[Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO
Jason Stajich
jason at cgt.duhs.duke.edu
Thu Jan 8 10:45:31 EST 2004
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/staden/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/staden/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
> >
> >
>
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>
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>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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