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BioC 3.2: CHECK report for RNAither on moscato1

This page was generated on 2016-04-23 10:16:46 -0700 (Sat, 23 Apr 2016).

Package 894/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAither 2.18.7
Lars Kaderali
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RNAither
Last Changed Rev: 115306 / Revision: 116712
Last Changed Date: 2016-03-27 15:03:31 -0700 (Sun, 27 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RNAither
Version: 2.18.7
Command: rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.18.7.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.18.7.tar.gz
StartedAt: 2016-04-23 06:55:56 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 07:06:10 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 614.4 seconds
RetCode: 0
Status:  OK  
CheckDir: RNAither.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.18.7.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.18.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/RNAither.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.18.7'
* 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 'RNAither' 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/extdata/CITATION
Most likely 'inst/CITATION' should be used instead.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'RankProd'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotSpatialDistrib: no visible global function definition for
  'brewer.pal'
RankProduct: no visible global function definition for 'RP'
compareReplicateSD: no visible global function definition for
  'brewer.pal'
compareReplicateSDPerScreen: no visible global function definition for
  'brewer.pal'
spatialDistrib: no visible global function definition for 'brewer.pal'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [109s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mainAnalysis 15.90   2.82   36.83
rnaither     12.42   2.70   26.08
gseaAnalysis  6.12   0.13   28.25
** running examples for arch 'x64' ... [127s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
mainAnalysis 19.43   2.62   42.12
rnaither     13.74   3.16   32.50
gseaAnalysis  7.63   0.12   32.42
* 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: 3 NOTEs
See
  'D:/biocbld/bbs-3.2-bioc/meat/RNAither.Rcheck/00check.log'
for details.


RNAither.Rcheck/00install.out:


install for i386

* installing *source* package 'RNAither' ...
** R
** data
** inst
** preparing package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

install for x64

* installing *source* package 'RNAither' ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'RNAither' as RNAither_2.18.7.zip
* DONE (RNAither)

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

nameusersystemelapsed
BScore0.050.000.05
DRQualControl0.110.000.11
LiWongRank0.070.000.08
MannWhitney0.040.000.03
RankProduct0.330.010.34
SNRQualControl0.010.020.03
Ttest0.040.000.03
ZPRIMEQualControl0.030.000.04
ZScore0.010.000.01
ZScorePerScreen0.020.000.02
ZScorePlot0.040.000.04
ZScorePlotTwo0.020.010.50
channelPlot0.020.020.03
closestToZero0.010.000.02
compareHits0.080.000.08
compareReplicaPlates0.010.000.01
compareReplicateSD0.150.000.14
compareReplicateSDPerScreen0.230.020.27
compareReplicates0.080.010.12
controlDensity0.030.000.03
controlDensityPerPlate0.110.030.16
controlDensityPerScreen0.050.020.06
controlNorm000
createSubset0.010.000.02
discardLabtek000
discardWells000
divNorm0.020.000.02
divideChannels000
eraseDataSetColumn000
findReplicates000
furthestFromZero000
generateDatasetFile0.020.000.01
generateRepMatNoFilter000
generateReplicateMat0.010.000.02
gseaAnalysis 6.12 0.1328.25
hitselectionPval0.030.000.03
hitselectionZscore0.030.000.03
hitselectionZscorePval0.020.000.02
incorporatepValVec0.010.010.03
indexSubset000
joinDatasetFiles0.020.020.03
joinDatasets000
lowessNorm0.010.000.02
mainAnalysis15.90 2.8236.83
makeBoxplot4PlateType0.030.000.03
makeBoxplotControls0.030.000.04
makeBoxplotControlsPerPlate0.090.000.09
makeBoxplotControlsPerScreen0.030.000.03
makeBoxplotPerPlate0.030.020.05
makeBoxplotPerScreen0.020.000.01
multTestAdjust000
numCellQualControl0.030.000.03
orderGeneIDs0.040.000.05
percCellQualControl0.030.000.03
plotBar0.100.010.11
plotControlHisto0.030.040.06
plotControlHistoPerplate0.230.060.65
plotControlHistoPerscreen0.140.000.14
plotHisto0.020.000.02
plotHistoPerplate0.030.030.06
plotHistoPerscreen0.030.000.03
plotQQ0.000.020.02
plotQQperplate0.050.010.06
plotQQperscreen0.010.020.03
quantileNormalization0.020.000.02
replicatesCV0.050.000.05
replicatesSpearmancor0.010.000.01
rms0.000.010.02
rnaither12.42 2.7026.08
saveDataset0.020.000.05
saveOldIntensityColumns000
savepValVec0.010.000.01
spatialDistrib0.440.030.47
spatialDistribHits0.370.111.00
subtractBackground0.020.000.01
sumChannels0.010.000.02
summarizeReps0.110.000.11
summarizeRepsNoFiltering0.060.000.06
trim000
varAdjust0.020.000.02
vennDiag0.060.020.07
volcanoPlot0.050.000.85

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

nameusersystemelapsed
BScore0.050.000.05
DRQualControl0.110.000.11
LiWongRank0.080.000.08
MannWhitney0.040.000.04
RankProduct0.420.010.44
SNRQualControl0.030.000.03
Ttest0.030.000.03
ZPRIMEQualControl0.030.000.03
ZScore0.020.000.01
ZScorePerScreen000
ZScorePlot0.060.000.07
ZScorePlotTwo0.000.000.03
channelPlot0.010.000.02
closestToZero0.020.000.01
compareHits0.060.000.66
compareReplicaPlates0.020.000.02
compareReplicateSD0.150.000.18
compareReplicateSDPerScreen0.240.000.25
compareReplicates0.100.020.16
controlDensity0.050.000.05
controlDensityPerPlate0.140.010.17
controlDensityPerScreen0.030.030.06
controlNorm0.010.000.02
createSubset000
discardLabtek0.000.020.02
discardWells000
divNorm0.020.000.01
divideChannels000
eraseDataSetColumn0.000.020.02
findReplicates000
furthestFromZero000
generateDatasetFile0.010.000.02
generateRepMatNoFilter0.020.000.01
generateReplicateMat0.010.000.02
gseaAnalysis 7.63 0.1232.42
hitselectionPval0.020.000.02
hitselectionZscore0.030.000.03
hitselectionZscorePval0.010.020.03
incorporatepValVec0.030.000.03
indexSubset000
joinDatasetFiles0.020.000.02
joinDatasets0.000.010.01
lowessNorm000
mainAnalysis19.43 2.6242.12
makeBoxplot4PlateType0.050.020.06
makeBoxplotControls0.020.010.03
makeBoxplotControlsPerPlate0.060.070.13
makeBoxplotControlsPerScreen0.040.010.06
makeBoxplotPerPlate0.070.000.06
makeBoxplotPerScreen0.030.000.03
multTestAdjust0.010.000.02
numCellQualControl0.040.020.04
orderGeneIDs0.070.000.08
percCellQualControl0.030.000.03
plotBar0.160.010.17
plotControlHisto0.070.000.08
plotControlHistoPerplate0.320.050.36
plotControlHistoPerscreen0.210.010.75
plotHisto0.040.000.03
plotHistoPerplate0.070.000.08
plotHistoPerscreen0.030.020.04
plotQQ0.020.000.01
plotQQperplate0.070.020.10
plotQQperscreen0.050.000.04
quantileNormalization0.030.000.04
replicatesCV0.030.030.06
replicatesSpearmancor0.030.000.03
rms000
rnaither13.74 3.1632.50
saveDataset0.020.000.02
saveOldIntensityColumns000
savepValVec0.020.000.02
spatialDistrib0.620.021.74
spatialDistribHits0.550.051.13
subtractBackground0.020.000.01
sumChannels0.010.000.02
summarizeReps0.100.000.09
summarizeRepsNoFiltering0.070.000.08
trim0.020.000.02
varAdjust0.010.000.01
vennDiag0.070.010.08
volcanoPlot0.040.000.05