BioC 3.2: CHECK report for minfi on zin1

Package: minfi

Version: 1.16.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.16.1.tar.gz

StartedAt: 2016-04-23 02:54:49 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:07:57 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 787.4 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.16.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.16.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’
  ‘SummarizedExperiment’ ‘Biostrings’ ‘bumphunter’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [22s/22s] 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 objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’
  ‘SummarizedExperiment:::.valid.SummarizedExperiment0.assays_ncol’
  ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [375s/376s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
gaphunter     252.747  0.087 253.218
bumphunter     37.180  1.400  38.578
compartments   26.845  0.091  27.032
read.450k.exp   5.675  0.004   5.678
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [179s/200s]
 [179s/200s] 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/minfi.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GenomicMethylSet-class	0.002	0.000	0.002
GenomicRatioSet-class	0.001	0.000	0.001
IlluminaMethylationManifest-class	2.789	0.076	2.863
MethylSet-class	0.001	0.000	0.001
RGChannelSet-class	0.001	0.000	0.002
RatioSet-class	0.001	0.000	0.001
bumphunter	37.180	1.400	38.578
compartments	26.845	0.091	27.032
controlStripPlot	1.603	0.008	1.617
densityBeanPlot	4.852	0.028	4.893
densityPlot	3.606	0.008	3.618
detectionP	4.714	0.000	4.713
dmpFinder	0.177	0.004	0.180
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.937	0.004	1.939
gaphunter	252.747	0.087	253.218
getAnnotation	0.969	0.000	0.970
getGenomicRatioSetFromGEO	0	0	0
getQC	0.410	0.000	0.411
getSex	1.824	0.000	1.825
logit2	0	0	0
makeGenomicRatioSetFromMatrix	0.979	0.000	0.979
mdsPlot	0.774	0.000	0.774
minfiQC	4.044	0.000	4.049
plotBetasByType	0.000	0.000	0.001
plotCpg	0.179	0.000	0.183
preprocessFunnorm	0.001	0.000	0.000
preprocessIllumina	3.425	0.008	3.469
preprocessNoob	0.000	0.000	0.001
preprocessQuantile	0.001	0.000	0.001
preprocessRaw	1.523	0.024	1.546
preprocessSwan	0.000	0.000	0.001
qcReport	0.067	0.000	0.071
read.450k	4.500	0.016	4.512
read.450k.exp	5.675	0.004	5.678
read.450k.sheet	0.068	0.000	0.068
readGEORawFile	0	0	0
readTCGA	0.001	0.000	0.001
utils	1.391	0.236	1.628