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Package 309/354HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.5.8
Biocore Team c/o BioC user list
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead
Last Changed Rev: 43433 / Revision: 43434
Last Changed Date: 2009-12-07 09:13:58 -0800 (Mon, 07 Dec 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK [ OK ]
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: ShortRead
Version: 1.5.8
Command: /Users/biocbuild/BBS/utils/build-universal.sh ShortRead_1.5.8.tar.gz /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R ShortRead.buildbin-libdir
StartedAt: 2009-12-07 19:49:56 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 19:50:41 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 44.7 seconds
RetCode: 0
Status: OK
PackageFile: ShortRead_1.5.8.tgz
PackageFileSize: 2.431 MiB

Command output

                INSTALLATION WITH 'R CMD INSTALL --preclean --library=ShortRead.buildbin-libdir ShortRead_1.5.8.tar.gz'

* 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 -c Biostrings_stubs.c -o Biostrings_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 -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 -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 -c alphabet.c -o alphabet.o
alphabet.c: In function ‘alphabet_as_int’:
alphabet.c:190: warning: ‘ians’ may be used uninitialized in this 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 -c io.c -o io.o
io.c: In function ‘_count_ipar_int_recs’:
io.c:118: warning: ‘bytes_read’ may be used uninitialized in this 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 -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 -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 -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 -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 -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 -c util.c -o util.o
util.c: In function ‘decoder’:
util.c:43: warning: ‘decode’ may be used uninitialized in this function
util.c: In function ‘encoder’:
util.c:59: warning: ‘encode’ may be used uninitialized in this function
util.c: In function ‘_char_as_strand_int’:
util.c:95: warning: ‘strand’ may be used uninitialized in this 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 -c xsnap.c -o xsnap.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -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
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'


	The following object(s) are masked from package:base :

	 Map,
	 cbind,
	 mapply,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 table 

** help
*** installing help indices
** building package indices ...
* DONE (ShortRead)

                INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=ShortRead.buildbin-libdir --libs-only ShortRead_1.5.8.tar.gz'

* 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 - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c alphabet.c -o alphabet.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c io.c -o io.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c io_bowtie.c -o io_bowtie.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c io_soap.c -o io_soap.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c pileup.c -o pileup.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c readBfaToc.cc -o readBfaToc.o
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c read_maq_map.cc -o read_maq_map.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c util.c -o util.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -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 -c xsnap.c -o xsnap.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -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
* DONE (ShortRead)