| Subject: | Bug installing Math::GSL, HELP PLEASE!!!!! |
| Date: | Tue, 18 May 2010 12:19:55 +0100 |
| To: | bug-Math-Gsl [...] rt.cpan.org, Jonathan Leto <jonathan [...] leto.net>, Thierry Moisan <thierry.moisan [...] gmail.com> |
| From: | inti pedroso <intipedroso [...] gmail.com> |
Dear,
I am having trouble to install Math::GSL. I really want to use it.
I had probems whne running perl Makefile.PL, which I solved by adding the
path to the CORE header.
Show quoted text
>sudo perl5.8.9 Makefile.PL
INC="/System/Library/Perl/5.8.9/darwin-thread-multi-2level/CORE"
i found this on the bugs forums of the module. Then I changed the Build.PL
at line 108,
my %gsl_pkgcfg = ExtUtils::PkgConfig->find ('gsl');
into
my %gsl_pkgcfg = ('modversion' => '1.13', 'cflags'=> '-I/usr/local/include',
'pkg' => 'gsl', 'libs' => '-L/usr/local/lib -lgsl -lgslcblas -lm' );
I took the information from the gsl-config because I do know why the
ExtUtils::PkgConfig could not find it but I know it is there.
Then I had problem when running ./Build
Show quoted text>sudo ./Build
Building Math-GSL
i686-apple-darwin10-gcc-4.2.1:
/System/Library/Perl/5.8.9/darwin-thread-multi-2level/CORE: linker input
file unused because linking not done
i686-apple-darwin10-gcc-4.2.1: -bundle not allowed with -dynamiclib
error building blib/arch/auto/Math/GSL/BLAS/BLAS.bundle file from
'xs/BLAS_wrap.o' at inc/GSLBuilder.pm line 132.
At this stage I just could not find out what the problem is, this goes
beyond my Perl/computing knowledge.
I have appended below the decription of the machine and of the perl I am
using.
I would be very very pleased if you could help me with this. thanks a lot
for building the module and in advance for help in getting it running.
Best Regards,
Inti Pedroso.
€€€€€€€€€€€€€€€€€
Show quoted text>uname -a
Darwin shiva.iop.kcl.ac.uk 10.3.0 Darwin Kernel Version 10.3.0: Fri Feb 26
11:57:13 PST 2010; root:xnu-1504.3.12~1/RELEASE_X86_64 x86_64
€€€€€€€€€€€€€€€€€€€€€€€€€
Show quoted text>perl5.8.9 -V
Summary of my perl5 (revision 5 version 8 subversion 9) configuration:
Platform:
osname=darwin, osvers=10.0, archname=darwin-thread-multi-2level
uname='darwin neige.apple.com 10.0 darwin kernel version 10.0.0d8: tue
may 5 19:29:59 pdt 2009; root:xnu-1437.2~2release_i386 i386 '
config_args='-ds -e -Dprefix=/usr -Dccflags=-g -pipe -Dldflags=
-Dman3ext=3pm -Duseithreads -Duseshrplib -Dinc_version_list=none
-Dcc=gcc-4.2'
hint=recommended, useposix=true, d_sigaction=define
usethreads=define use5005threads=undef useithreads=define
usemultiplicity=define
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=define use64bitall=define uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc-4.2', ccflags ='-arch i386 -arch ppc -g -pipe -fno-common
-DPERL_DARWIN -fno-strict-aliasing -I/usr/local/include',
optimize='-Os',
cppflags='-g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing
-I/usr/local/include'
ccversion='', gccversion='4.2.1 (Apple Inc. build 5646)',
gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t',
lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='gcc-4.2 -mmacosx-version-min=10.6', ldflags ='-arch i386 -arch ppc
-L/usr/local/lib'
libpth=/usr/local/lib /usr/lib
libs=-ldbm -ldl -lm -lutil -lc
perllibs=-ldl -lm -lutil -lc
libc=/usr/lib/libc.dylib, so=dylib, useshrplib=true,
libperl=libperl.dylib
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-arch i386 -arch ppc -bundle -undefined
dynamic_lookup -L/usr/local/lib'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
USE_FAST_STDIO USE_ITHREADS USE_LARGE_FILES
USE_PERLIO USE_REENTRANT_API
Locally applied patches:
/Library/Perl/Updates/<version> comes before system perl directories
installprivlib and installarchlib points to the Updates directory
6576362: fixed 5.8.9 binary compatibility issue: perlio mutex not
initialized
Built under darwin
Compiled at Jun 24 2009 00:35:17
%ENV:
PERL5LIB=":/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules:/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules:/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules:/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules:/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules:/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules:/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules:/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules"
@INC:
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Users/pedrosoi/Desktop/Installed_Apps/bioperl/bioperl-live/
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-compara/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-variation/modules
/Users/pedrosoi/Desktop/Installed_Apps/Ensembl/v57/ensembl-functgenomics/modules
/Library/Perl/Updates/5.8.9/darwin-thread-multi-2level
/Library/Perl/Updates/5.8.9
/System/Library/Perl/5.8.9/darwin-thread-multi-2level
/System/Library/Perl/5.8.9
/Library/Perl/5.8.9/darwin-thread-multi-2level
/Library/Perl/5.8.9
/Network/Library/Perl/5.8.9/darwin-thread-multi-2level
/Network/Library/Perl/5.8.9
/Network/Library/Perl
/System/Library/Perl/Extras/5.8.9/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.9
/Library/Perl/5.8.8
/Library/Perl/5.8.6
/Library/Perl/5.8.1
.
€€€€€€€€€€€€€€€€€€
--
Social, Genetic and Developmental
Psychiatry PhD programme,
NIHR BRC for Mental Health;
MRC SGDP Research Centre (PO82),
Institute of Psychiatry,
Kings College London.
SE5 8AF, London, UK.
Inti.PedrosoRovira@iop.kcl.ac.uk