[Bioperl-l] bioperl problem

[Brian Osborne]

Ying,

A directory like "/home/myhome/.cpan/build/libwww-perl-5.800/lib" is a build
directory, but it's not where the modules are installed after you issue the
"install" command in the CPAN shell. Where are your LWP modules after the
installation step? Example install:

cpan> install M/MK/MKHRAPOV/Chemistry-MolecularMass-0.1.tar.gz
Running make for M/MK/MKHRAPOV/Chemistry-MolecularMass-0.1.tar.gz
Fetching with LWP:

ftp://ftp.orst.edu/pub/CPAN/authors/id/M/MK/MKHRAPOV/Chemistry-MolecularMass
-0
.1.tar.gz
CPAN: Digest::MD5 loaded ok
Fetching with LWP:
  ftp://ftp.orst.edu/pub/CPAN/authors/id/M/MK/MKHRAPOV/CHECKSUMS
Checksum for
/home/bosborne/.cpan/sources/authors/id/M/MK/MKHRAPOV/Chemistry-Mol
ecularMass-0.1.tar.gz ok
Scanning cache /home/bosborne/.cpan/build for sizes
Chemistry/
Chemistry/MolecularMass/
Chemistry/MolecularMass/MolecularMass.xs
Chemistry/MolecularMass/MolecularMass.pm
Chemistry/MolecularMass/Makefile.PL
Chemistry/MolecularMass/test.pl
Chemistry/MolecularMass/Changes
Chemistry/MolecularMass/MANIFEST
Chemistry/MolecularMass/README
CPAN.pm: Going to build M/MK/MKHRAPOV/Chemistry-MolecularMass-0.1.tar.gz

Checking if your kit is complete...
Looks good
Writing Makefile for Chemistry::MolecularMass
Writing Makefile for Chemistry
make[1]: Entering directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'

cp MolecularMass.pm ../blib/lib/Chemistry/MolecularMass.pm
/bin/perl.exe /usr/lib/perl5/5.8.2/ExtUtils/xsubpp  -typemap
/usr/lib/perl5/5.8.
2/ExtUtils/typemap  MolecularMass.xs > MolecularMass.xsc && mv
MolecularMass.xsc
 MolecularMass.c
Please specify prototyping behavior for MolecularMass.xs (see perlxs manual)
gcc -c   -DPERL_USE_SAFE_PUTENV -fno-strict-aliasing -DUSEIMPORTLIB -O2   -D
VERS
ION=\"0.1\" -DXS_VERSION=\"0.1\"
"-I/usr/lib/perl5/5.8.2/cygwin-thread-multi-64
int/CORE"   MolecularMass.c
Running Mkbootstrap for Chemistry::MolecularMass ()
chmod 644 MolecularMass.bs
rm -f ../blib/arch/auto/Chemistry/MolecularMass/MolecularMass.dll
LD_RUN_PATH="" ld2  -s -L/usr/local/lib MolecularMass.o  -o
../blib/arch/auto/Ch
emistry/MolecularMass/MolecularMass.dll
/usr/lib/perl5/5.8.2/cygwin-thread-mult
i-64int/CORE/libperl.dll.a
gcc -shared -o
 MolecularMass.dll -Wl,--out-implib=libMolecularMass.dll.a -Wl,--
export-all-symbols -Wl,--enable-auto-import -Wl,--stack,8388608 \
-s -L/usr/local/lib MolecularMass.o
/usr/lib/perl5/5.8.2/cygwin-thread-multi-64
int/CORE/libperl.dll.a
Creating library file: libMolecularMass.dll.a
mv MolecularMass.dll libMolecularMass.dll.a
../blib/arch/auto/Chemistry/Molecula
rMass/
chmod 755 ../blib/arch/auto/Chemistry/MolecularMass/MolecularMass.dll
cp MolecularMass.bs
../blib/arch/auto/Chemistry/MolecularMass/MolecularMass.bs
chmod 644 ../blib/arch/auto/Chemistry/MolecularMass/MolecularMass.bs
make[1]: Leaving directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'
  /usr/bin/make  -- OK
Running make test
make[1]: Entering directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'

make[1]: Leaving directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'
make[1]: Entering directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'

/bin/perl.exe "-I../blib/lib" "-I../blib/arch" test.pl
1..10
ok 1
Parentheses don't match
ok 2
Parentheses don't match
ok 3
No such element: Nosuchelement
ok 4
Forbidden chars
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
make[1]: Leaving directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'
  /usr/bin/make test -- OK
Running make install
make[1]: Entering directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'

make[1]: Leaving directory
`/home/bosborne/.cpan/build/Chemistry/MolecularMass'
Installing
/usr/lib/perl5/site_perl/5.8.2/cygwin-thread-multi-64int/auto/Chemist
ry/MolecularMass/libMolecularMass.dll.a
Installing
/usr/lib/perl5/site_perl/5.8.2/cygwin-thread-multi-64int/auto/Chemist
ry/MolecularMass/MolecularMass.bs
Installing
/usr/lib/perl5/site_perl/5.8.2/cygwin-thread-multi-64int/auto/Chemist
ry/MolecularMass/MolecularMass.dll
Files found in blib/arch: installing files in blib/lib into architecture
depende
nt library tree
Installing
/usr/lib/perl5/site_perl/5.8.2/cygwin-thread-multi-64int/Chemistry/Mo
lecularMass.pm
Writing
/usr/lib/perl5/site_perl/5.8.2/cygwin-thread-multi-64int/auto/Chemistry/
.packlist
Appending installation info to
/usr/lib/perl5/5.8.2/cygwin-thread-multi-64int/pe
rllocal.pod
  /usr/bin/make install  -- OK

cpan>


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 Ying Sun
Sent: Monday, October 25, 2004 10:40 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] bioperl problem

Dear there:
Thank you for take time to see my problem in Bioperl.My problem is as
follows:
I use the Cygwin to run the Bioperl programme.
In my programme, I use module Bio::Perl  and function get_sequence. But when
I run this programme, I got error report: Your system does not have one of
LWP, HTTP::Request::Common, IO::String installed so the DB retrieval method
is not available.
Becusue the LWP in another pathway(my Bio::Perl module in
/home/myhome/.cpan/build/bioperl-1.4), so I add this script like that
use lib "/home/myhome/.cpan/build/libwww-perl-5.800/lib";
But it does not work.
So,I have no idea of how to use the modules and solve the problems.Could
someone give me a help?
Thanks a lot.

Best,
Ying