Hamed Haselimashhadi
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/PhenStat |
| Branch: RELEASE_3_9 |
| Last Commit: 6a8e0cd |
| Last Changed Date: 2019-07-15 18:47:47 -0400 (Mon, 15 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:03:42 -0400 (Wed, 16 Oct 2019).
| Package 1206/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhenStat 2.20.3 Hamed Haselimashhadi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: PhenStat |
| Version: 2.20.3 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PhenStat_2.20.3.tar.gz |
| StartedAt: 2019-10-16 03:54:17 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:56:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 151.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PhenStat.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PhenStat_2.20.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck’ * using R version 3.6.1 (2019-07-05) * 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 ‘2.20.3’ * 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-3.9-bioc/meat/PhenStat.Rcheck/00check.log’ for details.
PhenStat.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PhenStat ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 03:56:43 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
3.987 0.186 4.233
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.171 | 0.037 | 0.225 | |
| JSONOutput | 1.187 | 0.012 | 1.216 | |
| LRDataset | 0.096 | 0.000 | 0.107 | |
| PhenList-class | 0.279 | 0.008 | 0.353 | |
| PhenList | 0.338 | 0.000 | 0.354 | |
| PhenStatReport | 0.064 | 0.000 | 0.064 | |
| PhenTestResult-class | 0.983 | 0.008 | 0.992 | |
| PhenTestResult | 0.786 | 0.012 | 0.797 | |
| RRTest | 0.136 | 0.000 | 0.137 | |
| TFDataset | 0.528 | 0.000 | 0.528 | |
| analysedDataset | 0.901 | 0.012 | 0.912 | |
| analysisResults | 0.910 | 0.012 | 0.923 | |
| boxplotResidualBatch | 0.980 | 0.008 | 1.029 | |
| boxplotSexGenotype | 0.114 | 0.000 | 0.183 | |
| boxplotSexGenotypeBatch | 0.226 | 0.003 | 0.230 | |
| boxplotSexGenotypeBatchAdjusted | 0.119 | 0.000 | 0.175 | |
| boxplotSexGenotypeResult | 0.834 | 0.008 | 0.905 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.084 | 0.004 | 0.088 | |
| categoricalBarplot | 0.207 | 0.004 | 0.211 | |
| checkDataset | 0.048 | 0.000 | 0.047 | |
| classificationTag | 0.816 | 0.000 | 0.815 | |
| determiningLambda | 0.966 | 0.136 | 1.102 | |
| dim | 0.037 | 0.000 | 0.037 | |
| finalLRModel | 0.612 | 0.000 | 0.612 | |
| finalModel | 0.503 | 0.000 | 0.504 | |
| finalTFModel | 0.770 | 0.012 | 0.840 | |
| htestPhenStat-class | 0.253 | 0.000 | 0.253 | |
| modelFormula | 0.001 | 0.000 | 0.001 | |
| modelFormulaLR | 0.000 | 0.000 | 0.001 | |
| parserOutputSummary | 0.958 | 0.008 | 0.965 | |
| parserOutputSummaryLR | 1.126 | 0.004 | 1.131 | |
| parserOutputTFSummary | 0.167 | 0.000 | 0.189 | |
| performReverseTransformation | 0 | 0 | 0 | |
| performTransformation | 0 | 0 | 0 | |
| plot.PhenList | 2.929 | 0.036 | 2.977 | |
| plot.PhenTestResult | 2.863 | 0.028 | 2.891 | |
| plotResidualPredicted | 0.941 | 0.008 | 0.950 | |
| printLROutput | 0.81 | 0.00 | 0.81 | |
| printTabStyle | 0.001 | 0.000 | 0.001 | |
| qqplotGenotype | 0.951 | 0.008 | 0.958 | |
| qqplotRandomEffects | 0.929 | 0.004 | 0.934 | |
| qqplotRotatedResiduals | 4.065 | 0.032 | 4.153 | |
| recommendMethod | 0.334 | 0.000 | 0.333 | |
| scatterplotGenotypeWeight | 0.161 | 0.000 | 0.162 | |
| scatterplotGenotypeWeightResult | 1.548 | 0.008 | 1.556 | |
| scatterplotSexGenotypeBatch | 0.128 | 0.000 | 0.128 | |
| scatterplotSexGenotypeBatchResult | 1.233 | 0.004 | 1.237 | |
| startLRModel | 0.767 | 0.000 | 0.768 | |
| startModel | 0.67 | 0.00 | 0.67 | |
| startTFModel | 0.592 | 0.000 | 0.592 | |
| summaryOutput | 0.783 | 0.000 | 0.783 | |
| summaryPhenListResult | 0.777 | 0.004 | 0.780 | |
| testDataset | 1.990 | 0.024 | 2.014 | |
| testFinalLRModel | 0.829 | 0.000 | 0.828 | |
| testFinalModel | 1.115 | 0.000 | 1.116 | |
| vectorOutput | 1.103 | 0.000 | 1.170 | |
| vectorOutputMatrices | 0.197 | 0.000 | 0.199 | |