Hamed Haselimashhadi
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/PhenStat |
| Branch: RELEASE_3_7 |
| Last Commit: dcdc9c6 |
| Last Changed Date: 2018-09-07 12:00:59 -0400 (Fri, 07 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:52:18 -0400 (Wed, 17 Oct 2018).
| Package 1089/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhenStat 2.17.0 Hamed Haselimashhadi
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: PhenStat |
| Version: 2.17.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhenStat_2.17.0.tar.gz |
| StartedAt: 2018-10-16 23:13:40 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 23:16:20 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 160.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PhenStat_2.17.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/PhenStat.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PhenStat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PhenStat’ version ‘2.17.0’
* 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 ‘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
* 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: ‘SmoothWin’
All declared Imports should be used.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 5.096 0.037 5.156
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/PhenStat.Rcheck/00check.log’
for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘PhenStat’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (PhenStat)
PhenStat.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("PhenStat")
>=========================================================================<
This version of PhenStat includes *FEWER* functions than the previous ones
You *still* can use the previous functions by using `:::`. For example :
PhenStat:::boxplotSexGenotype or PhenStat:::FisherExactTest
*** Want to know what is new in this version? run PhenStat:::WhatIsNew()
>=========================================================================<
RUNIT TEST PROTOCOL -- Tue Oct 16 23:16:10 2018
***********************************************
Number of test functions: 0
Number of errors: 0
Number of failures: 0
1 Test Suite :
PhenStat RUnit Tests - 0 test functions, 0 errors, 0 failures
Number of test functions: 0
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
3.757 0.304 4.052
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.327 | 0.045 | 0.376 | |
| JSONOutput | 1.320 | 0.039 | 1.374 | |
| LRDataset | 0.086 | 0.004 | 0.089 | |
| PhenList-class | 0.244 | 0.009 | 0.257 | |
| PhenList | 0.282 | 0.007 | 0.298 | |
| PhenStatReport | 0.065 | 0.001 | 0.065 | |
| PhenTestResult-class | 1.033 | 0.016 | 1.052 | |
| PhenTestResult | 0.702 | 0.009 | 0.711 | |
| RRTest | 0.135 | 0.001 | 0.137 | |
| TFDataset | 0.453 | 0.018 | 0.474 | |
| analysedDataset | 1.068 | 0.021 | 1.096 | |
| analysisResults | 1.006 | 0.005 | 1.018 | |
| boxplotResidualBatch | 1.025 | 0.008 | 1.041 | |
| boxplotSexGenotype | 0.149 | 0.005 | 0.153 | |
| boxplotSexGenotypeBatch | 0.211 | 0.003 | 0.219 | |
| boxplotSexGenotypeBatchAdjusted | 0.117 | 0.004 | 0.123 | |
| boxplotSexGenotypeResult | 1.243 | 0.015 | 1.272 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.103 | 0.001 | 0.109 | |
| categoricalBarplot | 0.269 | 0.008 | 0.278 | |
| checkDataset | 0.081 | 0.001 | 0.081 | |
| classificationTag | 1.007 | 0.009 | 1.022 | |
| determiningLambda | 0.984 | 0.237 | 1.228 | |
| dim | 0.070 | 0.001 | 0.072 | |
| finalLRModel | 0.684 | 0.012 | 0.699 | |
| finalModel | 0.773 | 0.013 | 0.789 | |
| finalTFModel | 1.041 | 0.012 | 1.059 | |
| htestPhenStat-class | 0.272 | 0.006 | 0.279 | |
| modelFormula | 0.002 | 0.000 | 0.002 | |
| modelFormulaLR | 0.002 | 0.001 | 0.002 | |
| parserOutputSummary | 1.032 | 0.008 | 1.046 | |
| parserOutputSummaryLR | 0.964 | 0.018 | 0.988 | |
| parserOutputTFSummary | 0.195 | 0.001 | 0.200 | |
| performReverseTransformation | 0.002 | 0.000 | 0.002 | |
| performTransformation | 0.001 | 0.000 | 0.002 | |
| plot.PhenList | 3.046 | 0.046 | 3.119 | |
| plot.PhenTestResult | 3.072 | 0.040 | 3.151 | |
| plotResidualPredicted | 1.064 | 0.015 | 1.101 | |
| printLROutput | 0.735 | 0.006 | 0.751 | |
| printTabStyle | 0.003 | 0.000 | 0.003 | |
| qqplotGenotype | 1.010 | 0.003 | 1.023 | |
| qqplotRandomEffects | 1.029 | 0.005 | 1.039 | |
| qqplotRotatedResiduals | 5.096 | 0.037 | 5.156 | |
| recommendMethod | 0.482 | 0.003 | 0.487 | |
| scatterplotGenotypeWeight | 0.145 | 0.005 | 0.150 | |
| scatterplotGenotypeWeightResult | 1.274 | 0.015 | 1.295 | |
| scatterplotSexGenotypeBatch | 0.119 | 0.002 | 0.121 | |
| scatterplotSexGenotypeBatchResult | 1.313 | 0.009 | 1.330 | |
| startLRModel | 0.641 | 0.008 | 0.651 | |
| startModel | 0.778 | 0.003 | 0.785 | |
| startTFModel | 0.798 | 0.004 | 0.803 | |
| summaryOutput | 1.201 | 0.019 | 1.223 | |
| summaryPhenListResult | 1.181 | 0.022 | 1.206 | |
| testDataset | 2.776 | 0.034 | 2.826 | |
| testFinalLRModel | 0.698 | 0.007 | 0.709 | |
| testFinalModel | 1.198 | 0.005 | 1.206 | |
| vectorOutput | 1.295 | 0.016 | 1.315 | |
| vectorOutputMatrices | 0.279 | 0.004 | 0.284 | |