545*
*STACK: Bio::Assembly::IO::_load_format_module Bio/Assembly/IO.pm:296*
*STACK: Bio::Assembly::IO::new Bio/Assembly/IO.pm:138*
*STACK: t/Assembly/IO/sam.t:29*
*-----------------------------------------------------------*
*
*
*
*
*# Failed test 'init sam IO object'*
*# at t/Assembly/IO/sam.t line 29.*
*
*
*# Failed test 'The thing isa Bio::Assembly::IO'*
*# at t/Assembly/IO/sam.t line 32.*
*# The thing isn't defined*
*Can't call method "sam" on an undefined value at t/Assembly/IO/sam.t line
33.*
*# Tests were run but no plan was declared and done_testing() was not seen.*
*t/Assembly/IO/sam.t .......................... Dubious, test returned 255
(wstat 65280, 0xff00)*
*Failed 2/7 subtests *
*t/Assembly/core.t ............................ 1/890 *
*--------------------- WARNING ---------------------*
*MSG: Setting end to equal start[1]*
*---------------------------------------------------*
*
*
*--------------------- WARNING ---------------------*
*MSG: Setting end to equal start[1]*
*---------------------------------------------------*
*
*
*--------------------- WARNING ---------------------*
*MSG: Setting end to equal start[1]*
*---------------------------------------------------*
*
*
*--------------------- WARNING ---------------------*
*MSG: Setting end to equal start[1]*
*---------------------------------------------------*
*
*
*--------------------- WARNING ---------------------*
*MSG: Setting end to equal start[1]*
*---------------------------------------------------*
*t/Assembly/core.t ............................ ok *
*t/Biblio/Biblio.t ............................ ok *
*t/Biblio/References.t ........................ ok *
*...*
The rest of the tests pass so it looks like I'm having issues with GD and
Bio::DB::Sam. So I tried to upgrade to the most current version of these
modules. I've got GD version 2.45 installed and when I try to upgrade it to
the current 2.46, it fails with:
* LDS/GD-2.46.tar.gz*
* /usr/bin/make -- OK*
*Warning (usually harmless): 'YAML' not installed, will not store persistent
state*
*Running make test*
*PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t*
*t/GD.t ........ Can't find 'boot_GD' symbol in
./blib/arch/auto/GD/GD.bundle*
* at t/GD.t line 14*
*Compilation failed in require at t/GD.t line 14.*
*BEGIN failed--compilation aborted at t/GD.t line 14.*
*t/GD.t ........ Dubious, test returned 2 (wstat 512, 0x200)*
*Failed 12/12 subtests *
*t/Polyline.t .. Can't find 'boot_GD' symbol in
/Users/Matt/.cpan/build/GD-2.46-E2Ep66/blib/arch/auto/GD/GD.bundle*
* at /Users/Matt/.cpan/build/GD-2.46-E2Ep66/blib/lib/GD/Polyline.pm line 45*
*Compilation failed in require at
/Users/Matt/.cpan/build/GD-2.46-E2Ep66/blib/lib/GD/Polyline.pm line 45.*
*BEGIN failed--compilation aborted at
/Users/Matt/.cpan/build/GD-2.46-E2Ep66/blib/lib/GD/Polyline.pm line 45.*
*Compilation failed in require at t/Polyline.t line 10.*
*BEGIN failed--compilation aborted at t/Polyline.t line 10.*
*t/Polyline.t .. Dubious, test returned 2 (wstat 512, 0x200)*
*Failed 1/1 subtests *
I've got Bio::DB::Sam version 1.19 installed and when I try to upgrade to
the current 1.29 it also fails:
* CPAN.pm: Going to build L/LD/LDS/Bio-SamTools-1.29.tar.gz*
*
*
*This module requires samtools 0.1.9 or higher (samtools.sourceforge.net).*
*Please enter the location of the bam.h and compiled libbam.a files:
/Users/Matt/Desktop/Matt/software/samtools-0.1.16*
*
*
*Found /Users/Matt/Desktop/Matt/software/samtools-0.1.16/bam.h and
/Users/Matt/Desktop/Matt/software/samtools-0.1.16/libbam.a.*
*Creating new 'MYMETA.yml' with configuration results*
*Creating new 'Build' script for 'Bio-SamTools' version '1.29'*
*Could not read '/Users/Matt/.cpan/build/Bio-SamTools-1.29-o_guh5/META.yml'.
Falling back to other methods to determine prerequisites*
*CPAN: Module::Build loaded ok (v0.3603)*
*Building Bio-SamTools*
*gcc-4.2 -I/Users/Matt/Desktop/Matt/software/samtools-0.1.16
-I/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE
-DXS_VERSION="1.29" -DVERSION="1.29" -D_IOLIB=2 -D_FILE_OFFSET_BITS=64
-Wformat=0 -c -arch x86_64 -arch i386 -arch ppc -g -pipe -fno-common
-DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include -Os -o
lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c*
*ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')*
*env LD_RUN_PATH=/System/Library/Perl/5.10.0/darwin-thread-multi-2level/CORE
gcc-4.2 -mmacosx-version-min=10.6 -arch x86_64 -arch i386 -arch ppc -bundle
-undefined dynamic_lookup -L/usr/local/lib -o
blib/arch/auto/Bio/DB/Sam/Sam.bundle lib/Bio/DB/Sam.o
-L/Users/Matt/Desktop/Matt/software/samtools-0.1.16 -lbam -lz*
*ld: warning: in /Users/Matt/Desktop/Matt/software/samtools-0.1.16/libbam.a,
file was built for unsupported file format which is not the architecture
being linked (i386)*
*ld: warning: in /Users/Matt/Desktop/Matt/software/samtools-0.1.16/libbam.a,
file was built for unsupported file format which is not the architecture
being linked (ppc)*
* LDS/Bio-SamTools-1.29.tar.gz*
* ./Build -- OK*
*Warning (usually harmless): 'YAML' not installed, will not store persistent
state*
*Running Build test*
*t/01sam.t .. Can't load
'/Users/Matt/.cpan/build/Bio-SamTools-1.29-o_guh5/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle'
for module Bio::DB::Sam:
dlopen(/Users/Matt/.cpan/build/Bio-SamTools-1.29-o_guh5/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle,
1): Symbol not found: _bam_nt16_rev_table*
* Referenced from:
/Users/Matt/.cpan/build/Bio-SamTools-1.29-o_guh5/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle
*
* Expected in: flat namespace*
* in
/Users/Matt/.cpan/build/Bio-SamTools-1.29-o_guh5/t/../blib/arch/auto/Bio/DB/Sam/Sam.bundle
at /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line
207.*
* at t/01sam.t line 26*
*Compilation failed in require at t/01sam.t line 26.*
*BEGIN failed--compilation aborted at t/01sam.t line 26.*
*t/01sam.t .. Dubious, test returned 2 (wstat 512, 0x200)*
*Failed 112/112 subtests *
BioPerl fails to install and so GBrowse won't install either after this.
Interestingly, I'm able to install this on my development server which is a
very similar setup (same OS 10.6.7 server and Perl 5.10.0 universal binary),
but is 32-bit opposed to this server which is 64-bit. I can also upgrade GD
and Bio::DB::Sam on the 32-bit development server. I get all of the same
architecture warnings, so I'm not sure if that is the issue.. Any help
would be appreciated.
Thanks,
Matt
--
Matthew Conte
Bioinformatician
Department of Biology
University of Maryland
mconte at umd.edu
Bouillabase.org
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