Rsubread 0.99.2
Wei Shi
| Snapshot Date: 2011-04-06 11:17:57 -0700 (Wed, 06 Apr 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsubread | | Last Changed Rev: 54527 / Revision: 54545 | | Last Changed Date: 2011-04-05 23:43:27 -0700 (Tue, 05 Apr 2011) |
| lamb1 | Linux (openSUSE 11.3) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | ERROR | skipped | skipped |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | ERROR | skipped | skipped |
| pelham | Mac OS X Leopard (10.5.8) / i386 | [ ERROR ] | skipped | skipped |
* checking for file ‘Rsubread/DESCRIPTION’ ... OK
* preparing ‘Rsubread’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
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* installing *source* package ‘Rsubread’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -Wall -pedantic -c R_wrapper.c -o R_wrapper.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -g -O2 -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -fPIC -g -O2 -Wall -pedantic -c aligner.c -o aligner.o
aligner.c:211: error: expected specifier-qualifier-list before ‘pthread_spinlock_t’
aligner.c:215: error: expected declaration specifiers or ‘...’ before ‘pthread_spinlock_t’
aligner.c: In function ‘run_search’:
aligner.c:258: error: ‘input_lock’ undeclared (first use in this function)
aligner.c:258: error: (Each undeclared identifier is reported only once
aligner.c:258: error: for each function it appears in.)
aligner.c:259: warning: implicit declaration of function ‘pthread_spin_lock’
aligner.c:314: warning: implicit declaration of function ‘pthread_spin_unlock’
aligner.c: In function ‘run_search_thread’:
aligner.c:586: error: ‘struct gene_thread_data_transport’ has no member named ‘init_lock’
aligner.c:588: error: ‘struct gene_thread_data_transport’ has no member named ‘input_data_lock’
aligner.c:588: error: too many arguments to function ‘run_search’
aligner.c: In function ‘run_search_index’:
aligner.c:645: warning: passing argument 11 of ‘run_search’ makes integer from pointer without a cast
aligner.c:645: error: too many arguments to function ‘run_search’
aligner.c:651: error: ‘pthread_spinlock_t’ undeclared (first use in this function)
aligner.c:651: error: expected ‘;’ before ‘data_lock’
aligner.c:652: error: expected ‘;’ before ‘init_lock’
aligner.c:662: error: ‘struct gene_thread_data_transport’ has no member named ‘input_data_lock’
aligner.c:662: error: ‘data_lock’ undeclared (first use in this function)
aligner.c:663: error: ‘struct gene_thread_data_transport’ has no member named ‘init_lock’
aligner.c:663: error: ‘init_lock’ undeclared (first use in this function)
aligner.c:669: warning: implicit declaration of function ‘pthread_spin_init’
aligner.c:681: warning: implicit declaration of function ‘pthread_spin_destroy’
aligner.c: At top level:
gene-algorithms.h:27: warning: inline function ‘add_gene_vote_weighted’ declared but never defined
gene-algorithms.h:26: warning: inline function ‘add_gene_vote’ declared but never defined
make: *** [aligner.o] Error 1
ERROR: compilation failed for package ‘Rsubread’
* removing ‘/private/tmp/RtmpbyEXPs/Rinst56e57565/Rsubread’
-----------------------------------
ERROR: package installation failed