BioC 3.5: CHECK report for bsseq on tokay2

Package: bsseq

Version: 1.12.2

Command: rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.12.2.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.12.2.tar.gz

StartedAt: 2017-08-15 22:24:57 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:32:51 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 473.7 seconds

RetCode: 0

Status:  OK

CheckDir: bsseq.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf bsseq.buildbin-libdir bsseq.Rcheck && mkdir bsseq.buildbin-libdir bsseq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bsseq.buildbin-libdir bsseq_1.12.2.tar.gz >bsseq.Rcheck\00install.out 2>&1 && cp bsseq.Rcheck\00install.out bsseq-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=bsseq.buildbin-libdir --install="check:bsseq-install.out" --force-multiarch --no-vignettes --timings bsseq_1.12.2.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/bsseq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
BSmooth.tstat 10.96   1.75   14.86
getMeth        5.08   1.30    6.38
goodnessOfFit  3.80   1.25    5.20
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
BSmooth.tstat 8.07   1.54    9.61
getMeth       4.48   1.25    5.73
goodnessOfFit 4.09   1.33    5.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/bsseq.Rcheck/00check.log'
for details.

install for i386

* 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

install for x64

* installing *source* package 'bsseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bsseq' as bsseq_1.12.2.zip
* DONE (bsseq)

name	user	system	elapsed
BS.chr22	1.25	0.06	1.32
BSmooth	0	0	0
BSmooth.fstat	0	0	0
BSmooth.tstat	10.96	1.75	14.86
BSseq-class	2.40	0.09	2.63
BSseq	0.91	0.03	0.93
computeStat	0	0	0
data.frame2GRanges	0.03	0.00	0.03
dmrFinder	2.20	0.29	3.43
fisherTests	0.53	0.04	0.58
getCoverage	4.00	0.61	4.64
getMeth	5.08	1.30	6.38
getStats	0.37	0.10	0.47
goodnessOfFit	3.80	1.25	5.20
hasGRanges-class	0	0	0
read.bismark	1.79	0.14	3.40
read.umtab	0	0	0
smoothSds	0	0	0

name	user	system	elapsed
BS.chr22	2.03	0.03	2.06
BSmooth	0	0	0
BSmooth.fstat	0	0	0
BSmooth.tstat	8.07	1.54	9.61
BSseq-class	2.39	0.09	2.95
BSseq	0.82	0.01	0.83
computeStat	0	0	0
data.frame2GRanges	0.02	0.00	0.02
dmrFinder	1.50	0.19	1.69
fisherTests	0.45	0.03	0.48
getCoverage	3.16	0.58	3.88
getMeth	4.48	1.25	5.73
getStats	0.61	0.11	0.72
goodnessOfFit	4.09	1.33	5.42
hasGRanges-class	0	0	0
read.bismark	2.00	0.34	3.83
read.umtab	0	0	0
smoothSds	0	0	0