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Package 309/353HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.4.0
Biocore Team c/o BioC user list
Snapshot Date: 2010-04-02 23:28:25 -0700 (Fri, 02 Apr 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/ShortRead
Last Changed Rev: 42684 / Revision: 45705
Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009)
wilson2 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: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.10/Resources/bin/R CMD build ShortRead
StartedAt: 2010-04-03 03:24:22 -0700 (Sat, 03 Apr 2010)
EndedAt: 2010-04-03 03:25:42 -0700 (Sat, 03 Apr 2010)
EllapsedTime: 79.8 seconds
RetCode: 0
Status: OK
PackageFile: ShortRead_1.4.0.tar.gz
PackageFileSize: 1.851 MiB

Command output

* 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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/Biostrings/include"   -fPIC  -g -O2 -Wall -c pileup.c -o pileup.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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/2.10/Resources/include -I/Library/Frameworks/R.framework/Versions/2.10/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.10/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.10/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)
* 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_1.4.0.tar.gz'