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BioC 2.13: CHECK report for bsseq on perceval

This page was generated on 2014-04-05 09:52:53 -0700 (Sat, 05 Apr 2014).

Package 101/750HostnameOS / ArchBUILDCHECKBUILD BIN
bsseq 0.10.0
Kasper Daniel Hansen
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/bsseq
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: bsseq
Version: 0.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch bsseq_0.10.0.tar.gz
StartedAt: 2014-04-04 23:56:20 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-05 00:00:27 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 246.5 seconds
RetCode: 0
Status:  OK 
CheckDir: bsseq.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/bsseq.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘0.10.0’
* 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 ... [21s/21s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.bsGetCol’ ‘.bsPlotLines’ ‘.bsPlotTitle’ ‘.plotSmoothData’
  ‘plotAnnoTrack’ ‘read.bsmoothDirRaw’ ‘regionFinder3’
  ‘sampleRawToBSseq’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [39s/43s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
BSmooth.tstat 10.154  3.503  16.954
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/12s]
 [10s/13s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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.chr222.1250.1422.270
BSmooth0.0020.0040.006
BSmooth.tstat10.154 3.50316.954
BSseq-class0.4180.0900.508
BSseq0.3460.0080.354
data.frame2GRanges0.0490.0050.054
dmrFinder2.4950.9324.133
fisherTests0.2210.0160.242
getCoverage1.6280.6772.335
getMeth1.7511.4493.205
getStats0.8170.3781.197
goodnessOfFit2.1110.8193.108
hasGRanges-class0.0060.0080.014
read.bismark0.0020.0040.007
read.umtab0.0030.0050.008