BioC 2.12: CHECK report for RNAither on pelham

Package: RNAither

Version: 2.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAither_2.7.0.tar.gz

StartedAt: 2013-03-24 09:50:26 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 09:58:50 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 504.3 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 beta (2013-03-21 r62346)
* 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 '2.7.0'
* 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 ... [32s/33s] 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/179s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 58.437  4.544  70.569
rnaither     16.692  0.732  18.523
gseaAnalysis  6.995  0.171  60.570
* 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
   'vignetteRNAither.Rnw' 
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
* DONE (RNAither)

name	user	system	elapsed
BScore	0.088	0.008	0.103
DRQualControl	0.059	0.009	0.092
LiWongRank	0.129	0.007	0.140
MannWhitney	0.099	0.006	0.117
RankProduct	0.612	0.027	0.675
SNRQualControl	0.062	0.013	0.083
Ttest	0.065	0.007	0.072
ZPRIMEQualControl	0.088	0.016	0.114
ZScore	0.037	0.006	0.043
ZScorePerScreen	0.033	0.006	0.040
ZScorePlot	0.202	0.024	0.254
ZScorePlotTwo	0.071	0.009	0.082
channelPlot	0.082	0.008	0.093
closestToZero	0.012	0.006	0.018
compareHits	0.123	0.015	0.139
compareReplicaPlates	0.045	0.009	0.054
compareReplicateSD	0.323	0.021	0.352
compareReplicateSDPerScreen	0.509	0.031	0.556
compareReplicates	0.362	0.034	0.435
controlDensity	0.119	0.013	0.141
controlDensityPerPlate	0.366	0.029	0.412
controlDensityPerScreen	0.204	0.019	0.234
controlNorm	0.035	0.008	0.044
createSubset	0.017	0.004	0.021
discardLabtek	0.023	0.005	0.028
discardWells	0.016	0.005	0.020
divNorm	0.039	0.007	0.046
divideChannels	0.021	0.005	0.025
eraseDataSetColumn	0.034	0.004	0.038
findReplicates	0.030	0.008	0.041
furthestFromZero	0.019	0.006	0.024
generateDatasetFile	0.083	0.020	0.102
generateRepMatNoFilter	0.024	0.005	0.030
generateReplicateMat	0.034	0.005	0.038
gseaAnalysis	6.995	0.171	60.570
hitselectionPval	0.073	0.008	0.081
hitselectionZscore	0.077	0.007	0.084
hitselectionZscorePval	0.073	0.008	0.080
incorporatepValVec	0.065	0.008	0.074
indexSubset	0.026	0.004	0.030
joinDatasetFiles	0.057	0.007	0.065
joinDatasets	0.024	0.004	0.027
lowessNorm	0.049	0.006	0.055
mainAnalysis	58.437	4.544	70.569
makeBoxplot4PlateType	0.125	0.018	0.167
makeBoxplotControls	0.082	0.012	0.097
makeBoxplotControlsPerPlate	0.235	0.024	0.346
makeBoxplotControlsPerScreen	0.137	0.015	0.160
makeBoxplotPerPlate	0.131	0.016	0.150
makeBoxplotPerScreen	0.077	0.011	0.092
multTestAdjust	0.018	0.005	0.023
numCellQualControl	0.082	0.013	0.096
orderGeneIDs	0.110	0.009	0.119
percCellQualControl	0.076	0.012	0.095
plotBar	0.232	0.016	0.266
plotControlHisto	0.140	0.011	0.157
plotControlHistoPerplate	0.546	0.027	0.591
plotControlHistoPerscreen	0.269	0.018	0.308
plotHisto	0.073	0.013	0.090
plotHistoPerplate	0.209	0.025	0.247
plotHistoPerscreen	0.132	0.017	0.155
plotQQ	0.076	0.013	0.096
plotQQperplate	0.216	0.025	0.269
plotQQperscreen	0.116	0.014	0.135
quantileNormalization	0.065	0.009	0.073
replicatesCV	0.148	0.019	0.175
replicatesSpearmancor	0.059	0.010	0.073
rms	0.030	0.008	0.039
rnaither	16.692	0.732	18.523
saveDataset	0.039	0.009	0.049
saveOldIntensityColumns	0.020	0.007	0.027
savepValVec	0.015	0.006	0.022
spatialDistrib	0.945	0.057	1.027
spatialDistribHits	1.029	0.059	1.127
subtractBackground	0.023	0.009	0.035
sumChannels	0.041	0.008	0.049
summarizeReps	0.128	0.006	0.134
summarizeRepsNoFiltering	0.152	0.008	0.169
trim	0.022	0.009	0.031
varAdjust	0.032	0.010	0.042
vennDiag	0.201	0.028	0.234
volcanoPlot	0.134	0.021	0.160

Summary

Command output