[Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO

Brian Osborne brian_osborne at cognia.com
Thu Jan 8 12:58:00 EST 2004 

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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