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BioC 2.14: BUILD BIN report for ArrayExpressHTS on petty

This page was generated on 2014-10-08 08:59:33 -0700 (Wed, 08 Oct 2014).

Package 49/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ArrayExpressHTS 1.14.0
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ArrayExpressHTS
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED...
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: ArrayExpressHTS
Version: 1.14.0
Command: rm -rf ArrayExpressHTS.buildbin-libdir && mkdir ArrayExpressHTS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ArrayExpressHTS_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ArrayExpressHTS.buildbin-libdir
StartedAt: 2014-10-08 01:14:36 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:15:46 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 69.7 seconds
RetCode: 0
Status:  OK 
PackageFile: ArrayExpressHTS_1.14.0.tgz
PackageFileSize: 531.9 KiB

Command output

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###
### Running command:
###
###   rm -rf ArrayExpressHTS.buildbin-libdir && mkdir ArrayExpressHTS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ArrayExpressHTS_1.14.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R ArrayExpressHTS.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ArrayExpressHTS.buildbin-libdir ArrayExpressHTS_1.14.0.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/3.1/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/3.1/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/3.1/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/3.1/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/3.1/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/3.1/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/3.1/Resources/library/Rsamtools/usrlib//libbam.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libbcf.a /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rsamtools/usrlib//libtabix.a -lz -pthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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
Wed Oct  8 01:15:34 2014 [AEHTS] Setting Options Step 1
Wed Oct  8 01:15:34 2014 [AEHTS] Setting Options Step 2
Wed Oct  8 01:15:34 2014 [AEHTS] Setting Options Step 3
Wed Oct  8 01:15:34 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS]     fasta_formatter not found
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Wed Oct  8 01:15:34 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS]     cufflinks not found
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Wed Oct  8 01:15:34 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS]     samtools not found
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Wed Oct  8 01:15:34 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS]     bwa not found
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:34 2014 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Wed Oct  8 01:15:34 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:34 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS]     mmseq not found
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Wed Oct  8 01:15:35 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS]     bam2hits not found
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Wed Oct  8 01:15:35 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS]     bowtie not found
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Wed Oct  8 01:15:35 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] *** WARNING ***
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS]     tophat not found
Wed Oct  8 01:15:35 2014 [AEHTS] 
Wed Oct  8 01:15:35 2014 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Wed Oct  8 01:15:35 2014 [AEHTS] Use .Rprofile to make options persistent.
Wed Oct  8 01:15:35 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/3.1/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/3.1/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/3.1/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/3.1/Resources/lib/libreadline.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs//ArrayExpressHTS.so"