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 12:08:15 -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: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PhenStat_2.22.0.tar.gz |
| StartedAt: 2020-04-15 01:59:39 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 02:02:10 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 150.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PhenStat_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PhenStat.Rcheck’ * using R version 3.6.3 (2020-02-29) * 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 ‘2.22.0’ * 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 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-3.10-bioc/meat/PhenStat.Rcheck/00check.log’ for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-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 -- Wed Apr 15 02:02:04 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
3.772 0.140 3.984
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.260 | 0.016 | 0.291 | |
| JSONOutput | 1.080 | 0.012 | 1.107 | |
| LRDataset | 0.084 | 0.000 | 0.102 | |
| PhenList-class | 0.268 | 0.008 | 0.276 | |
| PhenList | 0.276 | 0.000 | 0.299 | |
| PhenStatReport | 0.048 | 0.004 | 0.050 | |
| PhenTestResult-class | 0.888 | 0.008 | 0.895 | |
| PhenTestResult | 0.716 | 0.004 | 0.726 | |
| RRTest | 0.148 | 0.000 | 0.147 | |
| TFDataset | 0.460 | 0.016 | 0.478 | |
| analysedDataset | 0.984 | 0.024 | 1.008 | |
| analysisResults | 0.940 | 0.004 | 0.944 | |
| boxplotResidualBatch | 1.020 | 0.012 | 1.037 | |
| boxplotSexGenotype | 0.128 | 0.000 | 0.205 | |
| boxplotSexGenotypeBatch | 0.228 | 0.000 | 0.228 | |
| boxplotSexGenotypeBatchAdjusted | 0.108 | 0.000 | 0.111 | |
| boxplotSexGenotypeResult | 1.364 | 0.004 | 1.370 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.112 | 0.000 | 0.112 | |
| categoricalBarplot | 0.276 | 0.000 | 0.275 | |
| checkDataset | 0.068 | 0.004 | 0.069 | |
| classificationTag | 0.860 | 0.004 | 0.868 | |
| determiningLambda | 0.652 | 0.144 | 0.800 | |
| dim | 0.068 | 0.000 | 0.068 | |
| finalLRModel | 0.732 | 0.000 | 0.731 | |
| finalModel | 0.764 | 0.000 | 0.792 | |
| finalTFModel | 0.860 | 0.000 | 0.895 | |
| htestPhenStat-class | 0.256 | 0.000 | 0.263 | |
| modelFormula | 0 | 0 | 0 | |
| modelFormulaLR | 0 | 0 | 0 | |
| parserOutputSummary | 0.964 | 0.004 | 0.983 | |
| parserOutputSummaryLR | 1.176 | 0.000 | 1.191 | |
| parserOutputTFSummary | 0.136 | 0.000 | 0.160 | |
| performReverseTransformation | 0.000 | 0.000 | 0.001 | |
| performTransformation | 0.000 | 0.000 | 0.001 | |
| plot.PhenList | 2.676 | 0.036 | 2.742 | |
| plot.PhenTestResult | 3.220 | 0.012 | 3.260 | |
| plotResidualPredicted | 0.972 | 0.000 | 0.972 | |
| printLROutput | 1.068 | 0.004 | 1.076 | |
| printTabStyle | 0.000 | 0.000 | 0.001 | |
| qqplotGenotype | 0.984 | 0.000 | 0.995 | |
| qqplotRandomEffects | 0.864 | 0.004 | 0.871 | |
| qqplotRotatedResiduals | 4.156 | 0.036 | 4.258 | |
| recommendMethod | 0.432 | 0.000 | 0.434 | |
| scatterplotGenotypeWeight | 0.156 | 0.000 | 0.159 | |
| scatterplotGenotypeWeightResult | 1.288 | 0.004 | 1.298 | |
| scatterplotSexGenotypeBatch | 0.128 | 0.000 | 0.127 | |
| scatterplotSexGenotypeBatchResult | 1.272 | 0.004 | 1.276 | |
| startLRModel | 0.768 | 0.000 | 0.770 | |
| startModel | 0.628 | 0.000 | 0.626 | |
| startTFModel | 0.664 | 0.000 | 0.665 | |
| summaryOutput | 1.168 | 0.004 | 1.178 | |
| summaryPhenListResult | 1.232 | 0.000 | 1.262 | |
| testDataset | 2.524 | 0.008 | 2.574 | |
| testFinalLRModel | 0.636 | 0.000 | 0.637 | |
| testFinalModel | 1.236 | 0.004 | 1.242 | |
| vectorOutput | 1.184 | 0.004 | 1.192 | |
| vectorOutputMatrices | 0.236 | 0.000 | 0.236 | |