>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ArrayExpressHTS.buildbin-libdir ArrayExpressHTS_1.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c addXS.c -o addXS.o
addXS.c: In function ‘addXS’:
addXS.c:42: warning: implicit declaration of function ‘Rprintf’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c fltbam.c -o fltbam.o
fltbam.c: In function ‘equalkeys’:
fltbam.c:40: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness
fltbam.c:40: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness
fltbam.c: In function ‘print_key’:
fltbam.c:45: warning: implicit declaration of function ‘Rprintf’
fltbam.c: In function ‘fltbam’:
fltbam.c:91: warning: implicit declaration of function ‘Rf_error’
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘__builtin___strcpy_chk’ differ in signedness
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘__inline_strcpy_chk’ differ in signedness
fltbam.c:126: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
fltbam.c: At top level:
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c functions.c -o functions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c hashtable.c -o hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c hashtable_itr.c -o hashtable_itr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/include" -fPIC -mtune=core2 -g -O2 -Wall -c hashtable_utility.c -o hashtable_utility.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: subseq
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: read.AnnotatedDataFrame
No methods found in "IRanges" for requests: subseq
Sat Apr 5 05:15:21 2014 [AEHTS] Setting Options Step 1
Sat Apr 5 05:15:21 2014 [AEHTS] Setting Options Step 2
Sat Apr 5 05:15:21 2014 [AEHTS] Setting Options Step 3
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] fasta_formatter not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] cufflinks not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] samtools not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] bwa not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] mmseq not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] bam2hits not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] bowtie not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] *** WARNING ***
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] tophat not found
Sat Apr 5 05:15:21 2014 [AEHTS]
Sat Apr 5 05:15:21 2014 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Sat Apr 5 05:15:21 2014 [AEHTS] Use .Rprofile to make options persistent.
Sat Apr 5 05:15:21 2014 [AEHTS]
* DONE (ArrayExpressHTS)
>>>>>>>
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs//ArrayExpressHTS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs//ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs//ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs//ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs//ArrayExpressHTS.so"