BioC 3.5: CHECK report for minfi on malbec2
This page was generated on 2017-08-16 13:14:12 -0400 (Wed, 16 Aug 2017).
minfi 1.22.1 Kasper Daniel Hansen
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/minfi | Last Changed Rev: 129326 / Revision: 131943 | 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: 2017-08-16 00:38:51 -0400 (Wed, 16 Aug 2017) |
EndedAt: 2017-08-16 00:48:55 -0400 (Wed, 16 Aug 2017) |
EllapsedTime: 604.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: minfi.Rcheck |
Warnings: 0 |
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.22.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/minfi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 62.120 10.700 77.482
bumphunter 31.276 7.460 38.893
densityPlot 8.412 0.056 8.475
read.metharray.exp 7.828 0.028 7.863
read.metharray 5.116 0.012 5.135
densityBeanPlot 4.888 0.212 5.108
* 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 | 0.000 | 0.000 | 0.002 |
|
GenomicRatioSet-class | 0.000 | 0.000 | 0.001 |
|
IlluminaMethylationManifest-class | 2.768 | 0.068 | 2.834 |
|
MethylSet-class | 0.000 | 0.000 | 0.001 |
|
RGChannelSet-class | 0.000 | 0.000 | 0.001 |
|
RatioSet-class | 0 | 0 | 0 |
|
bumphunter | 31.276 | 7.460 | 38.893 |
|
combineArrays | 62.120 | 10.700 | 77.482 |
|
compartments | 3.132 | 0.616 | 3.750 |
|
controlStripPlot | 3.112 | 0.512 | 4.198 |
|
convertArray | 1.212 | 0.004 | 1.216 |
|
densityBeanPlot | 4.888 | 0.212 | 5.108 |
|
densityPlot | 8.412 | 0.056 | 8.475 |
|
detectionP | 0.340 | 0.004 | 0.354 |
|
dmpFinder | 0.284 | 0.020 | 0.306 |
|
estimateCellCounts | 0.000 | 0.000 | 0.001 |
|
fixMethOutliers | 0.852 | 0.684 | 1.537 |
|
gaphunter | 0.132 | 0.000 | 0.157 |
|
getAnnotation | 1.708 | 0.168 | 1.875 |
|
getGenomicRatioSetFromGEO | 0.000 | 0.000 | 0.001 |
|
getQC | 0.232 | 0.004 | 0.235 |
|
getSex | 1.360 | 0.012 | 1.374 |
|
logit2 | 0.000 | 0.000 | 0.001 |
|
makeGenomicRatioSetFromMatrix | 0.488 | 0.000 | 0.487 |
|
mapToGenome-methods | 0.180 | 0.000 | 0.181 |
|
mdsPlot | 0.168 | 0.000 | 0.168 |
|
minfiQC | 3.072 | 0.140 | 3.217 |
|
plotBetasByType | 0.000 | 0.000 | 0.001 |
|
plotCpg | 0.100 | 0.000 | 0.098 |
|
preprocessFunnorm | 3.180 | 0.012 | 3.200 |
|
preprocessIllumina | 3.240 | 0.000 | 3.243 |
|
preprocessNoob | 0.844 | 0.000 | 0.850 |
|
preprocessQuantile | 0.508 | 0.000 | 0.510 |
|
preprocessRaw | 2.248 | 0.004 | 2.253 |
|
preprocessSwan | 0.42 | 0.00 | 0.42 |
|
qcReport | 0.048 | 0.004 | 0.050 |
|
ratioConvert-methods | 0.064 | 0.000 | 0.063 |
|
read.metharray | 5.116 | 0.012 | 5.135 |
|
read.metharray.exp | 7.828 | 0.028 | 7.863 |
|
read.metharray.sheet | 0.068 | 0.000 | 0.067 |
|
readGEORawFile | 0.000 | 0.000 | 0.001 |
|
readTCGA | 0 | 0 | 0 |
|
subsetByLoci | 0.388 | 0.000 | 0.387 |
|
utils | 0.132 | 0.004 | 0.138 |
|