ShortRead 1.6.2
Biocore Team c/o BioC user list
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/ShortRead | | Last Changed Rev: 46600 / Revision: 49923 | | Last Changed Date: 2010-04-28 10:21:31 -0700 (Wed, 28 Apr 2010) |
| wilson1 | Linux (openSUSE 11.1) / 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 |
* checking for file 'ShortRead/DESCRIPTION' ... OK
* preparing 'ShortRead':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* installing *source* package ‘ShortRead’ ...
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 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 size of unsigned long... 4
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
In file included from Biostrings_stubs.c:1:
/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include/_Biostrings_stubs.c:34: warning: ISO C does not allow extra ‘;’ outside of a function
/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include/_Biostrings_stubs.c:39: warning: ISO C does not allow extra ‘;’ outside of a function
/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include/_Biostrings_stubs.c:44: warning: ISO C does not allow extra ‘;’ outside of a function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c alphabet.c -o alphabet.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io.c -o io.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_bowtie.c -o io_bowtie.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c io_soap.c -o io_soap.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c pileup.c -o pileup.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c readBfaToc.cc -o readBfaToc.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -DHAVE_LIBZ=1 -fPIC -g -O2 -Wall -fasm-blocks -c read_maq_map.cc -o read_maq_map.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c util.c -o util.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Biostrings/include" -fPIC -g -O2 -Wall -pedantic -c xsnap.c -o xsnap.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o util.o xsnap.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /private/tmp/Rinst8091588616/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading
Attaching package: 'IRanges'
The following object(s) are masked from 'package:base':
Map, cbind, 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 (ShortRead)
* creating vignettes ... OK
* cleaning src
make: Nothing to be done for `clean'.
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'ShortRead_1.6.2.tar.gz'