Back to the "Multiple platform build/check report"[A] B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.12: CHECK report for ArrayExpressHTS on petty

This page was generated on 2013-10-09 09:39:59 -0700 (Wed, 09 Oct 2013).

Package 46/671HostnameOS / ArchBUILDCHECKBUILD BIN
ArrayExpressHTS 1.10.0
Angela Goncalves , Andrew Tikhonov
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ArrayExpressHTS
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
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 Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ArrayExpressHTS
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ArrayExpressHTS_1.10.0.tar.gz
StartedAt: 2013-10-08 21:35:49 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:42:43 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 413.6 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 3.0.1 (2013-05-16)
* 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 '1.10.0'
* 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 ... [46s/46s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [21s/21s] 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 -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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Tue Oct  8 21:36:36 2013 [AEHTS] Setting Options Step 1
Tue Oct  8 21:36:36 2013 [AEHTS] Setting Options Step 2
Tue Oct  8 21:36:36 2013 [AEHTS] Setting Options Step 3
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     fasta_formatter not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.fasta_formatter' = '/path/to/fasta_formatter') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     cufflinks not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.cufflinks' = '/path/to/cufflinks') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     samtools not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.samtools' = '/path/to/samtools') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     bwa not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.bwa' = '/path/to/bwa') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     mmseq not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.mmseq' = '/path/to/mmseq') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     bam2hits not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.bam2hits' = '/path/to/bam2hits') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     bowtie not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.bowtie' = '/path/to/bowtie') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] *** WARNING ***
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS]     tophat not found
Tue Oct  8 21:36:36 2013 [AEHTS] 
Tue Oct  8 21:36:36 2013 [AEHTS] Use options('ArrayExpressHTS.tophat' = '/path/to/tophat') to define the location.
Tue Oct  8 21:36:36 2013 [AEHTS] Use .Rprofile to make options persistent.
Tue Oct  8 21:36:36 2013 [AEHTS] 
* DONE (ArrayExpressHTS)

ArrayExpressHTS.Rcheck/ArrayExpressHTS-Ex.timings:

nameusersystemelapsed
ArrayExpressHTS0.4490.0100.474
ArrayExpressHTSFastQ0.0350.0120.048
isRCloud0.0160.0050.025
package-options0.0150.0070.021
prepareAnnotation0.0180.0060.027
prepareReference0.0230.0080.033
processing-options0.0100.0050.014