[Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO
Jason Stajich
jason at cgt.duhs.duke.edu
Thu Jan 8 14:22:00 EST 2004
Hey Brian - what version of perl? What about you Bonnie?
I get no errors with perl 5.8.0 on rh 9 or on OSX with perl 5.8.1-RC3 but
I do see this on perl 5.6.1 (rh 7.3) with the main-trunk live and 1.4 code
(released and 1.4 branch)
1..14
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm
line 130, <GEN1> line 13.
Use of uninitialized value in string eq at Bio/Restriction/IO/withrefm.pm
line 130, <GEN1> line 24.
ok 9
not ok 10
# Test 10 got: '9' (t/RestrictionIO.t at line 63)
# Expected: '11'
ok 11
ok 12
ok 13
ok 14
-jason
On Thu, 8 Jan 2004, Brian Osborne wrote:
> Rob,
>
> Partially fails for me as well, on Cygwin:
>
> ~/bioperl-live>perl t/RestrictionIO.t
> 1..14
> ok 1
> ok 2
> ok 3
> not ok 4
> # Test 4 got: '530' (t/RestrictionIO.t at line 43)
> # Expected: '532'
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> not ok 10
> # Test 10 got: '17' (t/RestrictionIO.t at line 63)
> # Expected: '11'
> ok 11
> ok 12
> not ok 13
> # Test 13 got: '19' (t/RestrictionIO.t at line 78)
> # Expected: '16'
> ok 14
>
> The 3 failing tests are $renzs->each_enzyme, where $renz is a RestrictionIO
> object, 3 different files.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Rob Edwards
> Sent: Thursday, January 08, 2004 12:03 PM
> To: Jason Stajich
> Cc: bhurwitz at twt.com; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO
>
> I am curious as to why this test is failing. Has anyone else had this fail?
>
> It passes for me (on Mac OS10.3)
>
> Rob
>
> On Thu, Jan 08, 2004 at 10:45:31AM -0500, Jason Stajich wrote:
> > Just ignore it.
> >
> > cpan> force install Bio::Perl
> >
> > if you like.
> >
> > On Wed, 7 Jan 2004 bhurwitz at twt.com wrote:
> >
> > >
> > > Hello,
> > >
> > > I am installing BioPerl 1.4 on a virtual machine through vmware that
> > > previously did not have bioperl (RedHat 7.3, perl 5.6.1). I am getting
> the
> > > following error from CPAN. Does anyone know what this could mean? I
> have
> > > installed the BioPerl Bundle prior to this successfully
> > > (C/CR/CRAFFI/Bundle-BioPerl-2.1.0.tar.gz)
> > >
> > > -Bonnie
> > >
> > >
> > > Failed Test Stat Wstat Total Fail Failed List of Failed
> >
> > --------------------------------------------------------------------------
> -----
> > > t/RestrictionIO.t 14 1 7.14% 10
> > > 121 subtests skipped.
> > > Failed 1/179 test scripts, 99.44% okay. 1/8268 subtests failed, 99.99%
> > > okay.
> > > make: *** [test_dynamic] Error 11
> > > /usr/bin/make test -- NOT OK
> > > Running make install
> > > make test had returned bad status, won't install without force
> > >
> > >
> > >
> > >
> > >
> > > Barry Moore
> > > <barry.moore at genetics.utah To: Jason
> Stajich <jason at cgt.duhs.duke.edu>
> > > .edu> cc:
> bioperl-l at bioperl.org
> > > Sent by: Subject: Re:
> [Bioperl-l] Trouble installing bioperl-ext-1.4
> > > bioperl-l-bounces at portal.o
> > > pen-bio.org
> > >
> > >
> > > 01/06/2004 05:15 PM
> > >
> > >
> > >
> > >
> > >
> > >
> > > Jason et al-
> > >
> > > ...while trying to install bioperl-ext-1.4 your suggestion for
> > > installing Inline::C first seems to have worked. Makefile.PL ran fine
> > > (highlighted below in green - if your reading HTML mail). However, now
> > > I get errors on running make. I've copied the entire output from the
> > > make command below (with some masking of low complexity regions). Sorry
> > > it's so long, but I'm having trouble spotting the problem, so I didn't
> > > want to leave out any of the important parts. The part indicating
> > > errors is at the end (highlighted in red).
> > >
> > > Barry
> > >
> > > [root at Tatshenshini bioperl-ext-1.4]# perl Makefile.PL
> > > Checking if your kit is complete...
> > > Looks good
> > > Writing Makefile for Bio::Ext::Align
> > > Please tell us where your Staden io_lib "read" library is installed:
> > > [/usr/local/lib]
> > > Please tell us where your Staden io_lib "Read.h" header is installed:
> > > [/usr/local/include/io_lib]
> > > Writing Makefile for Bio::SeqIO::staden::read
> > > Writing Makefile for Bio
> > > One or more DATA sections were not processed by Inline.
> > >
> > > [root at Tatshenshini bioperl-ext-1.4]# make
> > > cp Bio/Ext/Align/libs/hscore.h blib/lib/Bio/Ext/Align/libs/hscore.h
> > > ###Removed alot of cp commands to shorten e-mail post###
> > > cp Bio/Ext/Align/libs/wisefile.h blib/lib/Bio/Ext/Align/libs/wisefile.h
> > > make[1]: Entering directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align'
> > > cp Align.pm ../blib/lib/Bio/Ext/Align.pm
> > > DEFINE='-DPOSIX -DNOERROR'; CC='gcc'; export DEFINE INC CC; \
> > > cd libs && make CC=gcc libsw.a -e
> > > make[2]: Entering directory
> > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs'
> > > gcc -c -O -c -o aln.o aln.c
> > > ###Removed alot of gcc commands to shorten e-mail post###
> > > gcc -c -O -c -o linspc.o linspc.c
> > > ar ru libsw.a aln.o alnconvert.o alnrange.o asciibtcanvas.o basematrix.o
> > > btcanvas.o commandline.o complexconsensi.o
> > > complexevalset.o complexsequence.o compmat.o codon.o dna.o dnamatrix.o
> > > dpenvelope.o dynlibcross.o histogram.o hscore.o linesubs.o packaln.o
> > > probability.o protein.o proteindb.o proteinsw.o seqaligndisplay.o
> > > sequence.o sequencedb.o sw_wrap.o wiseerror.o wisefile.o wisememman.o
> > > wiseoverlay.o wiserandom.o wisestring.o wisetime.o dpalign.o linspc.o
> > > make[2]: Leaving directory
> > > `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align/libs'
> > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap
> > > /usr/lib/perl5/5.8.0/ExtUtils/typemap -typemap typemap
> > > Align.xs > Align.xsc && mv Align.xsc Align.c
> > > gcc -c -I./libs -D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS
> > > -DDEBUGGING -fno-strict-aliasing -I/usr/local/include
> > > -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm -O2
> > > -march=i386 -mcpu=i686 -g -DVERSION=\"0.1\" -DXS_VERSION=\"0.1\" -fPIC
> > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/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
> > > LD_RUN_PATH="" gcc -shared -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]: Leaving directory `/home/bmoore/bioperl-ext-1.4/Bio/Ext/Align'
> > > make[1]: Entering directory
> `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden'
> > > cp read.pm ../blib/lib/Bio/SeqIO/staden/read.pm
> > > /usr/bin/perl -Mblib -MInline=NOISY,_INSTALL_ -MBio::SeqIO::staden::read
> > > -e1 0.01 ../blib/arch
> > > Starting Build Prepocess Stage
> > > Finished Build Prepocess Stage
> > >
> > > Starting Build Parse Stage
> > > Finished Build Parse Stage
> > >
> > > Starting Build Glue 1 Stage
> > > Finished Build Glue 1 Stage
> > >
> > > Starting Build Glue 2 Stage
> > > Finished Build Glue 2 Stage
> > >
> > > Starting Build Glue 3 Stage
> > > Finished Build Glue 3 Stage
> > >
> > > Starting Build Compile Stage
> > > Starting "perl Makefile.PL" Stage
> > > Note (probably harmless): No library found for -lread
> > > Writing Makefile for Bio::SeqIO::staden::read
> > > Finished "perl Makefile.PL" Stage
> > >
> > > Starting "make" Stage
> > > make[2]: Entering directory
> > >
> `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade
> n/read'
> > >
> > > /usr/bin/perl /usr/lib/perl5/5.8.0/ExtUtils/xsubpp -typemap
> > > /usr/lib/perl5/5.8.0/ExtUtils/typemap read.xs > read.xsc && mv
> > > read.xsc read.c
> > > gcc -c -I/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden
> > > -I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE
> > > -DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing
> > > -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
> > > -I/usr/include/gdbm -O2 -march=i386 -mcpu=i686 -g -DVERSION=\"0.01\"
> > > -DXS_VERSION=\"0.01\" -fPIC
> > > "-I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE" read.c
> > > read.xs:5:18: Read.h: No such file or directory
> > > read.xs: In function `staden_write_trace':
> > > read.xs:9: `Read' undeclared (first use in this function)
> > > read.xs:9: (Each undeclared identifier is reported only once
> > > read.xs:9: for each function it appears in.)
> > > read.xs:15: invalid lvalue in assignment
> > > read.xs:16: request for member `base' in something not a structure or
> union
> > > read.xs:18: request for member `ident' in something not a structure or
> > > union
> > > read.xs:21: request for member `ident' in something not a structure or
> > > union
> > > read.xs:23: request for member `info' in something not a structure or
> union
> > > read.xs:26: request for member `info' in something not a structure or
> union
> > > read.xs:28: request for member `format' in something not a structure or
> > > union
> > > read.xs:29: request for member `leftCutoff' in something not a structure
> > > or union
> > > read.xs:30: request for member `rightCutoff' in something not a
> > > structure or union
> > > read.xs:32: warning: assignment from incompatible pointer type
> > > read.xs:38: request for member `base' in something not a structure or
> union
> > > read.xs:41: request for member `prob_A' in something not a structure or
> > > union
> > > read.xs:45: request for member `prob_C' in something not a structure or
> > > union
> > > read.xs:49: request for member `prob_G' in something not a structure or
> > > union
> > > read.xs:53: request for member `prob_T' in something not a structure or
> > > union
> > > read.xs:58: request for member `prob_A' in something not a structure or
> > > union
> > > read.xs:58: request for member `prob_C' in something not a structure or
> > > union
> > > read.xs:59: request for member `prob_G' in something not a structure or
> > > union
> > > read.xs:59: request for member `prob_T' in something not a structure or
> > > union
> > > read.xs:62: request for member `prob_A' in something not a structure or
> > > union
> > > read.xs:62: request for member `prob_C' in something not a structure or
> > > union
> > > read.xs:63: request for member `prob_G' in something not a structure or
> > > union
> > > read.xs:63: request for member `prob_T' in something not a structure or
> > > union
> > > read.xs: In function `staden_read_trace':
> > > read.xs:76: `Read' undeclared (first use in this function)
> > > read.xs:81: invalid lvalue in assignment
> > > read.xs:83: `NULLRead' undeclared (first use in this function)
> > > read.xs:88: request for member `leftCutoff' in something not a structure
> > > or union
> > > read.xs:90: request for member `rightCutoff' in something not a
> > > structure or union
> > > read.xs:91: request for member `NBases' in something not a structure or
> > > union
> > > read.xs:91: request for member `NBases' in something not a structure or
> > > union
> > > read.xs:93: request for member `base' in something not a structure or
> union
> > > read.xs:94: request for member `prob_A' in something not a structure or
> > > union
> > > read.xs:94: request for member `prob_C' in something not a structure or
> > > union
> > > read.xs:95: request for member `prob_G' in something not a structure or
> > > union
> > > read.xs:95: request for member `prob_T' in something not a structure or
> > > union
> > > read.xs:144: request for member `ident' in something not a structure or
> > > union
> > > read.xs:145: request for member `info' in something not a structure or
> > > union
> > > make[2]: *** [read.o] Error 1
> > > make[2]: Leaving directory
> > >
> `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/stade
> n/read'
> > >
> > >
> > > A problem was encountered while attempting to compile and install your
> > > Inline
> > > C code. The command that failed was:
> > > make
> > >
> > > The build directory was:
> > >
> /home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/_Inline/build/Bio/SeqIO/staden
> /read
> > >
> > >
> > > To debug the problem, cd to the build directory, and inspect the output
> > > files.
> > >
> > > at -e line 0
> > > INIT failed--call queue aborted.
> > > make[1]: *** [read.inl] Error 2
> > > make[1]: Leaving directory
> `/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden'
> > > make: *** [subdirs] Error 2
> > >
> > >
> > > Jason Stajich wrote:
> > >
> > > >Hey Barry!
> > > > You need to have installed Inline::C first.
> > > >
> > > > You don't need bioperl-ext unless you want the specialized stuff in
> there
> > > >(a smith-waterman implementation and access to the staden io library
> for
> > > > reading in trace files directly through perl).
> > > >
> > > >-jason
> > > >On Tue, 6 Jan 2004, Barry Moore wrote:
> > > >
> > > >
> > > >
> > > >>I'm installing bioperl 1.4 on my linux machine (RedHat 9.0, Perl 5.8).
> > > >>Bioperl-1.4 (the core) and bioperl-run-1.4 installed fine. I get the
> > > >>following errors when trying to install bioperl-ext-1.4:
> > > >>
> > > >>[root at Tatshenshini bioperl-ext-1.4]# perl Makefile.PL
> > > >>Checking if your kit is complete...
> > > >>Looks good
> > > >>Writing Makefile for Bio::Ext::Align
> > > >>ERROR from evaluation of
> > > >>/home/bmoore/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't
> locate
> > > >>Inline/MakeMaker.pm in @INC
> > > >>(@INC contains: /usr/lib/perl5/5.8.0/i386-linux-thread-multi
> > > >>/usr/lib/perl5/5.8.0
> > > >>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
> > > >>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
> > > >>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
> > > >>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl
> > > >>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
> > > >>/home/bmoore/bioperl-ext-1.4 .) at ./Makefile.PL line 1.
> > > >>BEGIN failed--compilation aborted at ./Makefile.PL line 1.
> > > >>[root at Tatshenshini bioperl-ext-1.4]# >>
> > > >>I'm a bit linux challenged so any pointers, no matter how remedial,
> will
> > > >>be greatly appreciated.
> > > >>
> > > >>Barry Moore
> > > >>Dept. Human Genetics
> > > >>University of Utah
> > > >>
> > > >>_______________________________________________
> > > >>Bioperl-l mailing list
> > > >>Bioperl-l at portal.open-bio.org
> > > >>http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > > >>
> > > >>
> > > >>
> > > >
> > > >--
> > > >Jason Stajich
> > > >Duke University
> > > >jason at cgt.mc.duke.edu
> > > >_______________________________________________
> > > >Bioperl-l mailing list
> > > >Bioperl-l at portal.open-bio.org
> > > >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > > >
> > > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> _______________________________________________
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>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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