Gabriel E. Hoffman
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/variancePartition |
| Branch: master |
| Last Commit: 9b09895 |
| Last Changed Date: 2019-03-20 14:51:09 -0400 (Wed, 20 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:43:30 -0400 (Tue, 09 Apr 2019).
| Package 1668/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| variancePartition 1.13.6 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: variancePartition |
| Version: 1.13.6 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings variancePartition_1.13.6.tar.gz |
| StartedAt: 2019-04-09 04:15:16 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:20:49 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 332.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: variancePartition.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:variancePartition.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings variancePartition_1.13.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘variancePartition/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘variancePartition’ version ‘1.13.6’
* 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 for sufficient/correct file permissions ... 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
* 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 ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
fitVarPartModel-method 26.763 1.648 44.827
extractVarPart 13.394 0.777 24.982
getVarianceComponents 6.919 1.214 15.398
varPartConfInf 5.948 0.813 21.817
residuals-VarParFitList-method 4.541 0.967 13.022
plotCompareP-method 1.223 0.675 15.159
plotCorrStructure 1.234 0.608 7.244
plotVarPart-method 1.124 0.573 10.837
plotPercentBars 1.015 0.679 11.043
fitExtractVarPartModel-method 1.104 0.412 18.636
sortCols-method 0.713 0.655 10.323
dream-method 0.939 0.115 7.303
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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
‘/home/biocbuild/bbs-3.9-bioc/meat/variancePartition.Rcheck/00check.log’
for details.
variancePartition.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL variancePartition ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * 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’ ** help *** installing help indices ** 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 * DONE (variancePartition)
variancePartition.Rcheck/tests/runTests.Rout
R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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 memory usage: > 4.6 Mb
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
Finished...
Total: 12 s
Projected memory usage: > 4.6 Mb
Finished...
Total: 13 s
Projected memory usage: > 4.6 Mb
Finished...
Total: 15 s
RUNIT TEST PROTOCOL -- Tue Apr 9 04:20:45 2019
***********************************************
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
44.517 0.194 44.727
variancePartition.Rcheck/variancePartition-Ex.timings
| name | user | system | elapsed | |
| ESS-method | 0.252 | 0.004 | 0.284 | |
| as.data.frame-varPartResults-method | 0.361 | 0.016 | 0.377 | |
| as.matrix-varPartResults-method | 0.378 | 0.000 | 0.378 | |
| calcVarPart-method | 0.069 | 0.000 | 0.069 | |
| canCorPairs | 0.063 | 0.000 | 0.063 | |
| colinearityScore | 0.434 | 0.000 | 0.434 | |
| dream-method | 0.939 | 0.115 | 7.303 | |
| extractVarPart | 13.394 | 0.777 | 24.982 | |
| fitExtractVarPartModel-method | 1.104 | 0.412 | 18.636 | |
| fitVarPartModel-method | 26.763 | 1.648 | 44.827 | |
| getContrast-method | 0.175 | 0.020 | 0.195 | |
| getVarianceComponents | 6.919 | 1.214 | 15.398 | |
| ggColorHue | 0.001 | 0.000 | 0.001 | |
| plotCompareP-method | 1.223 | 0.675 | 15.159 | |
| plotContrasts | 0.484 | 0.012 | 0.496 | |
| plotCorrMatrix | 0.111 | 0.012 | 0.123 | |
| plotCorrStructure | 1.234 | 0.608 | 7.244 | |
| plotPercentBars | 1.015 | 0.679 | 11.043 | |
| plotStratify | 1.099 | 0.056 | 1.155 | |
| plotStratifyBy | 0.973 | 0.035 | 1.008 | |
| plotVarPart-method | 1.124 | 0.573 | 10.837 | |
| residuals-VarParFitList-method | 4.541 | 0.967 | 13.022 | |
| sortCols-method | 0.713 | 0.655 | 10.323 | |
| varPartConfInf | 5.948 | 0.813 | 21.817 | |