Hamed Haselimashhadi
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/PhenStat |
| Branch: master |
| Last Commit: afedf2a |
| Last Changed Date: 2019-10-29 13:37:15 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:38:09 -0500 (Thu, 16 Jan 2020).
| Package 1256/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhenStat 2.23.0 Hamed Haselimashhadi
| malbec2 | Linux (Ubuntu 18.04.3 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: 2.23.0 |
| 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_2.23.0.tar.gz |
| StartedAt: 2020-01-16 07:26:10 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:29:47 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 217.3 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_2.23.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.23.0’
* 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 (user + system) or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 5.305 0.069 5.374
* 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-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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 -- Thu Jan 16 07:29:37 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
5.415 0.682 6.046
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.442 | 0.042 | 0.486 | |
| JSONOutput | 1.358 | 0.087 | 1.446 | |
| LRDataset | 0.151 | 0.041 | 0.194 | |
| PhenList-class | 0.365 | 0.032 | 0.397 | |
| PhenList | 0.370 | 0.015 | 0.385 | |
| PhenStatReport | 0.086 | 0.002 | 0.088 | |
| PhenTestResult-class | 1.324 | 0.049 | 1.373 | |
| PhenTestResult | 0.881 | 0.047 | 0.929 | |
| RRTest | 0.168 | 0.009 | 0.177 | |
| TFDataset | 0.544 | 0.020 | 0.565 | |
| analysedDataset | 1.078 | 0.077 | 1.156 | |
| analysisResults | 1.056 | 0.029 | 1.085 | |
| boxplotResidualBatch | 1.453 | 0.035 | 1.488 | |
| boxplotSexGenotype | 0.146 | 0.012 | 0.160 | |
| boxplotSexGenotypeBatch | 0.239 | 0.012 | 0.253 | |
| boxplotSexGenotypeBatchAdjusted | 0.130 | 0.005 | 0.136 | |
| boxplotSexGenotypeResult | 1.459 | 0.038 | 1.498 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.137 | 0.003 | 0.141 | |
| categoricalBarplot | 0.382 | 0.022 | 0.404 | |
| checkDataset | 0.073 | 0.001 | 0.075 | |
| classificationTag | 1.117 | 0.049 | 1.166 | |
| determiningLambda | 1.742 | 0.952 | 2.694 | |
| dim | 0.087 | 0.007 | 0.093 | |
| finalLRModel | 0.891 | 0.045 | 0.938 | |
| finalModel | 0.901 | 0.032 | 0.934 | |
| finalTFModel | 1.285 | 0.026 | 1.313 | |
| htestPhenStat-class | 0.368 | 0.023 | 0.390 | |
| modelFormula | 0.001 | 0.000 | 0.001 | |
| modelFormulaLR | 0.000 | 0.001 | 0.000 | |
| parserOutputSummary | 0.913 | 0.026 | 0.941 | |
| parserOutputSummaryLR | 0.769 | 0.034 | 0.804 | |
| parserOutputTFSummary | 0.177 | 0.002 | 0.179 | |
| performReverseTransformation | 0.001 | 0.001 | 0.001 | |
| performTransformation | 0.001 | 0.000 | 0.001 | |
| plot.PhenList | 3.446 | 0.062 | 3.526 | |
| plot.PhenTestResult | 3.257 | 0.065 | 3.338 | |
| plotResidualPredicted | 1.103 | 0.012 | 1.116 | |
| printLROutput | 0.810 | 0.023 | 0.833 | |
| printTabStyle | 0.002 | 0.000 | 0.001 | |
| qqplotGenotype | 1.039 | 0.019 | 1.060 | |
| qqplotRandomEffects | 1.146 | 0.029 | 1.176 | |
| qqplotRotatedResiduals | 5.305 | 0.069 | 5.374 | |
| recommendMethod | 0.629 | 0.019 | 0.661 | |
| scatterplotGenotypeWeight | 0.194 | 0.006 | 0.204 | |
| scatterplotGenotypeWeightResult | 1.646 | 0.043 | 1.690 | |
| scatterplotSexGenotypeBatch | 0.170 | 0.004 | 0.175 | |
| scatterplotSexGenotypeBatchResult | 1.264 | 0.040 | 1.351 | |
| startLRModel | 1.083 | 0.030 | 1.113 | |
| startModel | 0.711 | 0.010 | 0.722 | |
| startTFModel | 0.855 | 0.008 | 0.863 | |
| summaryOutput | 1.317 | 0.012 | 1.329 | |
| summaryPhenListResult | 1.285 | 0.032 | 1.316 | |
| testDataset | 3.187 | 0.063 | 3.270 | |
| testFinalLRModel | 0.742 | 0.033 | 0.776 | |
| testFinalModel | 1.295 | 0.018 | 1.314 | |
| vectorOutput | 1.508 | 0.034 | 1.542 | |
| vectorOutputMatrices | 0.328 | 0.006 | 0.333 | |