Hamed Haselimashhadi
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/PhenStat |
| Branch: master |
| Last Commit: 0c62560 |
| Last Changed Date: 2019-04-04 05:49:29 -0400 (Thu, 04 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:09:22 -0400 (Tue, 09 Apr 2019).
| Package 1182/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PhenStat 2.19.0 Hamed Haselimashhadi
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: PhenStat |
| Version: 2.19.0 |
| 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_2.19.0.tar.gz |
| StartedAt: 2019-04-09 04:22:32 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:25:46 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 193.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PhenStat.Rcheck |
| Warnings: 1 |
##############################################################################
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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_2.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.19.0’
* 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 ... NOTE
testDataset: no visible binding for global variable ‘check’
Undefined global functions or variables:
check
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'testDataset':
testDataset
Code: function(phenList = NULL, depVariable = NULL, equation =
"withWeight", outputMessages = TRUE, pThreshold =
0.05, method = "MM", modelWeight = NULL, callAll =
TRUE, keepList = NULL, dataPointsThreshold = 4,
RR_naturalVariation = 95, RR_controlPointsThreshold =
60, transformValues = FALSE, useUnfiltered = FALSE,
threshold = 10^-18, upper = 5)
Docs: function(phenList = NULL, depVariable = NULL, equation =
"withWeight", outputMessages = TRUE, pThreshold =
0.05, method = "MM", modelWeight = NULL, callAll =
TRUE, keepList = NULL, dataPointsThreshold = 4,
RR_naturalVariation = 95, RR_controlPointsThreshold =
60, transformValues = FALSE, useUnfiltered = FALSE,
threshold = 10^-18, check = 1, upper = 5)
Argument names in docs not in code:
check
Mismatches in argument names:
Position: 16 Code: upper Docs: check
* 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 5.372 0.124 5.497
* 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 WARNING, 2 NOTEs
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 Under development (unstable) (2019-03-18 r76245) -- "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 -- Tue Apr 9 04:25:36 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
4.438 0.582 4.969
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.446 | 0.078 | 0.526 | |
| JSONOutput | 1.425 | 0.093 | 1.518 | |
| LRDataset | 0.107 | 0.004 | 0.112 | |
| PhenList-class | 0.362 | 0.032 | 0.395 | |
| PhenList | 0.339 | 0.020 | 0.360 | |
| PhenStatReport | 0.073 | 0.002 | 0.075 | |
| PhenTestResult-class | 1.342 | 0.038 | 1.381 | |
| PhenTestResult | 0.933 | 0.057 | 0.990 | |
| RRTest | 0.182 | 0.003 | 0.185 | |
| TFDataset | 0.585 | 0.036 | 0.621 | |
| analysedDataset | 0.761 | 0.034 | 0.795 | |
| analysisResults | 1.069 | 0.040 | 1.108 | |
| boxplotResidualBatch | 1.283 | 0.068 | 1.351 | |
| boxplotSexGenotype | 0.126 | 0.008 | 0.135 | |
| boxplotSexGenotypeBatch | 0.242 | 0.015 | 0.258 | |
| boxplotSexGenotypeBatchAdjusted | 0.134 | 0.011 | 0.146 | |
| boxplotSexGenotypeResult | 1.416 | 0.038 | 1.455 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.117 | 0.002 | 0.119 | |
| categoricalBarplot | 0.375 | 0.037 | 0.413 | |
| checkDataset | 0.075 | 0.001 | 0.077 | |
| classificationTag | 1.362 | 0.026 | 1.388 | |
| determiningLambda | 1.196 | 0.562 | 1.759 | |
| dim | 0.062 | 0.006 | 0.068 | |
| finalLRModel | 0.866 | 0.048 | 0.916 | |
| finalModel | 0.892 | 0.038 | 0.930 | |
| finalTFModel | 1.148 | 0.043 | 1.191 | |
| htestPhenStat-class | 0.221 | 0.034 | 0.256 | |
| modelFormula | 0.000 | 0.000 | 0.001 | |
| modelFormulaLR | 0 | 0 | 0 | |
| parserOutputSummary | 0.916 | 0.033 | 0.950 | |
| parserOutputSummaryLR | 1.105 | 0.038 | 1.144 | |
| parserOutputTFSummary | 0.246 | 0.011 | 0.258 | |
| performReverseTransformation | 0.000 | 0.001 | 0.001 | |
| performTransformation | 0.000 | 0.001 | 0.001 | |
| plot.PhenList | 3.036 | 0.107 | 3.148 | |
| plot.PhenTestResult | 3.305 | 0.124 | 3.436 | |
| plotResidualPredicted | 1.078 | 0.031 | 1.109 | |
| printLROutput | 0.693 | 0.051 | 0.744 | |
| printTabStyle | 0.002 | 0.001 | 0.002 | |
| qqplotGenotype | 1.062 | 0.016 | 1.078 | |
| qqplotRandomEffects | 1.067 | 0.023 | 1.090 | |
| qqplotRotatedResiduals | 5.372 | 0.124 | 5.497 | |
| recommendMethod | 0.599 | 0.021 | 0.620 | |
| scatterplotGenotypeWeight | 0.182 | 0.005 | 0.188 | |
| scatterplotGenotypeWeightResult | 1.331 | 0.028 | 1.361 | |
| scatterplotSexGenotypeBatch | 0.155 | 0.028 | 0.185 | |
| scatterplotSexGenotypeBatchResult | 1.461 | 0.030 | 1.490 | |
| startLRModel | 0.745 | 0.041 | 0.786 | |
| startModel | 0.790 | 0.025 | 0.815 | |
| startTFModel | 1.041 | 0.047 | 1.087 | |
| summaryOutput | 1.170 | 0.041 | 1.211 | |
| summaryPhenListResult | 1.381 | 0.047 | 1.428 | |
| testDataset | 3.362 | 0.127 | 3.551 | |
| testFinalLRModel | 0.809 | 0.085 | 0.895 | |
| testFinalModel | 1.584 | 0.036 | 1.620 | |
| vectorOutput | 1.232 | 0.049 | 1.280 | |
| vectorOutputMatrices | 0.277 | 0.010 | 0.287 | |