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BioC 2.12: CHECK report for bsseq on george2

This page was generated on 2013-10-09 09:37:54 -0700 (Wed, 09 Oct 2013).

Package 90/671HostnameOS / ArchBUILDCHECKBUILD BIN
bsseq 0.8.0
Kasper Daniel Hansen
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/bsseq
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: bsseq
Version: 0.8.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_0.8.0.tar.gz
StartedAt: 2013-10-09 00:35:55 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:40:21 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 266.0 seconds
RetCode: 0
Status:  OK 
CheckDir: bsseq.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/bsseq.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘0.8.0’
* 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 ... [20s/20s] 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
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 ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [45s/49s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BSmooth.tstat 14.821  1.436  17.284
goodnessOfFit  4.164  0.340   5.219
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [11s/12s] 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

NOTE: There was 1 note.
See
  ‘/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
** testing if installed package can be loaded
* DONE (bsseq)

bsseq.Rcheck/bsseq-Ex.timings:

nameusersystemelapsed
BS.chr222.1680.0922.381
BSmooth0.0000.0040.009
BSmooth.tstat14.821 1.43617.284
BSseq-class0.4520.0000.470
BSseq0.3200.0000.327
data.frame2GRanges0.0520.0000.050
dmrFinder3.5960.1123.865
fisherTests1.7160.0242.001
getCoverage2.0090.0602.313
getMeth1.7120.7402.633
getStats2.1600.1202.354
goodnessOfFit4.1640.3405.219
hasGRanges-class0.0120.0000.012
read.bismark0.0040.0000.006
read.umtab0.0040.0000.007