BioC 3.5: CHECK report for bsseq on malbec2

Package: bsseq

Version: 1.12.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_1.12.2.tar.gz

StartedAt: 2017-10-17 21:39:51 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:44:00 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 249.3 seconds

RetCode: 0

Status:  OK

CheckDir: bsseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/bsseq.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.12.2’
* package encoding: UTF-8
* 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 ‘bsseq’ 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
Namespace in Imports field not imported from: ‘HDF5Array’
  All declared Imports should be used.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
BSmooth.tstat 7.184  1.996   9.884
* 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/bsseq.Rcheck/00check.log’
for details.

* installing *source* package ‘bsseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bsseq)

name	user	system	elapsed
BS.chr22	1.440	0.184	1.623
BSmooth	0	0	0
BSmooth.fstat	0	0	0
BSmooth.tstat	7.184	1.996	9.884
BSseq-class	1.992	0.016	2.101
BSseq	0.696	0.000	0.695
computeStat	0	0	0
data.frame2GRanges	0.020	0.000	0.018
dmrFinder	1.576	0.104	2.319
fisherTests	0.388	0.000	0.387
getCoverage	2.440	0.044	2.486
getMeth	2.868	0.596	3.468
getStats	0.392	0.096	0.489
goodnessOfFit	2.856	0.156	3.221
hasGRanges-class	0.000	0.000	0.001
read.bismark	1.148	0.004	1.150
read.umtab	0	0	0
smoothSds	0.000	0.000	0.001