[Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO
jun hu
junhu54 at hotmail.com
Thu Jan 8 15:42:28 EST 2004
I saw similar problems when I was in intall bioperl-live on both RH9 (with
perl 5.8) and RH7.3 (with perl 5.6). Some problems can be fixed after you
track download the exact package that gives you problem =>then download and
install tarball instead of using "perl -MCPAN -e shell". However, sometimes
you just have to force install some packages ... which might lead to those
failed tests...
Jun Hu
>From: Jason Stajich <jason at cgt.duhs.duke.edu>
>To: Brian Osborne <brian_osborne at cognia.com>
>CC: Rob Edwards <redwards at utmem.edu>, bhurwitz at twt.com,
>bioperl-l at bioperl.org
>Subject: RE: [Bioperl-l] Trouble installing bioperl-1.4 due to
>RestrictionIO
>Date: Thu, 8 Jan 2004 14:22:00 -0500 (EST)
>
>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
> > _______________________________________________
> > 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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