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 12:15:20 -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: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhenStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PhenStat_2.19.0.tar.gz |
| StartedAt: 2019-04-09 04:54:51 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:58:33 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 223.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PhenStat.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PhenStat.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PhenStat_2.19.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
qqplotRotatedResiduals 5.27 0.03 5.29
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.9-bioc/meat/PhenStat.Rcheck/00check.log'
for details.
PhenStat.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PhenStat_2.19.0.tar.gz && rm -rf PhenStat.buildbin-libdir && mkdir PhenStat.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PhenStat.buildbin-libdir PhenStat_2.19.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PhenStat_2.19.0.zip && rm PhenStat_2.19.0.tar.gz PhenStat_2.19.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 733k 100 733k 0 0 10.6M 0 --:--:-- --:--:-- --:--:-- 11.7M
install for i386
* installing *source* package 'PhenStat' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PhenStat'
finding HTML links ... done
FisherExactTest html
JSONOutput html
LRDataset html
LargeDataObject-class html
PhenList-class html
PhenList html
PhenStatReport html
PhenTestResult-class html
PhenTestResult html
RRTest html
TFDataset html
analysedDataset html
analysedDatasetPhenList html
analysedSubset html
analysisResults html
batchIn html
boxplotResidualBatch html
boxplotSexGenotype html
boxplotSexGenotypeBatch html
boxplotSexGenotypeBatchAdjusted html
boxplotSexGenotypeResult html
boxplotSexGenotypeWeightBatchAdjusted html
categoricalBarplot html
checkDataset html
classificationTag html
columnChecks html
columnLevels html
comparison html
dataset html
determiningLambda html
dim html
finalLRModel html
finalModel html
finalTFModel html
formulaDeterminingLambda html
generateGraphs html
getColumn html
getColumnBatchAdjusted html
getColumnView html
getColumnWeightBatchAdjusted html
getCountMatrices html
getDataset html
getGenotypeEffect html
getMatrix html
getPercentageMatrix html
getStat html
getVariable html
getVariables html
hemiGenotype html
htest-class html
htestPhenStat-class html
matrixCount html
method html
methodText html
modelFormula html
modelFormulaLR html
multipleBatches html
noSexes html
parameters html
parserOutputSummary html
parserOutputSummaryLR html
parserOutputTFSummary html
performReverseTransformation html
performTransformation html
plot.PhenList html
plot.PhenTestResult html
plotResidualPredicted html
printLROutput html
printTabStyle html
pvalue html
qqplotGenotype html
qqplotRandomEffects html
qqplotRotatedResiduals html
recommendMethod html
refGenotype html
scatterplotGenotypeWeight html
scatterplotGenotypeWeightResult html
scatterplotSexGenotypeBatch html
scatterplotSexGenotypeBatchResult html
setBatch html
setGenotype html
setMissingValue html
setSex html
setWeight html
startLRModel html
startModel html
startTFModel html
subsetText html
summaryOutput html
summaryPhenListResult html
testDataset html
testFinalLRModel html
testFinalModel html
testGenotype html
transformation html
transformationJSON html
transformationText html
vectorOutput html
vectorOutputMatrices html
weightIn html
** 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
install for x64
* installing *source* package 'PhenStat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PhenStat' as PhenStat_2.19.0.zip
* DONE (PhenStat)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PhenStat' successfully unpacked and MD5 sums checked
|
PhenStat.Rcheck/tests_i386/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 09 04:58:21 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
3.48 0.25 3.71
|
PhenStat.Rcheck/tests_x64/runTests.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 09 04:58:25 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
2.89 0.23 3.11
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PhenStat.Rcheck/examples_i386/PhenStat-Ex.timings
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PhenStat.Rcheck/examples_x64/PhenStat-Ex.timings
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