BioC 3.5: CHECK report for minfi on malbec2
This page was generated on 2017-10-18 14:14:21 -0400 (Wed, 18 Oct 2017).
minfi 1.22.1 Kasper Daniel Hansen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/minfi | Branch: RELEASE_3_5 | Last Commit: b2faf84 | Last Changed Date: 2017-05-01 11:23:50 -0400 (Mon, 01 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
Summary
Package: minfi |
Version: 1.22.1 |
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz |
StartedAt: 2017-10-18 00:51:08 -0400 (Wed, 18 Oct 2017) |
EndedAt: 2017-10-18 01:00:47 -0400 (Wed, 18 Oct 2017) |
EllapsedTime: 579.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
Command output
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###
### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.22.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘minfi’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘bumphunter:::.getEstimate’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
combineArrays 61.624 7.816 72.158
bumphunter 29.432 2.528 32.104
read.metharray.exp 7.548 0.016 7.566
densityBeanPlot 5.440 0.316 5.758
* 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-3.5-bioc/meat/minfi.Rcheck/00check.log’
for details.
minfi.Rcheck/00install.out:
* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (minfi)
minfi.Rcheck/minfi-Ex.timings:
name | user | system | elapsed
|
GenomicMethylSet-class | 0.004 | 0.000 | 0.003 |
|
GenomicRatioSet-class | 0.004 | 0.000 | 0.001 |
|
IlluminaMethylationManifest-class | 2.764 | 0.052 | 2.819 |
|
MethylSet-class | 0.000 | 0.000 | 0.001 |
|
RGChannelSet-class | 0.000 | 0.000 | 0.001 |
|
RatioSet-class | 0 | 0 | 0 |
|
bumphunter | 29.432 | 2.528 | 32.104 |
|
combineArrays | 61.624 | 7.816 | 72.158 |
|
compartments | 2.932 | 0.356 | 3.286 |
|
controlStripPlot | 2.884 | 0.248 | 3.747 |
|
convertArray | 1.260 | 0.004 | 1.264 |
|
densityBeanPlot | 5.440 | 0.316 | 5.758 |
|
densityPlot | 4.668 | 0.004 | 4.671 |
|
detectionP | 0.236 | 0.000 | 0.235 |
|
dmpFinder | 0.288 | 0.000 | 0.289 |
|
estimateCellCounts | 0 | 0 | 0 |
|
fixMethOutliers | 1.632 | 0.000 | 1.633 |
|
gaphunter | 0.084 | 0.000 | 0.084 |
|
getAnnotation | 0.972 | 0.000 | 0.969 |
|
getGenomicRatioSetFromGEO | 0.000 | 0.000 | 0.001 |
|
getQC | 0.240 | 0.000 | 0.238 |
|
getSex | 4.712 | 0.004 | 4.721 |
|
logit2 | 0 | 0 | 0 |
|
makeGenomicRatioSetFromMatrix | 0.396 | 0.000 | 0.395 |
|
mapToGenome-methods | 0.172 | 0.000 | 0.170 |
|
mdsPlot | 1.084 | 0.052 | 1.136 |
|
minfiQC | 2.940 | 0.024 | 2.969 |
|
plotBetasByType | 0.000 | 0.000 | 0.001 |
|
plotCpg | 0.104 | 0.000 | 0.103 |
|
preprocessFunnorm | 3.292 | 0.000 | 3.312 |
|
preprocessIllumina | 4.484 | 0.156 | 4.645 |
|
preprocessNoob | 0.736 | 0.000 | 0.736 |
|
preprocessQuantile | 0.496 | 0.004 | 0.501 |
|
preprocessRaw | 2.972 | 0.072 | 3.048 |
|
preprocessSwan | 0.424 | 0.020 | 0.446 |
|
qcReport | 0.060 | 0.000 | 0.063 |
|
ratioConvert-methods | 0.060 | 0.000 | 0.059 |
|
read.metharray | 4.812 | 0.020 | 4.832 |
|
read.metharray.exp | 7.548 | 0.016 | 7.566 |
|
read.metharray.sheet | 0.068 | 0.000 | 0.066 |
|
readGEORawFile | 0 | 0 | 0 |
|
readTCGA | 0.000 | 0.000 | 0.001 |
|
subsetByLoci | 0.376 | 0.000 | 0.376 |
|
utils | 0.944 | 0.196 | 1.142 |
|