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BioC 3.5: CHECK report for bsseq on tokay2

This page was generated on 2017-10-18 14:21:56 -0400 (Wed, 18 Oct 2017).

Package 155/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.12.2
Kasper Daniel Hansen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/bsseq
Branch: RELEASE_3_5
Last Commit: 765dec7
Last Changed Date: 2017-07-21 09:26:45 -0400 (Fri, 21 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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: 2017-10-17 22:27:07 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:34:57 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 470.2 seconds
RetCode: 0
Status:  OK  
CheckDir: bsseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/bsseq.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 8.86   1.86   11.97
getMeth       4.62   1.11    5.73
goodnessOfFit 3.94   1.29    5.53
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
BSmooth.tstat 7.97   1.47    9.44
getMeth       4.42   1.22    5.64
goodnessOfFit 4.05   1.23    5.28
* 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.


bsseq.Rcheck/00install.out:


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)

bsseq.Rcheck/examples_i386/bsseq-Ex.timings:

nameusersystemelapsed
BS.chr221.260.061.33
BSmooth000
BSmooth.fstat000
BSmooth.tstat 8.86 1.8611.97
BSseq-class2.130.093.75
BSseq0.800.050.84
computeStat000
data.frame2GRanges0.030.000.03
dmrFinder1.970.222.34
fisherTests0.370.010.40
getCoverage3.050.573.68
getMeth4.621.115.73
getStats0.410.140.55
goodnessOfFit3.941.295.53
hasGRanges-class000
read.bismark1.640.183.39
read.umtab000
smoothSds000

bsseq.Rcheck/examples_x64/bsseq-Ex.timings:

nameusersystemelapsed
BS.chr221.820.081.89
BSmooth000
BSmooth.fstat000
BSmooth.tstat7.971.479.44
BSseq-class2.390.042.78
BSseq0.910.020.92
computeStat000
data.frame2GRanges0.010.000.02
dmrFinder1.550.091.64
fisherTests0.420.060.48
getCoverage3.250.553.97
getMeth4.421.225.64
getStats0.470.110.58
goodnessOfFit4.051.235.28
hasGRanges-class000
read.bismark1.750.223.48
read.umtab000
smoothSds000