BioC 3.4: CHECK report for minfi on zin1

Package: minfi

Version: 1.19.14

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.19.14.tar.gz

StartedAt: 2016-09-20 09:22:34 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:31:48 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 553.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: minfi.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.19.14.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/minfi.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.19.14’
* 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 ... 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.SummarizedExperiment.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 ... WARNING
Undocumented code objects:
  ‘subsetByLoci’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gaphunter          42.268  0.028  42.300
compartments       34.188  0.016  34.205
bumphunter         30.356  0.984  31.558
combineArrays      17.864  0.100  18.603
densityBeanPlot     7.308  0.000   7.310
read.metharray.exp  7.088  0.016   7.105
detectionP          5.572  0.000   5.575
read.metharray      5.224  0.008   5.231
* 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 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-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	0.004	0.000	0.002
GenomicRatioSet-class	0.000	0.000	0.001
IlluminaMethylationManifest-class	2.456	0.048	2.508
MethylSet-class	0.000	0.000	0.001
RGChannelSet-class	0.000	0.004	0.001
RatioSet-class	0.000	0.000	0.001
bumphunter	30.356	0.984	31.558
combineArrays	17.864	0.100	18.603
compartments	34.188	0.016	34.205
controlStripPlot	1.280	0.004	1.284
convertArray	4.388	0.052	4.443
densityBeanPlot	7.308	0.000	7.310
densityPlot	3.224	0.000	3.226
detectionP	5.572	0.000	5.575
dmpFinder	0.100	0.000	0.101
estimateCellCounts	0.000	0.000	0.001
fixMethOutliers	1.904	0.008	1.910
gaphunter	42.268	0.028	42.300
getAnnotation	0.876	0.000	0.878
getGenomicRatioSetFromGEO	0.000	0.000	0.001
getQC	0.212	0.000	0.209
getSex	1.708	0.032	1.740
logit2	0	0	0
makeGenomicRatioSetFromMatrix	0.960	0.060	1.018
mdsPlot	0.336	0.000	0.336
minfiQC	4.076	0.116	4.193
plotBetasByType	0.004	0.000	0.001
plotCpg	0.116	0.000	0.117
preprocessFunnorm	0.000	0.000	0.001
preprocessIllumina	4.252	0.004	4.254
preprocessNoob	0	0	0
preprocessQuantile	0.004	0.000	0.001
preprocessRaw	4.352	0.000	4.351
preprocessSwan	0	0	0
qcReport	0.032	0.000	0.031
read.metharray	5.224	0.008	5.231
read.metharray.exp	7.088	0.016	7.105
read.metharray.sheet	0.036	0.000	0.035
readGEORawFile	0.000	0.000	0.001
readTCGA	0	0	0
utils	0.104	0.000	0.106