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. -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez 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 electr?nico, y en s...{{dropped}}

Apologies. Please disregard the previous message; I got the packages mixed-up (in Debian libpthread is for the emulation). So this probably has nothing to do with genefilter. R. On Thursday 01 March 2007 15:12, Ramon Diaz-Uriarte wrote: > 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. -- Ram?n D?az-Uriarte Statistical Computing Team Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez 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 electr?nico, y en s...{{dropped}}