Hamed Haselimashhadi
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PhenStat |
| Branch: RELEASE_3_8 |
| Last Commit: 30a1e0e |
| Last Changed Date: 2019-04-15 10:05:53 -0400 (Mon, 15 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:50:20 -0400 (Tue, 16 Apr 2019).
| Package 1152/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhenStat 2.18.1 Hamed Haselimashhadi
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: PhenStat |
| Version: 2.18.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PhenStat_2.18.1.tar.gz |
| StartedAt: 2019-04-16 02:04:58 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:07:00 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 121.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings PhenStat_2.18.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/PhenStat.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-pc-linux-gnu (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 ‘2.18.1’ * 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 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 ‘/home/biocbuild/bbs-3.8-bioc/meat/PhenStat.Rcheck/00check.log’ for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 Apr 16 02:06:54 2019
***********************************************
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
3.524 0.088 3.610
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.284 | 0.016 | 0.318 | |
| JSONOutput | 1.168 | 0.004 | 1.185 | |
| LRDataset | 0.056 | 0.000 | 0.057 | |
| PhenList-class | 0.176 | 0.000 | 0.179 | |
| PhenList | 0.192 | 0.000 | 0.192 | |
| PhenStatReport | 0.040 | 0.000 | 0.039 | |
| PhenTestResult-class | 0.644 | 0.004 | 0.646 | |
| PhenTestResult | 0.472 | 0.008 | 0.479 | |
| RRTest | 0.088 | 0.000 | 0.089 | |
| TFDataset | 0.264 | 0.004 | 0.269 | |
| analysedDataset | 0.588 | 0.012 | 0.598 | |
| analysisResults | 0.596 | 0.008 | 0.604 | |
| boxplotResidualBatch | 0.664 | 0.000 | 0.664 | |
| boxplotSexGenotype | 0.072 | 0.004 | 0.077 | |
| boxplotSexGenotypeBatch | 0.212 | 0.000 | 0.212 | |
| boxplotSexGenotypeBatchAdjusted | 0.116 | 0.004 | 0.123 | |
| boxplotSexGenotypeResult | 1.064 | 0.012 | 1.078 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.088 | 0.000 | 0.092 | |
| categoricalBarplot | 0.200 | 0.000 | 0.202 | |
| checkDataset | 0.048 | 0.000 | 0.048 | |
| classificationTag | 0.880 | 0.000 | 0.879 | |
| determiningLambda | 0.504 | 0.136 | 0.641 | |
| dim | 0.036 | 0.000 | 0.037 | |
| finalLRModel | 0.560 | 0.000 | 0.558 | |
| finalModel | 0.548 | 0.004 | 0.553 | |
| finalTFModel | 0.492 | 0.004 | 0.500 | |
| htestPhenStat-class | 0.228 | 0.000 | 0.228 | |
| modelFormula | 0.004 | 0.000 | 0.001 | |
| modelFormulaLR | 0.000 | 0.000 | 0.001 | |
| parserOutputSummary | 0.852 | 0.004 | 0.857 | |
| parserOutputSummaryLR | 1.056 | 0.000 | 1.053 | |
| parserOutputTFSummary | 0.100 | 0.000 | 0.117 | |
| performReverseTransformation | 0 | 0 | 0 | |
| performTransformation | 0 | 0 | 0 | |
| plot.PhenList | 1.872 | 0.000 | 1.882 | |
| plot.PhenTestResult | 2.180 | 0.012 | 2.199 | |
| plotResidualPredicted | 0.796 | 0.004 | 0.801 | |
| printLROutput | 0.860 | 0.000 | 0.861 | |
| printTabStyle | 0.004 | 0.000 | 0.002 | |
| qqplotGenotype | 0.636 | 0.004 | 0.641 | |
| qqplotRandomEffects | 0.780 | 0.000 | 0.781 | |
| qqplotRotatedResiduals | 3.412 | 0.024 | 3.437 | |
| recommendMethod | 0.308 | 0.004 | 0.312 | |
| scatterplotGenotypeWeight | 0.100 | 0.000 | 0.098 | |
| scatterplotGenotypeWeightResult | 0.800 | 0.004 | 0.802 | |
| scatterplotSexGenotypeBatch | 0.080 | 0.000 | 0.082 | |
| scatterplotSexGenotypeBatchResult | 0.792 | 0.004 | 0.797 | |
| startLRModel | 0.472 | 0.000 | 0.471 | |
| startModel | 0.444 | 0.000 | 0.443 | |
| startTFModel | 0.460 | 0.000 | 0.462 | |
| summaryOutput | 0.760 | 0.000 | 0.763 | |
| summaryPhenListResult | 1.272 | 0.004 | 1.280 | |
| testDataset | 2.100 | 0.016 | 2.119 | |
| testFinalLRModel | 0.484 | 0.000 | 0.483 | |
| testFinalModel | 0.860 | 0.000 | 0.862 | |
| vectorOutput | 0.920 | 0.000 | 0.921 | |
| vectorOutputMatrices | 0.156 | 0.000 | 0.157 | |