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 11:37:11 -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: /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_2.19.0.tar.gz |
| StartedAt: 2019-04-09 02:40:45 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:43:05 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 139.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PhenStat.Rcheck |
| Warnings: 1 |
##############################################################################
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###
### 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_2.19.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.19.0’
* 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 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 WARNING, 2 NOTEs
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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 -- Tue Apr 9 02:42:59 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
4.164 0.196 4.345
PhenStat.Rcheck/PhenStat-Ex.timings
| name | user | system | elapsed | |
| FisherExactTest | 0.263 | 0.027 | 0.308 | |
| JSONOutput | 1.252 | 0.016 | 1.278 | |
| LRDataset | 0.086 | 0.000 | 0.155 | |
| PhenList-class | 0.303 | 0.000 | 0.553 | |
| PhenList | 0.309 | 0.005 | 0.313 | |
| PhenStatReport | 0.069 | 0.000 | 0.070 | |
| PhenTestResult-class | 1.254 | 0.000 | 1.255 | |
| PhenTestResult | 0.774 | 0.007 | 0.782 | |
| RRTest | 0.140 | 0.000 | 0.141 | |
| TFDataset | 0.462 | 0.012 | 0.474 | |
| analysedDataset | 0.975 | 0.008 | 0.984 | |
| analysisResults | 0.643 | 0.004 | 0.647 | |
| boxplotResidualBatch | 0.753 | 0.004 | 0.757 | |
| boxplotSexGenotype | 0.107 | 0.004 | 0.112 | |
| boxplotSexGenotypeBatch | 0.216 | 0.000 | 0.216 | |
| boxplotSexGenotypeBatchAdjusted | 0.106 | 0.000 | 0.106 | |
| boxplotSexGenotypeResult | 1.218 | 0.004 | 1.223 | |
| boxplotSexGenotypeWeightBatchAdjusted | 0.109 | 0.000 | 0.109 | |
| categoricalBarplot | 0.255 | 0.004 | 0.260 | |
| checkDataset | 0.064 | 0.000 | 0.064 | |
| classificationTag | 0.927 | 0.004 | 0.931 | |
| determiningLambda | 0.705 | 0.108 | 0.812 | |
| dim | 0.074 | 0.000 | 0.074 | |
| finalLRModel | 0.868 | 0.000 | 0.870 | |
| finalModel | 0.778 | 0.000 | 0.778 | |
| finalTFModel | 0.863 | 0.000 | 0.863 | |
| htestPhenStat-class | 0.243 | 0.012 | 0.255 | |
| modelFormula | 0 | 0 | 0 | |
| modelFormulaLR | 0 | 0 | 0 | |
| parserOutputSummary | 0.954 | 0.004 | 0.959 | |
| parserOutputSummaryLR | 0.981 | 0.000 | 0.981 | |
| parserOutputTFSummary | 0.098 | 0.000 | 0.105 | |
| performReverseTransformation | 0.000 | 0.000 | 0.001 | |
| performTransformation | 0 | 0 | 0 | |
| plot.PhenList | 1.856 | 0.012 | 1.873 | |
| plot.PhenTestResult | 1.895 | 0.016 | 1.918 | |
| plotResidualPredicted | 0.585 | 0.004 | 0.589 | |
| printLROutput | 0.468 | 0.003 | 0.472 | |
| printTabStyle | 0.001 | 0.000 | 0.001 | |
| qqplotGenotype | 0.688 | 0.004 | 0.693 | |
| qqplotRandomEffects | 0.57 | 0.00 | 0.57 | |
| qqplotRotatedResiduals | 3.655 | 0.048 | 3.703 | |
| recommendMethod | 0.235 | 0.000 | 0.235 | |
| scatterplotGenotypeWeight | 0.092 | 0.000 | 0.092 | |
| scatterplotGenotypeWeightResult | 0.737 | 0.000 | 0.737 | |
| scatterplotSexGenotypeBatch | 0.085 | 0.000 | 0.085 | |
| scatterplotSexGenotypeBatchResult | 1.190 | 0.000 | 1.192 | |
| startLRModel | 0.693 | 0.000 | 0.693 | |
| startModel | 0.707 | 0.000 | 0.707 | |
| startTFModel | 0.795 | 0.000 | 0.795 | |
| summaryOutput | 0.823 | 0.000 | 0.823 | |
| summaryPhenListResult | 1.100 | 0.008 | 1.108 | |
| testDataset | 2.656 | 0.024 | 2.681 | |
| testFinalLRModel | 0.557 | 0.000 | 0.561 | |
| testFinalModel | 0.703 | 0.004 | 0.707 | |
| vectorOutput | 0.706 | 0.000 | 0.707 | |
| vectorOutputMatrices | 0.138 | 0.000 | 0.138 | |