Gabriel E. Hoffman
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: RELEASE_3_7 |
| Last Commit: 4455edd |
| Last Changed Date: 2018-10-11 19:15:43 -0400 (Thu, 11 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:40:54 -0400 (Wed, 17 Oct 2018).
| Package 1530/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.10.4 Gabriel E. Hoffman
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: variancePartition |
| Version: 1.10.4 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings variancePartition_1.10.4.tar.gz |
| StartedAt: 2018-10-17 05:21:41 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:33:57 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 736.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:variancePartition.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings variancePartition_1.10.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/variancePartition.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.10.4'
* 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 ... 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
fitVarPartModel-method 23.78 7.23 63.10
extractVarPart 13.00 3.15 30.44
getVarianceComponents 6.76 1.30 31.75
residuals-VarParFitList-method 4.80 0.89 15.91
varPartConfInf 4.98 0.22 21.49
fitExtractVarPartModel-method 1.36 0.60 22.04
plotPercentBars 1.22 0.08 14.18
plotCompareP-method 1.14 0.05 19.85
plotCorrStructure 1.04 0.09 10.34
sortCols-method 0.99 0.03 14.58
plotVarPart-method 0.64 0.08 13.79
dream-method 0.47 0.05 9.64
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 31.41 2.60 51.78
extractVarPart 14.44 1.16 31.84
getVarianceComponents 6.89 0.52 19.55
residuals-VarParFitList-method 5.63 0.61 17.08
varPartConfInf 5.16 0.08 20.04
fitExtractVarPartModel-method 1.29 0.15 22.83
plotCompareP-method 1.34 0.06 21.98
sortCols-method 1.23 0.03 14.24
plotCorrStructure 1.17 0.08 9.21
plotVarPart-method 1.00 0.06 35.18
plotPercentBars 1.04 0.01 14.37
dream-method 0.64 0.02 9.58
* 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: OK
variancePartition.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/variancePartition_1.10.4.tar.gz && rm -rf variancePartition.buildbin-libdir && mkdir variancePartition.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=variancePartition.buildbin-libdir variancePartition_1.10.4.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL variancePartition_1.10.4.zip && rm variancePartition_1.10.4.tar.gz variancePartition_1.10.4.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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100 1362k 100 1362k 0 0 17.0M 0 --:--:-- --:--:-- --:--:-- 19.0M
install for i386
* installing *source* package 'variancePartition' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'eBayes' 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
as.data.frame-varPartResults-method html
as.matrix-varPartResults-method html
calcVarPart-method html
canCorPairs html
colinearityScore 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
plotCorrMatrix html
plotCorrStructure html
plotPercentBars html
plotStratify html
plotStratifyBy html
plotVarPart-method html
residuals-VarParFitList-method html
sortCols-method html
sub-.MArrayLM2 html
varPartConfInf html
varPartDEdata html
varPartData html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'variancePartition' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'variancePartition' as variancePartition_1.10.4.zip
* DONE (variancePartition)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'variancePartition' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
variancePartition.Rcheck/tests_i386/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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")'.
Projected run time: ˜ 0.4 min
Loading required package: Matrix
Attaching package: 'lmerTest'
The following object is masked from 'package:lme4':
lmer
The following object is masked from 'package:stats':
step
Projected run time: ˜ 0.1 min
Projected run time: ˜ 0.2 min
RUNIT TEST PROTOCOL -- Wed Oct 17 05:33:05 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
variancePartition RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
executing %dopar% sequentially: no parallel backend registered
>
> proc.time()
user system elapsed
32.10 0.32 32.48
|
variancePartition.Rcheck/tests_x64/runTests.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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")'.
Projected run time: ˜ 0.4 min
Loading required package: Matrix
Attaching package: 'lmerTest'
The following object is masked from 'package:lme4':
lmer
The following object is masked from 'package:stats':
step
Projected run time: ˜ 0.2 min
Projected run time: ˜ 0.2 min
RUNIT TEST PROTOCOL -- Wed Oct 17 05:33:41 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
variancePartition RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning message:
executing %dopar% sequentially: no parallel backend registered
>
> proc.time()
user system elapsed
35.79 0.42 36.21
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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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