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Package 85/631HostnameOS / ArchBUILDCHECKBUILD BIN
bsseq 0.7.4
Kasper Daniel Hansen
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq
Last Changed Rev: 71547 / Revision: 72575
Last Changed Date: 2012-11-29 07:04:40 -0800 (Thu, 29 Nov 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ WARNINGS ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: bsseq
Version: 0.7.4
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_0.7.4.tar.gz
StartedAt: 2013-01-16 01:08:56 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:12:02 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 185.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: bsseq.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘0.7.4’
* 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 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.bsPlotPoints: no visible binding for global variable ‘pointsMinCov’
.plotSmoothData: no visible binding for global variable ‘Bsseq’
plotRegion: no visible binding for global variable ‘positions’
plotRegion: no visible binding for global variable ‘plotRange’
* 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 ... WARNING
Files not of a type allowed in a ‘data’ directory:
  ‘CpG_context_test_data.fastq_bismark.bedGraph’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BSmooth.tstat 10.581   0.78  11.832
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck/00check.log’
for details.

bsseq.Rcheck/00install.out:

* 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
   ‘bsseq.Rnw’ 
   ‘bsseq_analysis.Rnw’ 
** testing if installed package can be loaded

* DONE (bsseq)

bsseq.Rcheck/bsseq-Ex.timings:

nameusersystemelapsed
BS.chr221.4600.0521.518
BSmooth0.0000.0040.005
BSmooth.tstat10.581 0.78011.832
BSseq-class0.5320.0080.543
BSseq0.2200.0000.219
data.frame2GRanges0.0280.0000.030
dmrFinder2.1760.0402.407
fisherTests1.0400.0001.044
getCoverage1.3680.0161.390
getMeth1.1240.5321.654
getStats1.5400.0321.575
goodnessOfFit2.8840.1043.084
hasGRanges-class0.0080.0000.007
read.bismark0.0000.0000.004
read.umtab0.0040.0000.024