[BioC] genefilter and libpthread

[Ramon Diaz-Uriarte]

Dear All,

I cannot install genefilter (genefilter_1.12.0.tar.gz) if I have libpthread 
installed. I do not understand why. And a package that explicitly uses 
libpthread functionality (Rmpi) installs fine with or without libpthread. As 
soon as I remove the pthread libraries (and recompile R) everything seems 
fine. With and without libpthread R check was OK. Details follow:


* Installing *source* package 'genefilter' ...
** libs
gcc -std=gnu99 -I/http/R-patched-new/R-patched/include -I/http/R-patched-new/R-patched/include  -I/usr/local/include    -fpic  -g -O2 -c 
genedist.c -o genedist.o
g++ -I/http/R-patched-new/R-patched/include -I/http/R-patched-new/R-patched/include  -I/usr/local/include    -fpic  -g -O2 -c 
half_range_mode.cpp -o half_range_mode.o
/usr/include/pthread.h:285: error: conflicting declaration 'typedef struct 
pthread_st* pthread_t'
/usr/include/bits/pthreadtypes.h:50: error: 'pthread_t' has a previous 
declaration as 'typedef long unsigned int pthread_t'
/usr/include/pthread.h:286: error: conflicting declaration 'typedef struct 
pthread_attr_st* pthread_attr_t'
/usr/include/bits/pthreadtypes.h:57: error: 'pthread_attr_t' has a previous 
declaration as 'typedef union pthread_attr_t pthread_attr_t'
/usr/include/pthread.h:287: error: conflicting declaration 'typedef int 
pthread_key_t'
/usr/include/bits/pthreadtypes.h:118: error: 'pthread_key_t' has a previous 
declaration as 'typedef unsigned int pthread_key_t'
/usr/include/pthread.h:289: error: conflicting declaration 'typedef int 
pthread_mutexattr_t'
/usr/include/bits/pthreadtypes.h:88: error: 'pthread_mutexattr_t' has a 
previous declaration as 'typedef union pthread_mutexattr_t 
pthread_mutexattr_t'
/usr/include/pthread.h:290: error: conflicting declaration 'typedef struct 
pthread_mutex_st* pthread_mutex_t'
/usr/include/bits/pthreadtypes.h:82: error: 'pthread_mutex_t' has a previous 
declaration as 'typedef union pthread_mutex_t pthread_mutex_t'
/usr/include/pthread.h:291: error: conflicting declaration 'typedef int 
pthread_condattr_t'
/usr/include/bits/pthreadtypes.h:114: error: 'pthread_condattr_t' has a 
previous declaration as 'typedef union pthread_condattr_t pthread_condattr_t'
/usr/include/pthread.h:292: error: conflicting declaration 'typedef struct 
pthread_cond_st* pthread_cond_t'
/usr/include/bits/pthreadtypes.h:108: error: 'pthread_cond_t' has a previous 
declaration as 'typedef union pthread_cond_t pthread_cond_t'
/usr/include/pthread.h:293: error: conflicting declaration 'typedef int 
pthread_rwlockattr_t'
/usr/include/bits/pthreadtypes.h:170: error: 'pthread_rwlockattr_t' has a 
previous declaration as 'typedef union pthread_rwlockattr_t 
pthread_rwlockattr_t'
/usr/include/pthread.h:294: error: conflicting declaration 'typedef struct 
pthread_rwlock_st* pthread_rwlock_t'
/usr/include/bits/pthreadtypes.h:164: error: 'pthread_rwlock_t' has a previous 
declaration as 'typedef union pthread_rwlock_t pthread_rwlock_t'
make: *** [half_range_mode.o] Error 1
ERROR: compilation failed for package 'genefilter'


This is a Debian GNU/Linux system:

Linux karl03 2.6.8-11-amd64-k8-smp #1 SMP Wed Jun 1 00:01:27 CEST 2005 x86_64 
GNU/Linux


The pthread packages are:

ii  libpthread-dev                      2.0.7-4               
ii  libpthread20                        2.0.7-4                

gcc and g++:
gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21)


This propblem I just reproduced in the latest R-patched: version 2.4.1 Patched 
(2007-02-28 r40809).


Best,


R.


-- 
Ramón Díaz-Uriarte
Statistical Computing Team
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)



**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en s...{{dropped}}