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 12:52:26 -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: /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_2.20.3.tar.gz |
| StartedAt: 2019-10-16 05:31:55 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:35:28 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 213.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PhenStat.Rcheck |
| Warnings: 0 |
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### 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_2.20.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.20.3’
* 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 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 or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 5.991 0.109 6.101
* 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-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 05:35:15 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
5.411 0.702 6.064
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.410 | 0.057 | 0.469 | |
| JSONOutput | 1.401 | 0.080 | 1.482 | |
| LRDataset | 0.109 | 0.005 | 0.116 | |
| PhenList-class | 0.323 | 0.030 | 0.353 | |
| PhenList | 0.323 | 0.027 | 0.350 | |
| PhenStatReport | 0.052 | 0.002 | 0.053 | |
| PhenTestResult-class | 1.206 | 0.035 | 1.241 | |
| PhenTestResult | 0.971 | 0.005 | 0.977 | |
| RRTest | 0.149 | 0.003 | 0.152 | |
| TFDataset | 0.622 | 0.011 | 0.633 | |
| analysedDataset | 1.174 | 0.024 | 1.198 | |
| analysisResults | 1.155 | 0.018 | 1.174 | |
| boxplotResidualBatch | 1.255 | 0.025 | 1.281 | |
| boxplotSexGenotype | 0.165 | 0.008 | 0.175 | |
| boxplotSexGenotypeBatch | 0.292 | 0.006 | 0.298 | |
| boxplotSexGenotypeBatchAdjusted | 0.144 | 0.003 | 0.147 | |
| boxplotSexGenotypeResult | 1.608 | 0.015 | 1.625 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.133 | 0.003 | 0.137 | |
| categoricalBarplot | 0.361 | 0.039 | 0.400 | |
| checkDataset | 0.084 | 0.007 | 0.090 | |
| classificationTag | 1.473 | 0.008 | 1.481 | |
| determiningLambda | 1.263 | 0.529 | 1.793 | |
| dim | 0.092 | 0.010 | 0.102 | |
| finalLRModel | 0.884 | 0.024 | 0.916 | |
| finalModel | 0.905 | 0.021 | 0.926 | |
| finalTFModel | 1.121 | 0.025 | 1.146 | |
| htestPhenStat-class | 0.277 | 0.022 | 0.299 | |
| modelFormula | 0.001 | 0.000 | 0.001 | |
| modelFormulaLR | 0.001 | 0.000 | 0.000 | |
| parserOutputSummary | 1.201 | 0.037 | 1.240 | |
| parserOutputSummaryLR | 1.349 | 0.055 | 1.403 | |
| parserOutputTFSummary | 0.249 | 0.003 | 0.252 | |
| performReverseTransformation | 0.001 | 0.001 | 0.001 | |
| performTransformation | 0.001 | 0.000 | 0.001 | |
| plot.PhenList | 3.281 | 0.082 | 3.371 | |
| plot.PhenTestResult | 3.781 | 0.064 | 3.853 | |
| plotResidualPredicted | 1.140 | 0.007 | 1.147 | |
| printLROutput | 0.845 | 0.022 | 0.867 | |
| printTabStyle | 0.002 | 0.001 | 0.003 | |
| qqplotGenotype | 1.189 | 0.019 | 1.208 | |
| qqplotRandomEffects | 1.084 | 0.004 | 1.088 | |
| qqplotRotatedResiduals | 5.991 | 0.109 | 6.101 | |
| recommendMethod | 0.638 | 0.003 | 0.642 | |
| scatterplotGenotypeWeight | 0.196 | 0.007 | 0.204 | |
| scatterplotGenotypeWeightResult | 1.607 | 0.026 | 1.634 | |
| scatterplotSexGenotypeBatch | 0.162 | 0.003 | 0.165 | |
| scatterplotSexGenotypeBatchResult | 1.577 | 0.037 | 1.615 | |
| startLRModel | 0.782 | 0.024 | 0.806 | |
| startModel | 0.909 | 0.016 | 0.925 | |
| startTFModel | 1.156 | 0.010 | 1.171 | |
| summaryOutput | 1.489 | 0.026 | 1.515 | |
| summaryPhenListResult | 1.762 | 0.024 | 1.786 | |
| testDataset | 3.412 | 0.096 | 3.514 | |
| testFinalLRModel | 0.807 | 0.027 | 0.836 | |
| testFinalModel | 1.361 | 0.028 | 1.390 | |
| vectorOutput | 1.475 | 0.017 | 1.492 | |
| vectorOutputMatrices | 0.311 | 0.034 | 0.345 | |