| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:26 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the variancePartition package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/variancePartition.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1994/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| variancePartition 1.22.0 (landing page) Gabriel E. Hoffman
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: variancePartition |
| Version: 1.22.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings variancePartition_1.22.0.tar.gz |
| StartedAt: 2021-10-15 07:06:43 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 07:25:06 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1103.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings variancePartition_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/variancePartition.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.22.0'
* 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 '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 ... NOTE
Unexported object imported by a ':::' call: 'lme4:::reOnly'
See the note in ?`:::` about the use of this operator.
* 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 (user + system) or elapsed time > 5s
user system elapsed
fitVarPartModel-method 44.82 8.00 104.86
extractVarPart 26.01 8.11 68.02
residuals-VarParFitList-method 14.72 2.49 35.81
fitExtractVarPartModel-method 11.43 3.09 50.23
plotCompareP-method 7.58 1.84 27.01
plotVarPart-method 5.85 1.45 24.14
plotPercentBars 5.85 1.21 24.01
sortCols-method 5.89 1.16 23.28
varPartConfInf 4.20 0.03 24.06
dream-method 2.39 0.09 21.90
voomWithDreamWeights 2.36 0.11 14.96
plotCorrStructure 1.60 0.06 7.46
as.data.frame-varPartResults-method 0.60 0.04 6.54
colinearityScore 0.50 0.08 7.25
as.matrix-varPartResults-method 0.53 0.04 6.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
fitVarPartModel-method 43.81 5.83 107.43
extractVarPart 24.31 3.60 65.48
residuals-VarParFitList-method 16.07 1.93 37.75
fitExtractVarPartModel-method 11.99 2.12 55.02
plotCompareP-method 7.66 1.17 27.89
sortCols-method 5.95 1.36 25.30
plotVarPart-method 5.33 1.40 25.37
plotPercentBars 5.33 1.14 24.03
varPartConfInf 4.08 0.01 29.27
dream-method 2.70 0.06 22.78
voomWithDreamWeights 2.10 0.06 17.25
plotCorrStructure 1.95 0.06 8.55
as.data.frame-varPartResults-method 0.79 0.03 6.81
colinearityScore 0.54 0.10 6.89
as.matrix-varPartResults-method 0.56 0.05 6.04
* 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-3.13-bioc/meat/variancePartition.Rcheck/00check.log'
for details.
variancePartition.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/variancePartition_1.22.0.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.22.0.zip && rm variancePartition_1.22.0.tar.gz variancePartition_1.22.0.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 1394k 100 1394k 0 0 2628k 0 --:--:-- --:--:-- --:--:-- 2631k
install for i386
* installing *source* package 'variancePartition' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'classifyTestsF' in package 'variancePartition'
** help
*** installing help indices
converting help for package 'variancePartition'
finding HTML links ... done
ESS-method html
FMT-class html
FMT html
FMT.ZI 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
eBayesFMT html
extractVarPart html
fitExtractVarPartModel-method html
fitVarPartModel-method html
getContrast-method html
get_prediction-method html
ggColorHue html
plotCompareP-method html
plotContrasts html
plotCorrMatrix html
plotCorrStructure html
plotPercentBars html
plotStratify html
plotStratifyBy html
plotVarPart-method html
residuals-MArrayLM-method html
residuals-MArrayLM2-method html
residuals-VarParFitList-method html
sortCols-method html
subset.MArrayLM2-method html
toptable-method html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/variancePartition.buildbin-libdir/00LOCK-variancePartition/00new/variancePartition/help/toptable+2CFMT-method.html
REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/variancePartition.buildbin-libdir/00LOCK-variancePartition/00new/variancePartition/help/toptable+2CMArrayLM2-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_1.22.0.zip
* DONE (variancePartition)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'variancePartition' successfully unpacked and MD5 sums checked
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variancePartition.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.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 1 chunks...
Total:7 s
Dividing work into 1 chunks...
Total:7 s
Dividing work into 1 chunks...
Total:7 s
> proc.time()
user system elapsed
5.96 0.42 26.78
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variancePartition.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.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 1 chunks...
Total:8 s
Dividing work into 1 chunks...
Total:7 s
Dividing work into 1 chunks...
Total:7 s
> proc.time()
user system elapsed
6.85 0.29 27.70
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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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