[Bioperl-l] upgrading GBrowse from 2.08 to 2.38, problems with BioPerl 1.6.901 upgrade

Fri Jun 17 18:52:13 UTC 2011

I normally would say that (from the BioPerl perspective) GD is an optional module, but you will need it for GBrowse.  Bio::DB::Sam likewise.  

Have you looked at the README for the two distributions?  They have pointers regarding issues installing both modules. In particular, I know Bio::Samtools may require adding the -fPIC flag and recompiling samtools:

http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.29/README

GD issues are a little more complex:

http://cpansearch.perl.org/src/LDS/GD-2.46/README

chris

On Jun 17, 2011, at 1:17 PM, Matthew Conte wrote:

> 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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> Bioperl-l at lists.open-bio.org
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