Jakob Willforss
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/NormalyzerDE |
| Branch: RELEASE_3_9 |
| Last Commit: 460392e |
| Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:42:20 -0400 (Wed, 16 Oct 2019).
| Package 1110/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NormalyzerDE 1.2.0 Jakob Willforss
| 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: NormalyzerDE |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormalyzerDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings NormalyzerDE_1.2.0.tar.gz |
| StartedAt: 2019-10-16 05:37:16 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:44:48 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 452.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NormalyzerDE.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NormalyzerDE.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings NormalyzerDE_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NormalyzerDE/DESCRIPTION' ... OK
* this is package 'NormalyzerDE' version '1.2.0'
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'NormalyzerDE' 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
Missing or unexported object: 'SummarizedExperiment::metadata'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generatePlots 15.28 1.44 16.79
getSmoothedRTNormalizedMatrix 7.38 0.01 7.40
writeNormalizedDatasets 5.95 0.19 6.15
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
generatePlots 19.14 0.67 19.82
writeNormalizedDatasets 6.57 0.00 6.58
NormalyzerEvaluationResults 6.14 0.09 6.24
getSmoothedRTNormalizedMatrix 5.33 0.00 5.33
analyzeNormalizations 5.09 0.00 5.10
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/NormalyzerDE.Rcheck/00check.log'
for details.
NormalyzerDE.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/NormalyzerDE_1.2.0.tar.gz && rm -rf NormalyzerDE.buildbin-libdir && mkdir NormalyzerDE.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NormalyzerDE.buildbin-libdir NormalyzerDE_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL NormalyzerDE_1.2.0.zip && rm NormalyzerDE_1.2.0.tar.gz NormalyzerDE_1.2.0.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 923k 100 923k 0 0 15.5M 0 --:--:-- --:--:-- --:--:-- 17.6M
install for i386
* installing *source* package 'NormalyzerDE' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'NormalyzerDE'
finding HTML links ... done
NormalyzerDataset html
NormalyzerEvaluationResults html
NormalyzerResults html
NormalyzerStatistics html
analyzeNormalizations html
calculateANOVAPValues html
calculateAvgMadMem html
calculateAvgReplicateVariation html
calculateContrasts html
calculateCorrSum html
calculateFeatureCV html
calculatePercentageAvgDiffInMat html
calculateReplicateCV html
calculateSummarizedCorrelationVector html
createDirectory html
detectSingleReplicate html
detectSingletonSample html
elapsedSecondsBetweenSystimes html
example_data html
example_data_only_values html
example_design html
example_stat_data html
example_stat_summarized_experiment html
example_summarized_experiment html
example_wide_data html
example_wide_design html
filterLowRep html
findLowlyVariableFeaturesCVs html
generateAnnotatedMatrix html
generatePlots html
generateStatsReport html
getCombinedMatrix html
getIndexList html
getLowCountSampleFiltered html
getRTNormalizedMatrix html
getReplicateSortedData html
getRowNAFilterContrast html
getSmoothedRTNormalizedMatrix html
getVerifiedNormalyzerObject html
getWidenedRTRange html
globalIntensityNormalization html
loadData html
loadDesign html
loadRawDataFromFile html
meanNormalization html
medianNormalization html
normMethods html
normalyzer html
normalyzerDE html
performCyclicLoessNormalization html
performGlobalRLRNormalization html
performNoNormalization html
performNormalizations html
performQuantileNormalization html
performSMADNormalization html
performVSNNormalization html
plotBoxPlot html
plotCVvsIntensity html
plotComparisonVenns html
plotContrastPCA html
plotContrastPHists html
plotCorrelation html
plotDendrograms html
plotDensity html
plotFrontPage html
plotMA html
plotMDS html
plotMeanSD html
plotPHist html
plotQQ html
plotRLE html
plotReplicateVarAndStableVariables html
plotReplicateVariance html
plotSampleOutlierSummary html
plotScatter html
plotSigScatter html
preprocessData html
printMeta html
printPlots html
reduceTechnicalReplicates html
setupJobDir html
setupPlotting html
setupRawContrastObject html
setupRawDataObject html
setupTestData html
validateSampleReplication html
verifyContrasts html
verifyDesignMatrix html
verifyMultipleSamplesPresent html
verifyValidNumbers html
writeNormalizedDatasets 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 'NormalyzerDE' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'NormalyzerDE' as NormalyzerDE_1.2.0.zip
* DONE (NormalyzerDE)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'NormalyzerDE' successfully unpacked and MD5 sums checked
|
NormalyzerDE.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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.
> library(testthat)
> library(NormalyzerDE)
> test_check("NormalyzerDE")
== testthat results ===========================================================
[ OK: 85 | SKIPPED: 0 | WARNINGS: 78 | FAILED: 0 ]
>
> proc.time()
user system elapsed
31.31 1.37 33.65
|
NormalyzerDE.Rcheck/tests_x64/testthat.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-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.
> library(testthat)
> library(NormalyzerDE)
> test_check("NormalyzerDE")
== testthat results ===========================================================
[ OK: 85 | SKIPPED: 0 | WARNINGS: 78 | FAILED: 0 ]
>
> proc.time()
user system elapsed
34.62 0.54 35.15
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NormalyzerDE.Rcheck/examples_i386/NormalyzerDE-Ex.timings
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NormalyzerDE.Rcheck/examples_x64/NormalyzerDE-Ex.timings
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