[Bioperl-l] Trouble installing bioperl-ext-1.4

Barry Moore barry.moore at genetics.utah.edu
Tue Jan 6 18:15:19 EST 2004


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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