BioC 3.1: CHECK report for minfi on zin2

Package: minfi

Version: 1.14.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.14.0.tar.gz

StartedAt: 2015-10-09 03:32:48 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:45:16 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 747.7 seconds

RetCode: 0

Status:  OK

CheckDir: minfi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings minfi_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/minfi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘GenomicRanges’ ‘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 ... [17s/17s] 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:
  ‘GenomicRanges:::.ShallowSimpleListAssays’
  ‘GenomicRanges:::.valid.SummarizedExperiment.colData_dims’
  ‘GenomicRanges:::clone’ ‘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 ... [422s/464s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
gaphunter          265.201  0.110 265.724
bumphunter          37.649  1.368  39.033
preprocessFunnorm   31.640  0.231  49.210
preprocessNoob      17.139  0.016  29.285
preprocessQuantile  12.864  0.124  19.747
read.450k.exp        5.848  0.019   7.903
minfiQC              5.769  0.009   5.773
detectionP           5.096  0.004   5.104
read.450k            4.696  0.009   6.350
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [96s/117s]
 [96s/118s] 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-3.1-bioc/meat/minfi.Rcheck/00check.log’
for details.

* installing *source* package ‘minfi’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (minfi)

name	user	system	elapsed
GenomicMethylSet-class	0.002	0.000	0.002
GenomicRatioSet-class	0.000	0.000	0.001
IlluminaMethylationManifest-class	2.405	0.056	2.467
MethylSet-class	0.002	0.000	0.001
RGChannelSet-class	0.001	0.000	0.001
RatioSet-class	0.001	0.000	0.001
bumphunter	37.649	1.368	39.033
controlStripPlot	1.351	0.008	1.358
densityBeanPlot	4.872	0.012	4.881
densityPlot	2.792	0.004	2.793
detectionP	5.096	0.004	5.104
dmpFinder	0.182	0.000	0.182
estimateCellCounts	0	0	0
fixMethOutliers	2.937	0.004	2.945
gaphunter	265.201	0.110	265.724
getAnnotation	0.970	0.039	1.011
getGenomicRatioSetFromGEO	0	0	0
getQC	0.448	0.004	0.464
getSex	2.007	0.036	2.042
logit2	0.001	0.000	0.000
makeGenomicRatioSetFromMatrix	1.027	0.004	1.031
mdsPlot	0.639	0.000	0.638
minfiQC	5.769	0.009	5.773
plotBetasByType	0	0	0
plotCpg	0.160	0.000	0.161
preprocessFunnorm	31.640	0.231	49.210
preprocessIllumina	2.216	0.091	3.876
preprocessNoob	17.139	0.016	29.285
preprocessQuantile	12.864	0.124	19.747
preprocessRaw	1.656	0.004	2.051
preprocessSwan	0.000	0.000	0.001
qcReport	0.061	0.000	0.062
read.450k	4.696	0.009	6.350
read.450k.exp	5.848	0.019	7.903
read.450k.sheet	0.068	0.000	0.068
readGEORawFile	0.001	0.000	0.000
readTCGA	0.000	0.000	0.001
utils	1.362	0.200	2.006