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Package 45/658HostnameOS / ArchBUILDCHECKBUILD BIN
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 

Summary

Package: ArrayExpressHTS
Version: 1.9.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayExpressHTS_1.9.2.tar.gz
StartedAt: 2013-03-24 02:23:19 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 02:29:45 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 385.8 seconds
RetCode: 0
Status:  OK 
CheckDir: ArrayExpressHTS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ArrayExpressHTS/DESCRIPTION' ... OK
* this is package 'ArrayExpressHTS' version '1.9.2'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ArrayExpressHTS' can be installed ... [37s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cleanupCluster: no visible global function definition for
  'cleanupClusters'
prepareCluster: no visible global function definition for
  'mergeClusters'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [19s/19s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ArrayExpressHTS.Rcheck/00check.log'
for details.

ArrayExpressHTS.Rcheck/00install.out:

* 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.Rcheck/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 02:23:59 2013 [AEHTS] Setting Options Step 1
Sun Mar 24 02:23:59 2013 [AEHTS] Setting Options Step 2
Sun Mar 24 02:23:59 2013 [AEHTS] Setting Options Step 3
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     fasta_formatter not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     cufflinks not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     samtools not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     bwa not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     mmseq not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     bam2hits not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     bowtie not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] *** WARNING ***
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS]     tophat not found
Sun Mar 24 02:23:59 2013 [AEHTS] 
Sun Mar 24 02:23:59 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Sun Mar 24 02:23:59 2013 [AEHTS] Use .Rprofile to make options persistent.
Sun Mar 24 02:23:59 2013 [AEHTS] 
* DONE (ArrayExpressHTS)

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings:

nameusersystemelapsed
ArrayExpressHTS0.0300.0080.037
ArrayExpressHTSFastQ0.0560.0150.071
isRCloud0.0250.0060.031
package-options0.0270.0070.034
prepareAnnotation0.0360.0070.044
prepareReference0.0290.0080.037
processing-options0.0190.0060.025