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Package 44/609HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpressHTS 1.8.0
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/ArrayExpressHTS
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: ArrayExpressHTS
Version: 1.8.0
Command: rm -rf ArrayExpressHTS.buildbin-libdir && mkdir ArrayExpressHTS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ArrayExpressHTS_1.8.0.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R ArrayExpressHTS.buildbin-libdir
StartedAt: 2013-03-25 01:46:36 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:47:15 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 39.2 seconds
RetCode: 0
Status:  OK 
PackageFile: ArrayExpressHTS_1.8.0.tgz
PackageFileSize: 574.9 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ArrayExpressHTS.buildbin-libdir ArrayExpressHTS_1.8.0.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/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c addXS.c -o addXS.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/2.15/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 'fltbam':
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/2.15/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/2.15/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/2.15/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/2.15/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/2.15/Resources/library/Rsamtools/usrlib/i386/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ArrayExpressHTS.Rnw' 
** testing if installed package can be loaded
Mon Mar 25 01:47:08 2013 [AEHTS] Setting Options Step 1
Mon Mar 25 01:47:08 2013 [AEHTS] Setting Options Step 2
Mon Mar 25 01:47:08 2013 [AEHTS] Setting Options Step 3
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     fasta_formatter not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     cufflinks not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     samtools not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     bwa not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     mmseq not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     bam2hits not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     bowtie not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] *** WARNING ***
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS]     tophat not found
Mon Mar 25 01:47:08 2013 [AEHTS] 
Mon Mar 25 01:47:08 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Mon Mar 25 01:47:08 2013 [AEHTS] Use .Rprofile to make options persistent.
Mon Mar 25 01:47:08 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/2.15/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/2.15/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/2.15/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/2.15/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_1.8.0.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/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c addXS.c -o addXS.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/2.15/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 'fltbam':
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/2.15/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/2.15/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/2.15/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/2.15/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/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbam.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbcf.a /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libtabix.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-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/2.15/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/2.15/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/2.15/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/2.15/Resources/lib/libreadline.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so"