BioC 2.13: CHECK report for RNAither on moscato1
This page was generated on 2014-04-05 09:49:45 -0700 (Sat, 05 Apr 2014).
RNAither 2.10.0
Nora Rieber
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/RNAither | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
| Package: RNAither
|
| Version: 2.10.0
|
| Command: rm -rf RNAither.buildbin-libdir && mkdir RNAither.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.10.0.tar.gz >RNAither-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.10.0.tar.gz && mv RNAither.buildbin-libdir/* RNAither.Rcheck/ && rmdir RNAither.buildbin-libdir
|
| StartedAt: 2014-04-05 06:25:29 -0700 (Sat, 05 Apr 2014)
|
| EndedAt: 2014-04-05 06:35:35 -0700 (Sat, 05 Apr 2014)
|
| EllapsedTime: 605.9 seconds
|
| RetCode: 0
|
| Status: OK
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| CheckDir: RNAither.Rcheck
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| Warnings: 0
|
Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/RNAither.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.10.0'
* 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 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
* 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 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'vignetteRNAither.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [154s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainAnalysis 34.18 2.82 93.12
rnaither 15.96 3.25 26.88
gseaAnalysis 6.22 0.03 14.66
** running examples for arch 'x64' ... [182s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainAnalysis 33.07 2.45 42.70
rnaither 12.16 2.62 21.37
gseaAnalysis 5.81 0.17 98.06
* 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
NOTE: There were 3 notes.
See
'D:/biocbld/bbs-2.13-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_2.10.0.zip
* DONE (RNAither)
RNAither.Rcheck/examples_i386/RNAither-Ex.timings:
| name | user | system | elapsed
|
| BScore | 0.05 | 0.01 | 0.06 |
|
| DRQualControl | 0.08 | 0.04 | 0.11 |
|
| LiWongRank | 0.09 | 0.00 | 0.09 |
|
| MannWhitney | 0.06 | 0.00 | 0.07 |
|
| RankProduct | 0.41 | 0.00 | 0.41 |
|
| SNRQualControl | 0.06 | 0.00 | 0.22 |
|
| Ttest | 0.08 | 0.00 | 0.07 |
|
| ZPRIMEQualControl | 0.25 | 0.01 | 0.26 |
|
| ZScore | 0.03 | 0.02 | 0.05 |
|
| ZScorePerScreen | 0.03 | 0.01 | 0.04 |
|
| ZScorePlot | 0.03 | 0.07 | 0.09 |
|
| ZScorePlotTwo | 0.03 | 0.00 | 0.06 |
|
| channelPlot | 0.04 | 0.03 | 0.06 |
|
| closestToZero | 0.03 | 0.00 | 0.03 |
|
| compareHits | 0.09 | 0.00 | 0.09 |
|
| compareReplicaPlates | 0.03 | 0.00 | 0.03 |
|
| compareReplicateSD | 0.17 | 0.00 | 0.17 |
|
| compareReplicateSDPerScreen | 0.23 | 0.01 | 0.25 |
|
| compareReplicates | 0.10 | 0.06 | 0.17 |
|
| controlDensity | 0.07 | 0.04 | 0.09 |
|
| controlDensityPerPlate | 0.28 | 0.01 | 0.47 |
|
| controlDensityPerScreen | 0.13 | 0.02 | 0.14 |
|
| controlNorm | 0.05 | 0.01 | 0.06 |
|
| createSubset | 0.01 | 0.00 | 0.01 |
|
| discardLabtek | 0.03 | 0.00 | 0.03 |
|
| discardWells | 0.02 | 0.00 | 0.02 |
|
| divNorm | 0.03 | 0.00 | 0.03 |
|
| divideChannels | 0 | 0 | 0 |
|
| eraseDataSetColumn | 0.02 | 0.00 | 0.02 |
|
| findReplicates | 0.02 | 0.00 | 0.02 |
|
| furthestFromZero | 0.01 | 0.00 | 0.02 |
|
| generateDatasetFile | 0.05 | 0.00 | 0.04 |
|
| generateRepMatNoFilter | 0.02 | 0.00 | 0.02 |
|
| generateReplicateMat | 0.02 | 0.00 | 0.02 |
|
| gseaAnalysis | 6.22 | 0.03 | 14.66 |
|
| hitselectionPval | 0.05 | 0.00 | 0.05 |
|
| hitselectionZscore | 0.06 | 0.00 | 0.06 |
|
| hitselectionZscorePval | 0.05 | 0.00 | 0.05 |
|
| incorporatepValVec | 0.06 | 0.00 | 0.06 |
|
| indexSubset | 0.02 | 0.00 | 0.02 |
|
| joinDatasetFiles | 0.03 | 0.02 | 0.05 |
|
| joinDatasets | 0.01 | 0.00 | 0.02 |
|
| lowessNorm | 0.04 | 0.00 | 0.05 |
|
| mainAnalysis | 34.18 | 2.82 | 93.12 |
|
| makeBoxplot4PlateType | 0.05 | 0.02 | 0.06 |
|
| makeBoxplotControls | 0.05 | 0.00 | 0.05 |
|
| makeBoxplotControlsPerPlate | 0.08 | 0.01 | 0.10 |
|
| makeBoxplotControlsPerScreen | 0.06 | 0.00 | 0.06 |
|
| makeBoxplotPerPlate | 0.03 | 0.04 | 0.07 |
|
| makeBoxplotPerScreen | 0.03 | 0.00 | 0.03 |
|
| multTestAdjust | 0.02 | 0.00 | 0.01 |
|
| numCellQualControl | 0.04 | 0.01 | 0.07 |
|
| orderGeneIDs | 0.06 | 0.00 | 0.06 |
|
| percCellQualControl | 0.03 | 0.02 | 0.05 |
|
| plotBar | 0.19 | 0.01 | 0.46 |
|
| plotControlHisto | 0.13 | 0.00 | 0.12 |
|
| plotControlHistoPerplate | 0.39 | 0.06 | 0.45 |
|
| plotControlHistoPerscreen | 0.19 | 0.02 | 0.21 |
|
| plotHisto | 0.03 | 0.00 | 0.03 |
|
| plotHistoPerplate | 0.06 | 0.02 | 0.08 |
|
| plotHistoPerscreen | 0.22 | 0.03 | 0.25 |
|
| plotQQ | 0.04 | 0.00 | 0.03 |
|
| plotQQperplate | 0.04 | 0.04 | 0.10 |
|
| plotQQperscreen | 0.04 | 0.00 | 0.05 |
|
| quantileNormalization | 0.05 | 0.00 | 0.05 |
|
| replicatesCV | 0.03 | 0.03 | 0.06 |
|
| replicatesSpearmancor | 0.05 | 0.00 | 0.05 |
|
| rms | 0.02 | 0.00 | 0.01 |
|
| rnaither | 15.96 | 3.25 | 26.88 |
|
| saveDataset | 0.05 | 0.00 | 0.04 |
|
| saveOldIntensityColumns | 0.02 | 0.00 | 0.01 |
|
| savepValVec | 0.01 | 0.00 | 0.02 |
|
| spatialDistrib | 0.59 | 0.11 | 0.70 |
|
| spatialDistribHits | 0.68 | 0.08 | 1.31 |
|
| subtractBackground | 0.03 | 0.00 | 0.03 |
|
| sumChannels | 0.05 | 0.00 | 0.05 |
|
| summarizeReps | 0.14 | 0.00 | 0.14 |
|
| summarizeRepsNoFiltering | 0.14 | 0.00 | 0.14 |
|
| trim | 0.03 | 0.00 | 0.03 |
|
| varAdjust | 0.01 | 0.01 | 0.03 |
|
| vennDiag | 0.19 | 0.02 | 0.20 |
|
| volcanoPlot | 0.09 | 0.01 | 0.10 |
|
RNAither.Rcheck/examples_x64/RNAither-Ex.timings:
| name | user | system | elapsed
|
| BScore | 0.09 | 0.00 | 0.09 |
|
| DRQualControl | 0.16 | 0.03 | 0.21 |
|
| LiWongRank | 0.17 | 0.00 | 0.17 |
|
| MannWhitney | 0.10 | 0.00 | 0.09 |
|
| RankProduct | 0.81 | 0.00 | 0.81 |
|
| SNRQualControl | 0.08 | 0.00 | 0.08 |
|
| Ttest | 0.10 | 0.00 | 0.09 |
|
| ZPRIMEQualControl | 0.03 | 0.01 | 0.04 |
|
| ZScore | 0.03 | 0.00 | 0.03 |
|
| ZScorePerScreen | 0.02 | 0.00 | 0.01 |
|
| ZScorePlot | 0.29 | 0.02 | 0.31 |
|
| ZScorePlotTwo | 0.05 | 0.00 | 0.08 |
|
| channelPlot | 0.04 | 0.00 | 0.03 |
|
| closestToZero | 0.01 | 0.00 | 0.02 |
|
| compareHits | 0.08 | 0.03 | 0.11 |
|
| compareReplicaPlates | 0.03 | 0.00 | 0.97 |
|
| compareReplicateSD | 0.17 | 0.00 | 0.17 |
|
| compareReplicateSDPerScreen | 0.26 | 0.02 | 0.30 |
|
| compareReplicates | 0.10 | 0.01 | 0.23 |
|
| controlDensity | 0.05 | 0.02 | 0.06 |
|
| controlDensityPerPlate | 0.14 | 0.04 | 0.74 |
|
| controlDensityPerScreen | 0.09 | 0.00 | 0.09 |
|
| controlNorm | 0.01 | 0.02 | 0.04 |
|
| createSubset | 0.02 | 0.00 | 0.01 |
|
| discardLabtek | 0.01 | 0.02 | 0.03 |
|
| discardWells | 0.01 | 0.00 | 0.02 |
|
| divNorm | 0.05 | 0.00 | 0.05 |
|
| divideChannels | 0.02 | 0.00 | 0.02 |
|
| eraseDataSetColumn | 0.03 | 0.00 | 0.03 |
|
| findReplicates | 0.03 | 0.00 | 0.04 |
|
| furthestFromZero | 0.00 | 0.01 | 0.01 |
|
| generateDatasetFile | 0.07 | 0.00 | 0.06 |
|
| generateRepMatNoFilter | 0.03 | 0.00 | 0.03 |
|
| generateReplicateMat | 0.29 | 0.00 | 0.30 |
|
| gseaAnalysis | 5.81 | 0.17 | 98.06 |
|
| hitselectionPval | 0.07 | 0.00 | 0.07 |
|
| hitselectionZscore | 0.06 | 0.02 | 0.08 |
|
| hitselectionZscorePval | 0.06 | 0.00 | 0.06 |
|
| incorporatepValVec | 0.06 | 0.00 | 0.06 |
|
| indexSubset | 0.03 | 0.00 | 0.03 |
|
| joinDatasetFiles | 0.28 | 0.00 | 0.28 |
|
| joinDatasets | 0 | 0 | 0 |
|
| lowessNorm | 0.01 | 0.01 | 0.03 |
|
| mainAnalysis | 33.07 | 2.45 | 42.70 |
|
| makeBoxplot4PlateType | 0.07 | 0.00 | 0.06 |
|
| makeBoxplotControls | 0.03 | 0.02 | 0.05 |
|
| makeBoxplotControlsPerPlate | 0.06 | 0.05 | 0.11 |
|
| makeBoxplotControlsPerScreen | 0.06 | 0.00 | 0.06 |
|
| makeBoxplotPerPlate | 0.06 | 0.00 | 0.06 |
|
| makeBoxplotPerScreen | 0.05 | 0.00 | 0.05 |
|
| multTestAdjust | 0.02 | 0.00 | 0.02 |
|
| numCellQualControl | 0.04 | 0.00 | 0.04 |
|
| orderGeneIDs | 0.06 | 0.01 | 0.08 |
|
| percCellQualControl | 0.05 | 0.00 | 0.04 |
|
| plotBar | 0.14 | 0.00 | 0.14 |
|
| plotControlHisto | 0.07 | 0.03 | 0.09 |
|
| plotControlHistoPerplate | 0.34 | 0.02 | 0.36 |
|
| plotControlHistoPerscreen | 0.16 | 0.03 | 0.19 |
|
| plotHisto | 0.03 | 0.00 | 0.03 |
|
| plotHistoPerplate | 0.05 | 0.01 | 0.06 |
|
| plotHistoPerscreen | 0.04 | 0.02 | 0.05 |
|
| plotQQ | 0.03 | 0.00 | 0.03 |
|
| plotQQperplate | 0.07 | 0.02 | 0.08 |
|
| plotQQperscreen | 0.03 | 0.03 | 0.06 |
|
| quantileNormalization | 0.01 | 0.01 | 0.03 |
|
| replicatesCV | 0.06 | 0.00 | 0.06 |
|
| replicatesSpearmancor | 0.03 | 0.00 | 0.03 |
|
| rms | 0.01 | 0.00 | 0.02 |
|
| rnaither | 12.16 | 2.62 | 21.37 |
|
| saveDataset | 0.01 | 0.02 | 0.03 |
|
| saveOldIntensityColumns | 0.02 | 0.00 | 0.02 |
|
| savepValVec | 0.01 | 0.00 | 0.02 |
|
| spatialDistrib | 0.45 | 0.03 | 0.48 |
|
| spatialDistribHits | 0.49 | 0.05 | 0.54 |
|
| subtractBackground | 0.01 | 0.00 | 0.02 |
|
| sumChannels | 0.03 | 0.00 | 0.03 |
|
| summarizeReps | 0.08 | 0.00 | 0.08 |
|
| summarizeRepsNoFiltering | 0.08 | 0.00 | 0.08 |
|
| trim | 0.01 | 0.00 | 0.02 |
|
| varAdjust | 0.02 | 0.00 | 0.02 |
|
| vennDiag | 0.09 | 0.03 | 0.12 |
|
| volcanoPlot | 0.08 | 0.00 | 0.08 |
|