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BioC 3.5: CHECK report for Biobase on veracruz2

This page was generated on 2017-10-18 14:27:14 -0400 (Wed, 18 Oct 2017).

Package 111/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Biobase 2.36.2
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/Biobase
Branch: RELEASE_3_5
Last Commit: 15f5091
Last Changed Date: 2017-05-02 18:47:56 -0400 (Tue, 02 May 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Biobase
Version: 2.36.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Biobase_2.36.2.tar.gz
StartedAt: 2017-10-18 00:57:14 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 00:58:43 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 88.3 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 Biobase_2.36.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Biobase.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Biobase/DESCRIPTION’ ... OK
* this is package ‘Biobase’ version ‘2.36.2’
* 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 ‘Biobase’ can be installed ... 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 ... OK
* 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 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
  Running ‘test-rowMedians.R’
 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
* DONE

Status: OK

Biobase.Rcheck/00install.out:

* installing *source* package ‘Biobase’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rinit.c -o Rinit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c anyMissing.c -o anyMissing.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c envir.c -o envir.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matchpt.c -o matchpt.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rowMedians.c -o rowMedians.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c sublist_extract.c -o sublist_extract.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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-3.5-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
Aggregate0.0360.0020.039
ScalarObject-class0.0090.0000.009
addVig2Menu0.0010.0000.001
anyMissing0.0020.0010.002
cache0.0050.0000.006
channel0.3360.0020.360
channelNames0.0860.0010.088
class.AnnotatedDataFrame0.0430.0010.045
class.ExpressionSet0.3430.0060.355
class.MIAxE0.0150.0000.016
class.MultiSet0.0230.0010.024
class.NChannelSet0.2200.0020.231
class.Versioned0.0540.0050.059
class.VersionedBiobase0.0220.0010.023
class.Versions0.0120.0000.012
class.VersionsNull0.0010.0000.001
class.container0.0010.0000.002
class.eSet0.0740.0010.076
classVersion0.0030.0000.004
contents0.0010.0000.002
copyEnv0.0200.0010.021
copySubstitute0.0970.0040.103
createPackage0.0060.0010.011
data.aaMap0.0030.0000.004
data.geneData0.0430.0030.050
data.reporter0.0020.0010.003
data.sample.ExpressionSet0.0130.0050.018
data.sample.MultiSet0.0050.0040.009
dumpPackTxt0.0030.0000.004
esApply1.3130.0141.362
getPkgVigs0.0070.0010.010
isCurrent0.0310.0000.033
isUnique0.0010.0000.000
isVersioned0.0080.0000.009
lcSuffix0.0320.0000.035
listLen0.0010.0000.002
makeDataPackage0.0910.0070.099
matchpt0.0210.0000.021
multiassign0.0220.0000.024
note0.0010.0000.001
openPDF000
openVignette0.0000.0000.001
package.version0.0020.0000.001
read.AnnotatedDataFrame0.0110.0000.013
read.MIAME0.030.000.03
readExpressionSet0.0780.0010.080
reverseSplit0.0010.0000.001
rowMedians0.0410.0030.043
rowQ0.0160.0070.023
selectChannels0.0370.0000.038
selectSome0.0010.0000.001
strbreak0.0280.0010.029
subListExtract0.7540.0220.801
testBioCConnection0.0020.0010.266
updateOldESet0.0010.0000.000
validMsg0.0010.0000.000