[Bioperl-l] Bio::SeqIO::staden::read make test error

Roy Chaudhuri roy at colibase.bham.ac.uk
Wed May 11 06:21:20 EDT 2005

Hi all.

I'm attempting to install bioperl-ext as I need to read in sequences
from abi files. However the Bio::SeqIO::staden::read module fails the
tests (the output from "perl Makefile.PL; make; make test" in the
bioperl-ext/Bio/SeqIO/staden directory is pasted below).

If I ignore the failed tests and make install anyway, I get the
following error with a simple abi2fasta script:

# abi2fasta a_A01_001.ab1
Can't locate object method "staden_read_trace" via package
"Bio::SeqIO::abi" at
line 115.
One or more DATA sections were not processed by Inline.

I know that this subject comes up regularly on the mailing list, but I
have searched the archives and tried all the suggestions, and I think my
problem is something that has not been raised before.

I am using a standard CPAN bioperl-1.4 install (with Bio::Tools::dpAlign
replaced with the cvs version, and the eval requiring
Bio::SeqIO::staden::read in Bio::SeqIO commented out) and the cvs
version of bioperl-ext (with read.pm modified to include -lz in LIBS).

The Staden io_lib is installed in /usr/local/include with the os.h and
config.h files copied into /usr/local/include/io_lib, and the os.h
<config.h> line changed to "config.h". The io_lib is detected correctly
during the perl Makefile.PL process.

Does anyone have any other suggestions?

# perl Makefile.PL
Found Staden io_lib "libread" in /usr/local/lib ...
Automatically using the Read.h found in /usr/local/include/io_lib ...
Writing Makefile for Bio::SeqIO::staden::read
# make
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
Writing Makefile for Bio::SeqIO::staden::read
  Finished "perl Makefile.PL" Stage

  Starting "make" Stage
make[1]: Entering directory
/usr/bin/perl /usr/lib/perl5/5.8.3/ExtUtils/xsubpp  -typemap
/usr/lib/perl5/5.8.3/ExtUtils/typemap   read.xs > read.xsc && mv
read.xsc read.c
gcc -c  -I/home/roy/bioperl-ext/Bio/SeqIO/staden
-I/usr/local/include/io_lib -D_REENTRANT -D_GNU_SOURCE
-DTHREADS_HAVE_PIDS -DDEBUGGING -fno-strict-aliasing
-I/usr/include/gdbm -O2 -g -pipe -march=i386 -mcpu=i686
-DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC
"-I/usr/lib/perl5/5.8.3/i386-linux-thread-multi/CORE"   read.c
In file included from /usr/local/include/io_lib/os.h:4,
                 from /usr/local/include/io_lib/Read.h:43,
                 from read.xs:5:
/usr/local/include/io_lib/config.h:45:1: warning: "VERSION" redefined
<command line>:10:1: warning: this is the location of the previous
read.xs: In function `staden_write_trace':
read.xs:32: warning: assignment from incompatible pointer type
Running Mkbootstrap for Bio::SeqIO::staden::read ()
chmod 644 read.bs
rm -f blib/arch/auto/Bio/SeqIO/staden/read/read.so
gcc  -shared -L/usr/local/lib read.o  -o
blib/arch/auto/Bio/SeqIO/staden/read/read.so   -L/usr/local/lib -lread
chmod 755 blib/arch/auto/Bio/SeqIO/staden/read/read.so
cp read.bs blib/arch/auto/Bio/SeqIO/staden/read/read.bs
chmod 644 blib/arch/auto/Bio/SeqIO/staden/read/read.bs
make[1]: Leaving directory
  Finished "make" Stage

  Starting "make install" Stage
make[1]: Entering directory
Files found in blib/arch: installing files in blib/lib into architecture
dependent library tree
make[1]: Leaving directory
  Finished "make install" Stage

  Starting Cleaning Up Stage
  Finished Cleaning Up Stage

Finished Build Compile Stage

Manifying blib/man3/Bio::SeqIO::staden::read.3pm
# make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" test.pl
test....The extension 'Bio::SeqIO::staden::read' is not properly
installed in path:

If this is a CPAN/distributed module, you may need to reinstall it on your

To allow Inline to compile the module in a temporary cache, simply
remove the
Inline config option 'VERSION=' from the Bio::SeqIO::staden::read module.

 at test.pl line 0
INIT failed--call queue aborted, <DATA> line 1.
        Test returned status 255 (wstat 65280, 0xff00)
Scalar found where operator expected at (eval 155) line 1, near "'int'
        (Missing operator before   $__val?)
DIED. FAILED tests 1-94
        Failed 94/94 tests, 0.00% okay
Failed Test Stat Wstat Total Fail  Failed  List of Failed
test.pl      255 65280    94  188 200.00%  1-94
Failed 1/1 test scripts, 0.00% okay. 94/94 subtests failed, 0.00% okay.
make: *** [test_dynamic] Error 2

Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, UK


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