ArrayExpressHTS 1.9.2
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2013-03-23 17:02:20 -0700 (Sat, 23 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 70419 / Revision: 74756 | | 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 |
| pelham | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] |
* 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 -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 -c fltbam.c -o fltbam.o
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: 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 -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 -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 -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 -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 -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-2.12-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs
** R
** inst
** preparing package for lazy loading
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.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
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Sun Mar 24 11:25:28 2013 [AEHTS] Setting Options Step 1
Sun Mar 24 11:25:28 2013 [AEHTS] Setting Options Step 2
Sun Mar 24 11:25:28 2013 [AEHTS] Setting Options Step 3
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] fasta_formatter not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] cufflinks not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] samtools not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] bwa not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] mmseq not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] bam2hits not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] bowtie not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] *** WARNING ***
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] tophat not found
Sun Mar 24 11:25:28 2013 [AEHTS]
Sun Mar 24 11:25:28 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Sun Mar 24 11:25:28 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 11:25:28 2013 [AEHTS]
packaged installation of 'ArrayExpressHTS' as 'ArrayExpressHTS_1.9.2.tgz'
* DONE (ArrayExpressHTS)