BioC 2.12: CHECK report for RNAither on petty

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: 2013-10-08 23:45:21 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:56:13 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 652.0 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 3.0.1 (2013-05-16)
* 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 ... [35s/36s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [140s/238s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
mainAnalysis 73.632  4.542  91.321
rnaither     19.824  0.593  21.186
gseaAnalysis 10.532  0.186  93.296
* 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	0.094	0.008	0.102
DRQualControl	0.062	0.008	0.080
LiWongRank	0.148	0.007	0.157
MannWhitney	0.079	0.006	0.087
RankProduct	1.174	0.036	1.220
SNRQualControl	0.070	0.010	0.087
Ttest	0.076	0.007	0.083
ZPRIMEQualControl	0.097	0.014	0.141
ZScore	0.048	0.006	0.055
ZScorePerScreen	0.040	0.004	0.044
ZScorePlot	0.241	0.026	0.295
ZScorePlotTwo	0.078	0.011	0.092
channelPlot	0.090	0.009	0.102
closestToZero	0.022	0.003	0.024
compareHits	0.168	0.011	0.178
compareReplicaPlates	0.045	0.007	0.052
compareReplicateSD	0.407	0.019	0.465
compareReplicateSDPerScreen	0.616	0.030	0.660
compareReplicates	0.435	0.035	0.508
controlDensity	0.142	0.012	0.197
controlDensityPerPlate	0.438	0.029	0.535
controlDensityPerScreen	0.214	0.020	0.250
controlNorm	0.043	0.007	0.049
createSubset	0.015	0.004	0.019
discardLabtek	0.025	0.004	0.029
discardWells	0.017	0.004	0.021
divNorm	0.042	0.006	0.049
divideChannels	0.022	0.004	0.027
eraseDataSetColumn	0.038	0.004	0.043
findReplicates	0.020	0.006	0.026
furthestFromZero	0.017	0.005	0.021
generateDatasetFile	0.071	0.013	0.096
generateRepMatNoFilter	0.022	0.004	0.026
generateReplicateMat	0.035	0.004	0.039
gseaAnalysis	10.532	0.186	93.296
hitselectionPval	0.095	0.006	0.101
hitselectionZscore	0.502	0.021	0.526
hitselectionZscorePval	0.07	0.01	0.08
incorporatepValVec	0.059	0.012	0.072
indexSubset	0.015	0.006	0.021
joinDatasetFiles	0.049	0.011	0.060
joinDatasets	0.018	0.006	0.025
lowessNorm	0.034	0.008	0.042
mainAnalysis	73.632	4.542	91.321
makeBoxplot4PlateType	0.136	0.018	0.158
makeBoxplotControls	0.081	0.013	0.096
makeBoxplotControlsPerPlate	0.276	0.022	0.308
makeBoxplotControlsPerScreen	0.141	0.015	0.161
makeBoxplotPerPlate	0.159	0.017	0.181
makeBoxplotPerScreen	0.079	0.012	0.095
multTestAdjust	0.020	0.007	0.026
numCellQualControl	0.071	0.012	0.087
orderGeneIDs	0.118	0.009	0.126
percCellQualControl	0.059	0.012	0.073
plotBar	0.276	0.018	0.304
plotControlHisto	0.157	0.015	0.175
plotControlHistoPerplate	0.647	0.033	0.887
plotControlHistoPerscreen	0.332	0.021	0.405
plotHisto	0.076	0.014	0.122
plotHistoPerplate	0.265	0.028	0.385
plotHistoPerscreen	0.129	0.016	0.154
plotQQ	0.077	0.013	0.094
plotQQperplate	0.245	0.025	0.292
plotQQperscreen	0.131	0.015	0.155
quantileNormalization	0.059	0.009	0.068
replicatesCV	0.156	0.017	0.184
replicatesSpearmancor	0.059	0.011	0.069
rms	0.017	0.008	0.025
rnaither	19.824	0.593	21.186
saveDataset	0.047	0.013	0.064
saveOldIntensityColumns	0.018	0.006	0.028
savepValVec	0.020	0.007	0.031
spatialDistrib	1.239	0.061	1.432
spatialDistribHits	1.339	0.064	1.517
subtractBackground	0.028	0.009	0.039
sumChannels	0.047	0.007	0.056
summarizeReps	0.168	0.007	0.189
summarizeRepsNoFiltering	0.165	0.008	0.184
trim	0.024	0.009	0.033
varAdjust	0.041	0.010	0.055
vennDiag	0.243	0.028	0.313
volcanoPlot	0.169	0.020	0.216