[Bioperl-l] Trouble installing bioperl-1.4 due to RestrictionIO
bhurwitz at twt.com
bhurwitz at twt.com
Wed Jan 7 22:17:48 EST 2004
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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