Rsamtools 1.2.3
Biocore Team c/o BioC user list
| Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/Rsamtools | | Last Changed Rev: 51873 / Revision: 54281 | | Last Changed Date: 2011-01-11 16:14:33 -0800 (Tue, 11 Jan 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/Rsamtools.Rcheck’
* using R version 2.12.2 Patched (2011-02-25 r54591)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsamtools’ version ‘1.2.3’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘Rsamtools’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘Rsamtools_unit_tests.R’
OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘Rsamtools’ ...
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 gzeof in -lz... yes
checking for bzero... yes
checking for memset... yes
checking for pow... yes
checking for sqrt... yes
checking for strcasecmp... yes
checking for strdup... yes
checking for strstr... yes
checking for strtol... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for ptrdiff_t... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c io_sam.c -o io_sam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c utilities.c -o utilities.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c encode.c -o encode.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c R_init_Rsamtools.c -o R_init_Rsamtools.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bam.c -o samtools/bam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bam_import.c -o samtools/bam_import.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bam_sort.c -o samtools/bam_sort.o
samtools/bam_sort.c: In function ‘__ks_insertsort_heap’:
samtools/bam_sort.c:53: warning: ‘heap_lt’ is static but used in inline function ‘__ks_insertsort_heap’ which is not static
samtools/bam_sort.c: In function ‘__ks_insertsort_sort’:
samtools/bam_sort.c:273: warning: ‘bam1_lt’ is static but used in inline function ‘__ks_insertsort_sort’ which is not static
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bam_index.c -o samtools/bam_index.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/kstring.c -o samtools/kstring.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bam_aux.c -o samtools/bam_aux.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/sam_header.c -o samtools/sam_header.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bgzf.c -o samtools/bgzf.o
samtools/bgzf.c: In function ‘deflate_block’:
samtools/bgzf.c:319: warning: pointer of type ‘void *’ used in arithmetic
samtools/bgzf.c: In function ‘inflate_block’:
samtools/bgzf.c:335: warning: pointer of type ‘void *’ used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function ‘_razf_buffered_write’:
samtools/razf.c:283: warning: pointer of type ‘void *’ used in arithmetic
samtools/razf.c: In function ‘razf_write’:
samtools/razf.c:297: warning: pointer of type ‘void *’ used in arithmetic
samtools/razf.c: In function ‘razf_open_r’:
samtools/razf.c:392: warning: pointer of type ‘void *’ used in arithmetic
samtools/razf.c:400: warning: pointer of type ‘void *’ used in arithmetic
samtools/razf.c: In function ‘_razf_open’:
samtools/razf.c:511: warning: ordered comparison of pointer with integer zero
samtools/razf.c: In function ‘razf_read’:
samtools/razf.c:631: warning: pointer of type ‘void *’ used in arithmetic
samtools/razf.c:637: warning: pointer of type ‘void *’ used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/knetfile.c -o samtools/knetfile.o
samtools/knetfile.c: In function ‘my_netread’:
samtools/knetfile.c:190: warning: pointer of type ‘void *’ used in arithmetic
samtools/knetfile.c: In function ‘knet_read’:
samtools/knetfile.c:520: warning: pointer of type ‘void *’ used in arithmetic
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/sam.c -o samtools/sam.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/bam_pileup.c -o samtools/bam_pileup.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.12/Resources/library/IRanges/include" -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -fPIC -g -O2 -Wall -pedantic -c samtools/faidx.c -o samtools/faidx.o
samtools/faidx.c:9: warning: type of bit-field ‘len’ is a GCC extension
samtools/faidx.c:9: warning: type of bit-field ‘line_len’ is a GCC extension
samtools/faidx.c:9: warning: type of bit-field ‘line_blen’ is a GCC extension
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rsamtools.so io_sam.o utilities.o encode.o Biostrings_stubs.o IRanges_stubs.o R_init_Rsamtools.o samtools/bam.o samtools/bam_import.o samtools/bam_sort.o samtools/bam_index.o samtools/kstring.o samtools/bam_aux.o samtools/sam_header.o samtools/bgzf.o samtools/razf.o samtools/knetfile.o samtools/sam.o samtools/bam_pileup.o samtools/faidx.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/Rsamtools.Rcheck/Rsamtools/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
pmin.int, rbind, rep.int, table
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* DONE (Rsamtools)