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Package 527/631HostnameOS / ArchBUILDCHECKBUILD BIN
RNAither 2.7.0
Nora Rieber
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RNAither
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: RNAither
Version: 2.7.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RNAither_2.7.0.tar.gz
StartedAt: 2013-01-16 06:00:34 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 06:06:10 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 336.2 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAither.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RNAither/DESCRIPTION’ ... OK
* this is package ‘RNAither’ version ‘2.7.0’
* 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 ‘RNAither’ can be installed ... 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 ... 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
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 33.386  0.836  36.393
rnaither     10.349  0.148  10.526
gseaAnalysis  6.017  0.060   8.464
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck/00check.log’
for details.

RNAither.Rcheck/00install.out:

* 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
   ‘vignetteRNAither.Rnw’ 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (RNAither)

RNAither.Rcheck/RNAither-Ex.timings:

nameusersystemelapsed
BScore0.0840.0000.084
DRQualControl0.0480.0040.052
LiWongRank0.1080.0080.118
MannWhitney0.0840.0000.082
RankProduct0.5160.0040.523
SNRQualControl0.0600.0000.061
Ttest0.0600.0120.069
ZPRIMEQualControl0.0840.0040.089
ZScore0.0480.0040.049
ZScorePerScreen0.0240.0080.033
ZScorePlot0.0760.0080.086
ZScorePlotTwo0.4280.0000.426
channelPlot0.0520.0080.062
closestToZero0.0160.0040.024
compareHits0.1120.0000.113
compareReplicaPlates0.0440.0040.046
compareReplicateSD0.2160.0040.220
compareReplicateSDPerScreen0.2960.0160.315
compareReplicates0.1560.0040.161
controlDensity0.0880.0040.092
controlDensityPerPlate0.2000.0040.203
controlDensityPerScreen0.1080.0040.109
controlNorm0.0360.0000.038
createSubset0.0280.0000.027
discardLabtek0.0240.0000.026
discardWells0.0240.0040.026
divNorm0.0400.0040.044
divideChannels0.0240.0000.022
eraseDataSetColumn0.0320.0000.036
findReplicates0.0280.0000.028
furthestFromZero0.0160.0000.016
generateDatasetFile0.0840.0000.082
generateRepMatNoFilter0.0240.0040.028
generateReplicateMat0.0320.0000.032
gseaAnalysis6.0170.0608.464
hitselectionPval0.0560.0040.062
hitselectionZscore0.0600.0040.072
hitselectionZscorePval0.0760.0120.086
incorporatepValVec0.0480.0120.057
indexSubset0.020.000.02
joinDatasetFiles0.0560.0080.066
joinDatasets0.0200.0040.024
lowessNorm0.0440.0000.044
mainAnalysis33.386 0.83636.393
makeBoxplot4PlateType0.0800.0000.087
makeBoxplotControls0.0640.0040.068
makeBoxplotControlsPerPlate0.1440.0040.147
makeBoxplotControlsPerScreen0.0880.0000.118
makeBoxplotPerPlate0.0960.0040.099
makeBoxplotPerScreen0.0600.0040.065
multTestAdjust0.0280.0000.030
numCellQualControl0.0360.0080.046
orderGeneIDs0.0680.0000.068
percCellQualControl0.0440.0000.044
plotBar0.1120.0040.119
plotControlHisto0.0760.0000.076
plotControlHistoPerplate0.2680.0040.273
plotControlHistoPerscreen0.1440.0080.148
plotHisto0.0360.0000.035
plotHistoPerplate0.0760.0080.083
plotHistoPerscreen0.0520.0000.052
plotQQ0.0360.0040.039
plotQQperplate0.0880.0040.092
plotQQperscreen0.0560.0040.060
quantileNormalization0.0400.0040.047
replicatesCV0.0640.0000.063
replicatesSpearmancor0.0320.0080.039
rms0.0240.0000.022
rnaither10.349 0.14810.526
saveDataset0.0360.0040.040
saveOldIntensityColumns0.0160.0000.020
savepValVec0.020.000.02
spatialDistrib0.5920.0000.590
spatialDistribHits0.6440.0000.643
subtractBackground0.0160.0080.028
sumChannels0.0440.0040.045
summarizeReps0.0920.0000.098
summarizeRepsNoFiltering0.1080.0000.109
trim0.0360.0000.034
varAdjust0.0320.0040.035
vennDiag0.1600.0080.168
volcanoPlot0.1080.0000.110