BioC 3.4: CHECK report for minfi on morelia

Package: minfi

Version: 1.20.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.20.2.tar.gz

StartedAt: 2017-04-15 05:04:06 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:16:25 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 738.9 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings minfi_1.20.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/minfi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘minfi/DESCRIPTION’ ... OK
* this is package ‘minfi’ version ‘1.20.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
combineArrays      63.937  3.496  71.898
bumphunter         35.208  7.007  42.275
read.metharray.exp 10.235  0.354  10.598
densityBeanPlot     9.704  0.629  10.346
read.metharray      6.630  0.305   6.964
preprocessIllumina  5.977  0.570   6.549
densityPlot         5.248  0.610   5.863
* 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: 2 NOTEs
See
  ‘/Users/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	0.003	0.001	0.004
GenomicRatioSet-class	0.002	0.000	0.002
IlluminaMethylationManifest-class	2.652	0.123	2.777
MethylSet-class	0.002	0.000	0.002
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.001	0.001	0.002
bumphunter	35.208	7.007	42.275
combineArrays	63.937	3.496	71.898
compartments	4.386	0.481	4.870
controlStripPlot	2.295	0.178	2.785
convertArray	1.878	0.100	1.980
densityBeanPlot	9.704	0.629	10.346
densityPlot	5.248	0.610	5.863
detectionP	1.096	0.171	1.268
dmpFinder	0.145	0.009	0.153
estimateCellCounts	0.001	0.000	0.001
fixMethOutliers	1.829	0.191	2.021
gaphunter	0.108	0.002	0.150
getAnnotation	2.176	0.250	2.427
getGenomicRatioSetFromGEO	0	0	0
getQC	0.153	0.007	0.159
getSex	1.980	0.174	2.155
logit2	0.001	0.000	0.001
makeGenomicRatioSetFromMatrix	0.863	0.068	0.931
mapToGenome-methods	0.307	0.008	0.315
mdsPlot	0.980	0.194	1.277
minfiQC	4.081	0.452	4.532
plotBetasByType	0.001	0.000	0.001
plotCpg	0.276	0.003	0.311
preprocessFunnorm	2.066	0.134	2.210
preprocessIllumina	5.977	0.570	6.549
preprocessNoob	0.731	0.046	0.778
preprocessQuantile	0.355	0.029	0.384
preprocessRaw	4.329	0.344	4.678
preprocessSwan	0.425	0.035	0.461
qcReport	0.046	0.001	0.047
ratioConvert-methods	0.090	0.001	0.091
read.metharray	6.630	0.305	6.964
read.metharray.exp	10.235	0.354	10.598
read.metharray.sheet	0.055	0.002	0.056
readGEORawFile	0.001	0.000	0.001
readTCGA	0	0	0
subsetByLoci	0.477	0.040	0.518
utils	0.162	0.067	0.229