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BioC 2.14: CHECK report for Biobase on petty

This page was generated on 2014-10-08 08:56:48 -0700 (Wed, 08 Oct 2014).

Package 83/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.24.0
Bioconductor Package Maintainer
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/Biobase
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  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: Biobase
Version: 2.24.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.24.0.tar.gz
StartedAt: 2014-10-07 20:54:16 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 20:57:28 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 191.2 seconds
RetCode: 0
Status:  OK 
CheckDir: Biobase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Biobase_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.24.0’
* 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 ‘Biobase’ can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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
cache: no visible binding for global variable ‘cache_old’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... 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 files in ‘vignettes’ ... OK
* checking examples ... [12s/12s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test-all.R’ [45s/45s]
  Running ‘test-rowMedians.R’ [36s/36s]
 [81s/82s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck/00check.log’
for details.

Biobase.Rcheck/00install.out:

* installing *source* package ‘Biobase’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Rinit.c -o Rinit.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c anyMissing.c -o anyMissing.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c envir.c -o envir.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c matchpt.c -o matchpt.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c rowMedians.c -o rowMedians.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c sublist_extract.c -o sublist_extract.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 Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-bioc/meat/Biobase.Rcheck/Biobase/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Biobase)

Biobase.Rcheck/Biobase-Ex.timings:

nameusersystemelapsed
Aggregate0.0210.0010.022
ScalarObject-class0.0310.0000.032
addVig2Menu0.0010.0000.002
anyMissing0.0030.0000.004
cache0.0060.0010.008
channel0.3510.0040.356
channelNames0.1400.0010.141
class.AnnotatedDataFrame0.0790.0020.080
class.ExpressionSet0.5550.0190.574
class.MIAxE0.0430.0010.044
class.MultiSet0.0790.0000.080
class.NChannelSet0.5530.0060.560
class.Versioned0.1410.0010.143
class.VersionedBiobase0.0630.0020.064
class.Versions0.0310.0010.031
class.VersionsNull0.0030.0000.003
class.container0.0110.0000.010
class.eSet0.2230.0020.225
classVersion0.0130.0010.012
contents0.0020.0000.003
copyEnv0.0020.0000.002
copySubstitute0.0210.0080.034
createPackage0.0140.0050.018
data.aaMap0.0050.0010.006
data.geneData0.0620.0050.068
data.reporter0.0090.0010.009
data.sample.ExpressionSet0.0240.0130.038
data.sample.MultiSet0.0090.0110.021
dumpPackTxt0.0030.0010.026
esApply3.1690.0193.191
getPkgVigs0.0820.0120.145
isCurrent0.0880.0010.089
isUnique0.0020.0010.002
isVersioned0.0350.0000.035
lcSuffix0.0060.0000.005
listLen0.0020.0010.003
makeDataPackage0.1180.0160.140
matchpt0.0090.0010.010
multiassign0.0020.0000.002
note0.0010.0010.002
openPDF0.0010.0000.000
openVignette0.0010.0000.001
package.version0.0050.0000.006
read.AnnotatedDataFrame0.0240.0030.026
read.MIAME0.0060.0000.005
readExpressionSet0.1440.0040.147
reverseSplit0.0010.0010.002
rowMedians0.1700.0030.172
rowQ0.0300.0160.052
selectChannels0.1320.0000.133
selectSome0.0010.0000.002
strbreak0.0030.0000.003
subListExtract2.7120.0562.771
testBioCConnection0.0040.0020.016
updateOldESet0.0010.0000.001
validMsg0.0010.0010.001