ArrayExpressHTS 1.9.2
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 70419 / Revision: 74774 | | Last Changed Date: 2012-10-11 09:58:19 -0700 (Thu, 11 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ArrayExpressHTS.buildbin-libdir ArrayExpressHTS_1.9.2.tar.gz'
>>>>>>>
* installing *source* package 'ArrayExpressHTS' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -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 -g -O2 -Wall -pedantic -c addXS.c -o addXS.o
addXS.c: In function 'addXS':
addXS.c:42: warning: implicit declaration of function 'Rprintf'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -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 -g -O2 -Wall -pedantic -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 'strcpy' 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
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -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 -g -O2 -Wall -pedantic -c functions.c -o functions.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -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 -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -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 -g -O2 -Wall -pedantic -c hashtable_itr.c -o hashtable_itr.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -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 -g -O2 -Wall -pedantic -c hashtable_utility.c -o hashtable_utility.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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/i386/libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/i386/libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386
** R
** inst
** preparing package for lazy loading
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
'ArrayExpressHTS.Rnw'
** testing if installed package can be loaded
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Mon Mar 25 05:18:11 2013 [AEHTS] Setting Options Step 1
Mon Mar 25 05:18:11 2013 [AEHTS] Setting Options Step 2
Mon Mar 25 05:18:11 2013 [AEHTS] Setting Options Step 3
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] fasta_formatter not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] cufflinks not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] samtools not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] bwa not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] mmseq not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] bam2hits not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] bowtie not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] *** WARNING ***
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] tophat not found
Mon Mar 25 05:18:11 2013 [AEHTS]
Mon Mar 25 05:18:11 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Mon Mar 25 05:18:11 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 05:18:11 2013 [AEHTS]
* DONE (ArrayExpressHTS)
>>>>>>>
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386/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/i386/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/i386/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/i386/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/i386/ArrayExpressHTS.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=ArrayExpressHTS.buildbin-libdir --libs-only ArrayExpressHTS_1.9.2.tar.gz'
>>>>>>>
* installing *source* package 'ArrayExpressHTS' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -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 -g -O2 -Wall -pedantic -c addXS.c -o addXS.o
addXS.c: In function 'addXS':
addXS.c:42: warning: implicit declaration of function 'Rprintf'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -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 -g -O2 -Wall -pedantic -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 'strcpy' 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
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -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 -g -O2 -Wall -pedantic -c functions.c -o functions.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -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 -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -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 -g -O2 -Wall -pedantic -c hashtable_itr.c -o hashtable_itr.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -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 -g -O2 -Wall -pedantic -c hashtable_utility.c -o hashtable_utility.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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/x86_64/libbam.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/x86_64/libbcf.a /Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rsamtools/usrlib/x86_64/libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64
* DONE (ArrayExpressHTS)
>>>>>>>
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/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/x86_64/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/x86_64/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/x86_64/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/x86_64/ArrayExpressHTS.so"