Hamed Haselimashhadi
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/PhenStat |
| Branch: RELEASE_3_10 |
| Last Commit: 85472df |
| Last Changed Date: 2019-10-29 13:08:51 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:39:31 -0400 (Wed, 15 Apr 2020).
| Package 1258/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhenStat 2.22.0 Hamed Haselimashhadi
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: PhenStat |
| Version: 2.22.0 |
| 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_2.22.0.tar.gz |
| StartedAt: 2020-04-15 04:35:28 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:38:15 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 166.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/PhenStat.Rcheck’ * using R version 3.6.3 (2020-02-29) * 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 ‘2.22.0’ * 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 * 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-3.10-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/3.6/Resources/library’ * installing *source* package ‘PhenStat’ ... ** using staged installation ** 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 from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PhenStat)
PhenStat.Rcheck/tests/runTests.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 -- Wed Apr 15 04:38:07 2020
***********************************************
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
4.272 0.325 4.571
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.312 | 0.028 | 0.342 | |
| JSONOutput | 1.276 | 0.041 | 1.324 | |
| LRDataset | 0.075 | 0.006 | 0.084 | |
| PhenList-class | 0.292 | 0.012 | 0.306 | |
| PhenList | 0.316 | 0.006 | 0.323 | |
| PhenStatReport | 0.067 | 0.001 | 0.072 | |
| PhenTestResult-class | 1.120 | 0.018 | 1.144 | |
| PhenTestResult | 0.866 | 0.011 | 0.884 | |
| RRTest | 0.158 | 0.002 | 0.164 | |
| TFDataset | 0.513 | 0.007 | 0.529 | |
| analysedDataset | 1.056 | 0.019 | 1.077 | |
| analysisResults | 0.980 | 0.010 | 0.998 | |
| boxplotResidualBatch | 1.128 | 0.019 | 1.162 | |
| boxplotSexGenotype | 0.121 | 0.003 | 0.124 | |
| boxplotSexGenotypeBatch | 0.249 | 0.004 | 0.255 | |
| boxplotSexGenotypeBatchAdjusted | 0.108 | 0.004 | 0.118 | |
| boxplotSexGenotypeResult | 1.291 | 0.011 | 1.327 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.109 | 0.001 | 0.111 | |
| categoricalBarplot | 0.299 | 0.008 | 0.308 | |
| checkDataset | 0.065 | 0.001 | 0.065 | |
| classificationTag | 0.969 | 0.005 | 0.975 | |
| determiningLambda | 0.948 | 0.262 | 1.211 | |
| dim | 0.060 | 0.001 | 0.061 | |
| finalLRModel | 0.733 | 0.016 | 0.751 | |
| finalModel | 0.799 | 0.013 | 0.817 | |
| finalTFModel | 1.054 | 0.013 | 1.092 | |
| htestPhenStat-class | 0.268 | 0.003 | 0.277 | |
| modelFormula | 0.001 | 0.000 | 0.000 | |
| modelFormulaLR | 0.001 | 0.000 | 0.001 | |
| parserOutputSummary | 1.001 | 0.017 | 1.031 | |
| parserOutputSummaryLR | 0.971 | 0.016 | 0.991 | |
| parserOutputTFSummary | 0.210 | 0.004 | 0.219 | |
| performReverseTransformation | 0 | 0 | 0 | |
| performTransformation | 0.001 | 0.000 | 0.001 | |
| plot.PhenList | 3.212 | 0.043 | 3.416 | |
| plot.PhenTestResult | 2.866 | 0.038 | 2.910 | |
| plotResidualPredicted | 0.929 | 0.005 | 0.936 | |
| printLROutput | 0.702 | 0.007 | 0.711 | |
| printTabStyle | 0.001 | 0.000 | 0.001 | |
| qqplotGenotype | 0.980 | 0.004 | 0.986 | |
| qqplotRandomEffects | 0.929 | 0.004 | 0.935 | |
| qqplotRotatedResiduals | 4.657 | 0.040 | 4.718 | |
| recommendMethod | 0.461 | 0.002 | 0.470 | |
| scatterplotGenotypeWeight | 0.156 | 0.002 | 0.160 | |
| scatterplotGenotypeWeightResult | 1.257 | 0.009 | 1.284 | |
| scatterplotSexGenotypeBatch | 0.145 | 0.002 | 0.150 | |
| scatterplotSexGenotypeBatchResult | 1.316 | 0.010 | 1.343 | |
| startLRModel | 0.674 | 0.007 | 0.693 | |
| startModel | 0.762 | 0.005 | 0.771 | |
| startTFModel | 0.864 | 0.005 | 0.876 | |
| summaryOutput | 1.167 | 0.012 | 1.196 | |
| summaryPhenListResult | 1.251 | 0.013 | 1.272 | |
| testDataset | 3.063 | 0.041 | 3.132 | |
| testFinalLRModel | 0.669 | 0.005 | 0.677 | |
| testFinalModel | 1.174 | 0.003 | 1.180 | |
| vectorOutput | 1.201 | 0.017 | 1.223 | |
| vectorOutputMatrices | 0.243 | 0.002 | 0.247 | |