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BioC 2.13: CHECK report for GeneRegionScan on moscato1

This page was generated on 2014-04-05 09:49:53 -0700 (Sat, 05 Apr 2014).

Package 289/750HostnameOS / ArchBUILDCHECKBUILD BIN
GeneRegionScan 1.18.0
Lasse Folkersen
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GeneRegionScan
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GeneRegionScan
Version: 1.18.0
Command: rm -rf GeneRegionScan.buildbin-libdir && mkdir GeneRegionScan.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GeneRegionScan.buildbin-libdir GeneRegionScan_1.18.0.tar.gz >GeneRegionScan-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GeneRegionScan.buildbin-libdir --install="check:GeneRegionScan-install.out" --force-multiarch --no-vignettes --timings GeneRegionScan_1.18.0.tar.gz && mv GeneRegionScan.buildbin-libdir/* GeneRegionScan.Rcheck/ && rmdir GeneRegionScan.buildbin-libdir
StartedAt: 2014-04-05 04:05:58 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:13:58 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 480.5 seconds
RetCode: 0
Status:  OK  
CheckDir: GeneRegionScan.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GeneRegionScan.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GeneRegionScan/DESCRIPTION' ... OK
* this is package 'GeneRegionScan' version '1.18.0'
* 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 whether package 'GeneRegionScan' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.4Mb
  sub-directories of 1Mb or more:
    exec  19.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biobase' 'Biostrings'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotOnGene,ExpressionSet: warning in plot.default(1, type = "n", xlab =
  "bp", ylab = ylab, frame = FALSE, xlim = xlim, ylim = ylim, main =
  paste("Expression of probes"), cex.main = 1): partial argument match
  of 'frame' to 'frame.plot'
readFASTA_replacement: no visible global function definition for
  'read.DNAStringSet'
plotCoexpression,ExpressionSet: no visible binding for global variable
  'interval'
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'GeneRegionScan.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [142s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   62.34   0.04   62.98
plotCoexpression 45.97   0.00   46.02
plotOnGene       14.54   0.03   14.57
exonStructure    10.31   0.03   10.35
** running examples for arch 'x64' ... [184s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
geneRegionScan   76.59   6.10   84.01
plotCoexpression 60.12   3.78   63.92
plotOnGene       15.32   0.01   15.33
exonStructure    10.29   0.06   10.36
* 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 were 5 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/GeneRegionScan.Rcheck/00check.log'
for details.

GeneRegionScan.Rcheck/00install.out:


install for i386

* installing *source* package 'GeneRegionScan' ...
** R
** data
** exec
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'GeneRegionScan' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GeneRegionScan' as GeneRegionScan_1.18.0.zip
* DONE (GeneRegionScan)

GeneRegionScan.Rcheck/examples_i386/GeneRegionScan-Ex.timings:

nameusersystemelapsed
addSnpPdata000
checkForFileInPath0.030.030.22
doProbeLinear1.980.001.98
doProbeTTest0.620.020.64
exampleProbeLevelSet0.030.020.04
excludeDoubleMatchingProbes000
exonStructure10.31 0.0310.35
findProbePositions0.530.000.53
findSequenceInGenome0.020.000.01
geneRegionScan62.34 0.0462.98
getLocalMetaprobeIntensities000
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest0.010.000.01
getProbeLevelAnnotationForExonArrays000
getProbesetsFromMetaprobeset000
getProbesetsFromRegionOfInterest000
getSequence0.030.000.04
getServerProbeIntensities000
plotCoexpression45.97 0.0046.02
plotOnGene14.54 0.0314.57
readGeneInput000
translateSampleNames0.060.000.06

GeneRegionScan.Rcheck/examples_x64/GeneRegionScan-Ex.timings:

nameusersystemelapsed
addSnpPdata000
checkForFileInPath0.060.020.07
doProbeLinear3.530.003.52
doProbeTTest0.970.000.97
exampleProbeLevelSet0.050.000.04
excludeDoubleMatchingProbes0.020.000.02
exonStructure10.29 0.0610.36
findProbePositions0.530.000.53
findSequenceInGenome0.020.000.01
geneRegionScan76.59 6.1084.01
getLocalMetaprobeIntensities000
getLocalProbeIntensities000
getMetaprobesetsFromRegionOfInterest000
getProbeLevelAnnotationForExonArrays0.020.000.01
getProbesetsFromMetaprobeset000
getProbesetsFromRegionOfInterest000
getSequence0.040.000.03
getServerProbeIntensities000
plotCoexpression60.12 3.7863.92
plotOnGene15.32 0.0115.33
readGeneInput000
translateSampleNames0.070.020.08