BioC 3.1: CHECK report for PhenStat on moscato2
This page was generated on 2015-10-09 09:30:52 -0700 (Fri, 09 Oct 2015).
PhenStat 2.2.0
Natasha Karp
| 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/PhenStat | | 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: PhenStat
|
| Version: 2.2.0
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| Command: rm -rf PhenStat.buildbin-libdir PhenStat.Rcheck && mkdir PhenStat.buildbin-libdir PhenStat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PhenStat.buildbin-libdir PhenStat_2.2.0.tar.gz >PhenStat.Rcheck\00install.out 2>&1 && cp PhenStat.Rcheck\00install.out PhenStat-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=PhenStat.buildbin-libdir --install="check:PhenStat-install.out" --force-multiarch --no-vignettes --timings PhenStat_2.2.0.tar.gz
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| StartedAt: 2015-10-09 04:47:41 -0700 (Fri, 09 Oct 2015)
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| EndedAt: 2015-10-09 04:51:04 -0700 (Fri, 09 Oct 2015)
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| EllapsedTime: 202.6 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: PhenStat.Rcheck
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| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf PhenStat.buildbin-libdir PhenStat.Rcheck && mkdir PhenStat.buildbin-libdir PhenStat.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=PhenStat.buildbin-libdir PhenStat_2.2.0.tar.gz >PhenStat.Rcheck\00install.out 2>&1 && cp PhenStat.Rcheck\00install.out PhenStat-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=PhenStat.buildbin-libdir --install="check:PhenStat-install.out" --force-multiarch --no-vignettes --timings PhenStat_2.2.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/PhenStat.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 'PhenStat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PhenStat' version '2.2.0'
* 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 'PhenStat' 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 ... OK
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 6.07 0.06 6.13
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 6.18 0.04 6.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R' [3s]
[3s] OK
** running tests for arch 'x64' ...
Running 'runTests.R' [3s]
[3s] OK
* 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: OK
PhenStat.Rcheck/00install.out:
install for i386
* installing *source* package 'PhenStat' ...
** R
** inst
** preparing package for lazy loading
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
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 'PhenStat' ...
** testing if installed package can be loaded
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 'PhenStat' as PhenStat_2.2.0.zip
* DONE (PhenStat)
PhenStat.Rcheck/examples_i386/PhenStat-Ex.timings:
| name | user | system | elapsed
|
| FisherExactTest | 0.34 | 0.00 | 0.34 |
|
| LRDataset | 0.11 | 0.00 | 0.11 |
|
| PhenList-class | 0.28 | 0.00 | 0.28 |
|
| PhenList | 0.3 | 0.0 | 0.3 |
|
| PhenTestResult-class | 2.19 | 0.06 | 2.24 |
|
| PhenTestResult | 1.45 | 0.09 | 1.55 |
|
| RRTest | 0.12 | 0.00 | 0.12 |
|
| TFDataset | 0.42 | 0.00 | 0.42 |
|
| boxplotResidualBatch | 1.25 | 0.10 | 1.35 |
|
| boxplotSexGenotype | 0.11 | 0.00 | 0.10 |
|
| boxplotSexGenotypeBatch | 0.19 | 0.01 | 0.21 |
|
| boxplotSexGenotypeBatchAdjusted | 0.11 | 0.00 | 0.11 |
|
| categoricalBarplot | 0.31 | 0.02 | 0.32 |
|
| checkDataset | 0.06 | 0.00 | 0.07 |
|
| classificationTag | 1.26 | 0.08 | 1.34 |
|
| determiningLambda | 1.05 | 0.03 | 1.07 |
|
| dim | 0.06 | 0.00 | 0.07 |
|
| finalLRModel | 0.42 | 0.01 | 0.43 |
|
| finalModel | 1.18 | 0.00 | 1.19 |
|
| finalTFModel | 1.05 | 0.00 | 1.04 |
|
| htestPhenStat-class | 0.23 | 0.00 | 0.23 |
|
| modelFormula | 0 | 0 | 0 |
|
| modelFormulaLR | 0 | 0 | 0 |
|
| parserOutputSummary | 1.27 | 0.00 | 1.27 |
|
| parserOutputSummaryLR | 0.42 | 0.02 | 0.43 |
|
| parserOutputTFSummary | 0.15 | 0.00 | 0.16 |
|
| plotResidualPredicted | 1.22 | 0.00 | 1.22 |
|
| printLROutput | 0.52 | 0.00 | 0.51 |
|
| printTabStyle | 0 | 0 | 0 |
|
| qqplotGenotype | 1.19 | 0.00 | 1.18 |
|
| qqplotRandomEffects | 1.43 | 0.00 | 1.44 |
|
| qqplotRotatedResiduals | 6.07 | 0.06 | 6.13 |
|
| recommendMethod | 0.36 | 0.00 | 0.36 |
|
| reverseTransformValues | 0 | 0 | 0 |
|
| scatterplotGenotypeWeight | 0.14 | 0.00 | 0.14 |
|
| scatterplotSexGenotypeBatch | 0.12 | 0.00 | 0.13 |
|
| startLRModel | 0.52 | 0.00 | 0.51 |
|
| startModel | 1.73 | 0.00 | 1.74 |
|
| startTFModel | 0.64 | 0.00 | 0.64 |
|
| summaryOutput | 1.33 | 0.00 | 1.32 |
|
| testDataset | 2.60 | 0.00 | 2.61 |
|
| testFinalLRModel | 0.42 | 0.01 | 0.43 |
|
| testFinalModel | 1.38 | 0.00 | 1.38 |
|
| transformValues | 0 | 0 | 0 |
|
| vectorOutput | 1.37 | 0.00 | 1.37 |
|
| vectorOutputMatrices | 0.2 | 0.0 | 0.2 |
|
PhenStat.Rcheck/examples_x64/PhenStat-Ex.timings:
| name | user | system | elapsed
|
| FisherExactTest | 0.39 | 0.00 | 0.39 |
|
| LRDataset | 0.10 | 0.00 | 0.09 |
|
| PhenList-class | 0.25 | 0.00 | 0.25 |
|
| PhenList | 0.25 | 0.01 | 0.27 |
|
| PhenTestResult-class | 1.81 | 0.00 | 1.81 |
|
| PhenTestResult | 1.81 | 0.04 | 1.84 |
|
| RRTest | 0.11 | 0.00 | 0.11 |
|
| TFDataset | 0.45 | 0.00 | 0.45 |
|
| boxplotResidualBatch | 1.25 | 0.00 | 1.25 |
|
| boxplotSexGenotype | 0.11 | 0.00 | 0.11 |
|
| boxplotSexGenotypeBatch | 0.37 | 0.00 | 0.37 |
|
| boxplotSexGenotypeBatchAdjusted | 0.09 | 0.00 | 0.10 |
|
| categoricalBarplot | 0.22 | 0.00 | 0.21 |
|
| checkDataset | 0.05 | 0.00 | 0.05 |
|
| classificationTag | 1.20 | 0.01 | 1.22 |
|
| determiningLambda | 0.75 | 0.02 | 0.76 |
|
| dim | 0.05 | 0.00 | 0.05 |
|
| finalLRModel | 0.42 | 0.00 | 0.43 |
|
| finalModel | 1.40 | 0.00 | 1.41 |
|
| finalTFModel | 0.80 | 0.00 | 0.79 |
|
| htestPhenStat-class | 0.2 | 0.0 | 0.2 |
|
| modelFormula | 0 | 0 | 0 |
|
| modelFormulaLR | 0 | 0 | 0 |
|
| parserOutputSummary | 1.31 | 0.00 | 1.33 |
|
| parserOutputSummaryLR | 0.57 | 0.00 | 0.57 |
|
| parserOutputTFSummary | 0.21 | 0.00 | 0.21 |
|
| plotResidualPredicted | 1.4 | 0.0 | 1.4 |
|
| printLROutput | 0.45 | 0.00 | 0.45 |
|
| printTabStyle | 0 | 0 | 0 |
|
| qqplotGenotype | 1.38 | 0.00 | 1.37 |
|
| qqplotRandomEffects | 1.24 | 0.00 | 1.25 |
|
| qqplotRotatedResiduals | 6.18 | 0.04 | 6.22 |
|
| recommendMethod | 0.43 | 0.00 | 0.44 |
|
| reverseTransformValues | 0 | 0 | 0 |
|
| scatterplotGenotypeWeight | 0.16 | 0.00 | 0.16 |
|
| scatterplotSexGenotypeBatch | 0.13 | 0.00 | 0.12 |
|
| startLRModel | 0.39 | 0.00 | 0.39 |
|
| startModel | 2.15 | 0.05 | 2.20 |
|
| startTFModel | 1.03 | 0.02 | 1.04 |
|
| summaryOutput | 1.41 | 0.00 | 1.40 |
|
| testDataset | 2.57 | 0.00 | 2.58 |
|
| testFinalLRModel | 0.42 | 0.01 | 0.44 |
|
| testFinalModel | 1.36 | 0.03 | 1.38 |
|
| transformValues | 0 | 0 | 0 |
|
| vectorOutput | 1.58 | 0.00 | 1.58 |
|
| vectorOutputMatrices | 0.21 | 0.00 | 0.22 |
|