Gabriel E. Hoffman
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_9 |
| Last Commit: 12a60fd |
| Last Changed Date: 2019-10-01 11:56:37 -0400 (Tue, 01 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:33:45 -0400 (Wed, 16 Oct 2019).
| Package 1705/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.14.1 Gabriel E. Hoffman
| 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: variancePartition |
| Version: 1.14.1 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings variancePartition_1.14.1.tar.gz |
| StartedAt: 2019-10-16 07:47:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 08:05:53 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1092.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.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:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings variancePartition_1.14.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/variancePartition.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 'variancePartition/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'variancePartition' version '1.14.1'
* 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 'variancePartition' 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 ... OK
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
[.MArrayLM2
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* 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
fitVarPartModel-method 21.56 3.45 71.42
extractVarPart 14.64 2.22 54.24
fitExtractVarPartModel-method 5.91 1.39 42.00
getVarianceComponents 5.75 0.88 25.23
residuals-VarParFitList-method 5.84 0.77 26.26
varPartConfInf 4.90 0.01 30.02
plotCompareP-method 3.98 0.61 27.78
plotPercentBars 3.44 0.58 29.51
sortCols-method 3.19 0.42 26.45
plotVarPart-method 2.65 0.72 26.74
voomWithDreamWeights 2.80 0.24 24.34
dream-method 2.02 0.14 24.68
plotCorrStructure 1.56 0.14 15.76
colinearityScore 0.65 0.12 9.43
as.data.frame-varPartResults-method 0.62 0.04 10.27
as.matrix-varPartResults-method 0.43 0.01 11.38
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 23.27 2.86 71.91
extractVarPart 13.14 1.79 50.85
residuals-VarParFitList-method 6.27 0.96 22.81
getVarianceComponents 6.00 0.83 22.63
fitExtractVarPartModel-method 5.32 1.46 43.78
plotCompareP-method 3.92 0.65 25.86
varPartConfInf 4.21 0.07 21.55
plotPercentBars 3.16 0.47 24.31
sortCols-method 2.93 0.69 24.47
plotVarPart-method 2.67 0.81 22.91
voomWithDreamWeights 2.57 0.25 20.06
dream-method 2.24 0.11 22.38
plotCorrStructure 1.70 0.11 16.94
as.data.frame-varPartResults-method 1.17 0.00 11.46
colinearityScore 0.70 0.16 9.72
as.matrix-varPartResults-method 0.64 0.00 10.49
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck/00check.log'
for details.
variancePartition.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/variancePartition_1.14.1.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.14.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.14.1.zip && rm variancePartition_1.14.1.tar.gz variancePartition_1.14.1.zip
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install for i386
* installing *source* package 'variancePartition' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'eBayes' from package 'limma' in package 'variancePartition'
Creating a new generic function for 'classifyTestsF' in package 'variancePartition'
Creating a generic function for 'topTable' from package 'limma' in package 'variancePartition'
** help
*** installing help indices
converting help for package 'variancePartition'
finding HTML links ... done
ESS-method html
MArrayLM2-class html
VarParCIList-class html
VarParFitList-class html
as.data.frame-varPartResults-method html
as.matrix-varPartResults-method html
calcVarPart-method html
canCorPairs html
classifyTestsF-MArrayLM2-method html
classifyTestsF html
colinearityScore html
dot-getAllUniContrasts html
dot-isMixedModelFormula html
dot-standard_transform html
dream-method html
eBayes-method html
extractVarPart html
fitExtractVarPartModel-method html
fitVarPartModel-method html
getContrast-method html
getVarianceComponents html
ggColorHue html
plotCompareP-method html
plotContrasts html
plotCorrMatrix html
plotCorrStructure html
plotPercentBars html
plotStratify html
plotStratifyBy html
plotVarPart-method html
residuals-VarParFitList-method html
sortCols-method html
subset.MArrayLM2-method html
toptable-method html
varParFrac-class html
varPartConfInf html
varPartDEdata html
varPartData html
varPartResults-class html
voomWithDreamWeights 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 'variancePartition' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'variancePartition' as variancePartition_1.14.1.zip
* DONE (variancePartition)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'variancePartition' successfully unpacked and MD5 sums checked
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variancePartition.Rcheck/tests_i386/runTests.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.
> BiocGenerics:::testPackage("variancePartition")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'variancePartition'
The following object is masked from 'package:limma':
classifyTestsF
Dividing work into 10 chunks...
Total: 10 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 11 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 13 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
> proc.time()
user system elapsed
5.39 0.59 38.87
Warning messages:
1: In dream(geneExpr[1:10, ], form, info, L1) :
Contrasts with only a single non-zero term are already evaluated by default.
2: In dream(geneExpr[1:10, ], form, info, L2) :
Contrasts with only a single non-zero term are already evaluated by default.
3: In dream(geneExpr[1:10, ], form, info, L) :
Contrasts with only a single non-zero term are already evaluated by default.
|
variancePartition.Rcheck/tests_x64/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-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("variancePartition")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'variancePartition'
The following object is masked from 'package:limma':
classifyTestsF
Dividing work into 10 chunks...
Total: 10 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 11 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
Dividing work into 10 chunks...
Total: 11 s
Empircal Bayes moderated test is no longer supported for dream analysis
Returning original results for use downstream
> proc.time()
user system elapsed
5.65 0.28 36.32
Warning messages:
1: In dream(geneExpr[1:10, ], form, info, L1) :
Contrasts with only a single non-zero term are already evaluated by default.
2: In dream(geneExpr[1:10, ], form, info, L2) :
Contrasts with only a single non-zero term are already evaluated by default.
3: In dream(geneExpr[1:10, ], form, info, L) :
Contrasts with only a single non-zero term are already evaluated by default.
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variancePartition.Rcheck/examples_i386/variancePartition-Ex.timings
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variancePartition.Rcheck/examples_x64/variancePartition-Ex.timings
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