BioC 2.12: CHECK report for RNAither on pelham

Package: RNAither

Version: 2.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.8.0.tar.gz

StartedAt: 2013-05-01 10:26:18 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 10:33:59 -0700 (Wed, 01 May 2013)

EllapsedTime: 460.5 seconds

RetCode: 0

Status: OK

CheckDir: RNAither.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.8.0'
* 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 ... [31s/32s] 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 ... [116s/136s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 57.796  4.495  70.546
rnaither     15.970  0.760  22.601
gseaAnalysis  7.994  0.190  12.828
* 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/RNAither.Rcheck/00check.log'
for details.

* 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.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.087	0.010	0.096
DRQualControl	0.066	0.010	0.077
LiWongRank	0.120	0.007	0.131
MannWhitney	0.072	0.007	0.079
RankProduct	1.036	0.027	1.079
SNRQualControl	0.064	0.013	0.080
Ttest	0.070	0.009	0.080
ZPRIMEQualControl	0.090	0.015	0.110
ZScore	0.046	0.007	0.056
ZScorePerScreen	0.038	0.007	0.047
ZScorePlot	0.200	0.023	0.241
ZScorePlotTwo	0.065	0.008	0.077
channelPlot	0.074	0.008	0.086
closestToZero	0.012	0.006	0.021
compareHits	0.124	0.017	0.141
compareReplicaPlates	0.039	0.007	0.047
compareReplicateSD	0.334	0.021	0.364
compareReplicateSDPerScreen	0.485	0.031	0.545
compareReplicates	0.375	0.037	0.447
controlDensity	0.133	0.015	0.162
controlDensityPerPlate	0.360	0.031	0.421
controlDensityPerScreen	0.202	0.021	0.241
controlNorm	0.036	0.007	0.043
createSubset	0.022	0.005	0.027
discardLabtek	0.016	0.004	0.020
discardWells	0.022	0.004	0.026
divNorm	0.042	0.006	0.048
divideChannels	0.020	0.003	0.023
eraseDataSetColumn	0.031	0.005	0.035
findReplicates	0.018	0.006	0.024
furthestFromZero	0.020	0.006	0.025
generateDatasetFile	0.058	0.014	0.072
generateRepMatNoFilter	0.027	0.005	0.031
generateReplicateMat	0.032	0.004	0.036
gseaAnalysis	7.994	0.190	12.828
hitselectionPval	0.574	0.017	0.595
hitselectionZscore	0.056	0.011	0.068
hitselectionZscorePval	0.057	0.011	0.069
incorporatepValVec	0.045	0.013	0.058
indexSubset	0.458	0.010	0.469
joinDatasetFiles	0.043	0.012	0.056
joinDatasets	0.018	0.008	0.026
lowessNorm	0.035	0.010	0.046
mainAnalysis	57.796	4.495	70.546
makeBoxplot4PlateType	0.110	0.017	0.175
makeBoxplotControls	0.071	0.013	0.087
makeBoxplotControlsPerPlate	0.229	0.024	0.291
makeBoxplotControlsPerScreen	0.133	0.017	0.197
makeBoxplotPerPlate	0.126	0.016	0.163
makeBoxplotPerScreen	0.068	0.012	0.083
multTestAdjust	0.017	0.006	0.024
numCellQualControl	0.062	0.012	0.074
orderGeneIDs	0.094	0.009	0.103
percCellQualControl	0.059	0.011	0.073
plotBar	0.210	0.016	0.234
plotControlHisto	0.134	0.014	0.161
plotControlHistoPerplate	0.526	0.030	0.586
plotControlHistoPerscreen	0.262	0.019	0.293
plotHisto	0.067	0.014	0.089
plotHistoPerplate	0.204	0.024	0.240
plotHistoPerscreen	0.112	0.016	0.135
plotQQ	0.068	0.013	0.084
plotQQperplate	0.203	0.024	0.245
plotQQperscreen	0.117	0.017	0.141
quantileNormalization	0.06	0.01	0.07
replicatesCV	0.127	0.015	0.163
replicatesSpearmancor	0.055	0.012	0.075
rms	0.020	0.008	0.029
rnaither	15.970	0.760	22.601
saveDataset	0.042	0.009	0.051
saveOldIntensityColumns	0.017	0.006	0.024
savepValVec	0.471	0.010	0.596
spatialDistrib	0.977	0.059	1.148
spatialDistribHits	1.057	0.073	1.172
subtractBackground	0.023	0.011	0.034
sumChannels	0.036	0.009	0.050
summarizeReps	0.118	0.008	0.127
summarizeRepsNoFiltering	0.113	0.006	0.120
trim	0.021	0.009	0.034
varAdjust	0.027	0.009	0.041
vennDiag	0.182	0.026	0.227
volcanoPlot	0.133	0.020	0.175

Summary

Command output