BioC 3.1: CHECK report for RNAither on moscato2
This page was generated on 2015-10-09 09:28:22 -0700 (Fri, 09 Oct 2015).
RNAither 2.16.0
Lars Kaderali
| Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/RNAither | | Last Changed Rev: 102591 / Revision: 109384 | | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK | |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: RNAither
|
| Version: 2.16.0
|
| Command: rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.16.0.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.16.0.tar.gz
|
| StartedAt: 2015-10-09 05:41:06 -0700 (Fri, 09 Oct 2015)
|
| EndedAt: 2015-10-09 05:48:56 -0700 (Fri, 09 Oct 2015)
|
| EllapsedTime: 469.9 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: RNAither.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf RNAither.buildbin-libdir RNAither.Rcheck && mkdir RNAither.buildbin-libdir RNAither.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAither.buildbin-libdir RNAither_2.16.0.tar.gz >RNAither.Rcheck\00install.out 2>&1 && cp RNAither.Rcheck\00install.out RNAither-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=RNAither.buildbin-libdir --install="check:RNAither-install.out" --force-multiarch --no-vignettes --timings RNAither_2.16.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/RNAither.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RNAither/DESCRIPTION' ... OK
* this is package 'RNAither' version '2.16.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
PlotSpatialDistrib: no visible global function definition for
'brewer.pal'
RankProduct: no visible global function definition for 'RP'
compareReplicateSD: no visible global function definition for
'brewer.pal'
compareReplicateSDPerScreen: no visible global function definition for
'brewer.pal'
spatialDistrib: no visible global function definition for 'brewer.pal'
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [81s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainAnalysis 32.26 3.27 40.81
rnaither 11.93 2.46 16.23
gseaAnalysis 7.02 0.13 9.64
** running examples for arch 'x64' ... [89s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
mainAnalysis 35.62 2.68 43.03
rnaither 13.79 3.15 19.22
gseaAnalysis 7.66 0.22 10.26
* 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
* DONE
Status: 3 NOTEs
See
'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
install for x64
* installing *source* package 'RNAither' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'RNAither' as RNAither_2.16.0.zip
* DONE (RNAither)
RNAither.Rcheck/examples_i386/RNAither-Ex.timings:
| name | user | system | elapsed
|
| BScore | 0.03 | 0.00 | 0.04 |
|
| DRQualControl | 0.10 | 0.03 | 0.14 |
|
| LiWongRank | 0.04 | 0.02 | 0.06 |
|
| MannWhitney | 0.03 | 0.00 | 0.03 |
|
| RankProduct | 0.27 | 0.02 | 0.28 |
|
| SNRQualControl | 0.03 | 0.01 | 0.05 |
|
| Ttest | 0.02 | 0.00 | 0.01 |
|
| ZPRIMEQualControl | 0.02 | 0.00 | 0.01 |
|
| ZScore | 0.00 | 0.02 | 0.02 |
|
| ZScorePerScreen | 0.01 | 0.00 | 0.02 |
|
| ZScorePlot | 0.05 | 0.00 | 0.04 |
|
| ZScorePlotTwo | 0.03 | 0.00 | 0.03 |
|
| channelPlot | 0.02 | 0.01 | 0.03 |
|
| closestToZero | 0.01 | 0.00 | 0.02 |
|
| compareHits | 0.05 | 0.00 | 0.05 |
|
| compareReplicaPlates | 0.02 | 0.02 | 0.03 |
|
| compareReplicateSD | 0.18 | 0.00 | 0.19 |
|
| compareReplicateSDPerScreen | 0.55 | 0.09 | 0.65 |
|
| compareReplicates | 0.12 | 0.02 | 0.31 |
|
| controlDensity | 0.07 | 0.01 | 0.08 |
|
| controlDensityPerPlate | 0.21 | 0.00 | 0.23 |
|
| controlDensityPerScreen | 0.08 | 0.02 | 0.09 |
|
| controlNorm | 0.01 | 0.00 | 0.02 |
|
| createSubset | 0 | 0 | 0 |
|
| discardLabtek | 0 | 0 | 0 |
|
| discardWells | 0 | 0 | 0 |
|
| divNorm | 0.02 | 0.00 | 0.02 |
|
| divideChannels | 0 | 0 | 0 |
|
| eraseDataSetColumn | 0.02 | 0.00 | 0.01 |
|
| findReplicates | 0.00 | 0.01 | 0.02 |
|
| furthestFromZero | 0 | 0 | 0 |
|
| generateDatasetFile | 0.03 | 0.00 | 0.03 |
|
| generateRepMatNoFilter | 0.01 | 0.00 | 0.01 |
|
| generateReplicateMat | 0.02 | 0.00 | 0.02 |
|
| gseaAnalysis | 7.02 | 0.13 | 9.64 |
|
| hitselectionPval | 0.03 | 0.00 | 0.03 |
|
| hitselectionZscore | 0.05 | 0.00 | 0.05 |
|
| hitselectionZscorePval | 0.03 | 0.00 | 0.03 |
|
| incorporatepValVec | 0.02 | 0.00 | 0.01 |
|
| indexSubset | 0.01 | 0.00 | 0.02 |
|
| joinDatasetFiles | 0.02 | 0.01 | 0.03 |
|
| joinDatasets | 0 | 0 | 0 |
|
| lowessNorm | 0.01 | 0.00 | 0.02 |
|
| mainAnalysis | 32.26 | 3.27 | 40.81 |
|
| makeBoxplot4PlateType | 0.04 | 0.00 | 0.05 |
|
| makeBoxplotControls | 0.03 | 0.00 | 0.03 |
|
| makeBoxplotControlsPerPlate | 0.11 | 0.01 | 0.12 |
|
| makeBoxplotControlsPerScreen | 0.06 | 0.00 | 0.07 |
|
| makeBoxplotPerPlate | 0.06 | 0.00 | 0.06 |
|
| makeBoxplotPerScreen | 0.03 | 0.00 | 0.03 |
|
| multTestAdjust | 0 | 0 | 0 |
|
| numCellQualControl | 0.03 | 0.02 | 0.05 |
|
| orderGeneIDs | 0.08 | 0.00 | 0.08 |
|
| percCellQualControl | 0.03 | 0.00 | 0.03 |
|
| plotBar | 0.11 | 0.00 | 0.11 |
|
| plotControlHisto | 0.06 | 0.00 | 0.06 |
|
| plotControlHistoPerplate | 0.28 | 0.01 | 0.30 |
|
| plotControlHistoPerscreen | 0.13 | 0.02 | 0.14 |
|
| plotHisto | 0.00 | 0.01 | 0.01 |
|
| plotHistoPerplate | 0.06 | 0.00 | 0.07 |
|
| plotHistoPerscreen | 0.03 | 0.00 | 0.03 |
|
| plotQQ | 0.02 | 0.00 | 0.01 |
|
| plotQQperplate | 0.06 | 0.02 | 0.08 |
|
| plotQQperscreen | 0.02 | 0.01 | 0.03 |
|
| quantileNormalization | 0.01 | 0.00 | 0.02 |
|
| replicatesCV | 0.03 | 0.02 | 0.05 |
|
| replicatesSpearmancor | 0.02 | 0.00 | 0.01 |
|
| rms | 0 | 0 | 0 |
|
| rnaither | 11.93 | 2.46 | 16.23 |
|
| saveDataset | 0.02 | 0.00 | 0.01 |
|
| saveOldIntensityColumns | 0 | 0 | 0 |
|
| savepValVec | 0.01 | 0.00 | 0.02 |
|
| spatialDistrib | 0.38 | 0.02 | 0.39 |
|
| spatialDistribHits | 0.34 | 0.09 | 0.60 |
|
| subtractBackground | 0.02 | 0.00 | 0.02 |
|
| sumChannels | 0 | 0 | 0 |
|
| summarizeReps | 0.08 | 0.00 | 0.08 |
|
| summarizeRepsNoFiltering | 0.06 | 0.00 | 0.06 |
|
| trim | 0 | 0 | 0 |
|
| varAdjust | 0.01 | 0.00 | 0.02 |
|
| vennDiag | 0.07 | 0.02 | 0.07 |
|
| volcanoPlot | 0.03 | 0.02 | 0.05 |
|
RNAither.Rcheck/examples_x64/RNAither-Ex.timings:
| name | user | system | elapsed
|
| BScore | 0.03 | 0.00 | 0.03 |
|
| DRQualControl | 0.11 | 0.00 | 0.69 |
|
| LiWongRank | 0.06 | 0.00 | 0.06 |
|
| MannWhitney | 0.05 | 0.00 | 0.05 |
|
| RankProduct | 0.48 | 0.00 | 0.48 |
|
| SNRQualControl | 0.05 | 0.00 | 0.05 |
|
| Ttest | 0.03 | 0.00 | 0.03 |
|
| ZPRIMEQualControl | 0.03 | 0.00 | 0.03 |
|
| ZScore | 0.36 | 0.00 | 0.36 |
|
| ZScorePerScreen | 0 | 0 | 0 |
|
| ZScorePlot | 0.04 | 0.02 | 0.04 |
|
| ZScorePlotTwo | 0.00 | 0.01 | 0.18 |
|
| channelPlot | 0.03 | 0.00 | 0.03 |
|
| closestToZero | 0 | 0 | 0 |
|
| compareHits | 0.06 | 0.00 | 0.06 |
|
| compareReplicaPlates | 0.02 | 0.02 | 0.03 |
|
| compareReplicateSD | 0.20 | 0.03 | 0.24 |
|
| compareReplicateSDPerScreen | 0.19 | 0.01 | 0.21 |
|
| compareReplicates | 0.10 | 0.00 | 0.13 |
|
| controlDensity | 0.05 | 0.00 | 0.05 |
|
| controlDensityPerPlate | 0.13 | 0.04 | 0.17 |
|
| controlDensityPerScreen | 0.06 | 0.00 | 0.06 |
|
| controlNorm | 0.02 | 0.00 | 0.02 |
|
| createSubset | 0 | 0 | 0 |
|
| discardLabtek | 0 | 0 | 0 |
|
| discardWells | 0.02 | 0.00 | 0.02 |
|
| divNorm | 0 | 0 | 0 |
|
| divideChannels | 0 | 0 | 0 |
|
| eraseDataSetColumn | 0 | 0 | 0 |
|
| findReplicates | 0.00 | 0.01 | 0.02 |
|
| furthestFromZero | 0 | 0 | 0 |
|
| generateDatasetFile | 0.02 | 0.00 | 0.01 |
|
| generateRepMatNoFilter | 0 | 0 | 0 |
|
| generateReplicateMat | 0.01 | 0.00 | 0.02 |
|
| gseaAnalysis | 7.66 | 0.22 | 10.26 |
|
| hitselectionPval | 0.02 | 0.00 | 0.02 |
|
| hitselectionZscore | 0.03 | 0.00 | 0.03 |
|
| hitselectionZscorePval | 0.03 | 0.00 | 0.03 |
|
| incorporatepValVec | 0.02 | 0.00 | 0.03 |
|
| indexSubset | 0 | 0 | 0 |
|
| joinDatasetFiles | 0.02 | 0.00 | 0.02 |
|
| joinDatasets | 0.01 | 0.00 | 0.01 |
|
| lowessNorm | 0 | 0 | 0 |
|
| mainAnalysis | 35.62 | 2.68 | 43.03 |
|
| makeBoxplot4PlateType | 0.03 | 0.03 | 0.06 |
|
| makeBoxplotControls | 0.03 | 0.00 | 0.03 |
|
| makeBoxplotControlsPerPlate | 0.11 | 0.00 | 0.11 |
|
| makeBoxplotControlsPerScreen | 0.07 | 0.00 | 0.06 |
|
| makeBoxplotPerPlate | 0.06 | 0.00 | 0.06 |
|
| makeBoxplotPerScreen | 0.01 | 0.03 | 0.05 |
|
| multTestAdjust | 0 | 0 | 0 |
|
| numCellQualControl | 0.04 | 0.02 | 0.05 |
|
| orderGeneIDs | 0.06 | 0.00 | 0.06 |
|
| percCellQualControl | 0.03 | 0.00 | 0.03 |
|
| plotBar | 0.19 | 0.00 | 0.19 |
|
| plotControlHisto | 0.11 | 0.00 | 0.11 |
|
| plotControlHistoPerplate | 0.37 | 0.08 | 0.78 |
|
| plotControlHistoPerscreen | 0.20 | 0.01 | 0.21 |
|
| plotHisto | 0.00 | 0.02 | 0.02 |
|
| plotHistoPerplate | 0.10 | 0.00 | 0.09 |
|
| plotHistoPerscreen | 0.03 | 0.02 | 0.05 |
|
| plotQQ | 0.03 | 0.00 | 0.03 |
|
| plotQQperplate | 0.06 | 0.03 | 0.10 |
|
| plotQQperscreen | 0.05 | 0.00 | 0.04 |
|
| quantileNormalization | 0.03 | 0.00 | 0.03 |
|
| replicatesCV | 0.06 | 0.00 | 0.07 |
|
| replicatesSpearmancor | 0.02 | 0.01 | 0.03 |
|
| rms | 0 | 0 | 0 |
|
| rnaither | 13.79 | 3.15 | 19.22 |
|
| saveDataset | 0.03 | 0.00 | 0.03 |
|
| saveOldIntensityColumns | 0 | 0 | 0 |
|
| savepValVec | 0.00 | 0.02 | 0.01 |
|
| spatialDistrib | 0.44 | 0.00 | 0.44 |
|
| spatialDistribHits | 0.40 | 0.01 | 0.44 |
|
| subtractBackground | 0.02 | 0.00 | 0.01 |
|
| sumChannels | 0.01 | 0.00 | 0.02 |
|
| summarizeReps | 0.08 | 0.00 | 0.08 |
|
| summarizeRepsNoFiltering | 0.08 | 0.00 | 0.07 |
|
| trim | 0.02 | 0.00 | 0.02 |
|
| varAdjust | 0 | 0 | 0 |
|
| vennDiag | 0.04 | 0.04 | 0.08 |
|
| volcanoPlot | 0.03 | 0.01 | 0.05 |
|