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BioC 3.0: CHECK report for bsseq on zin1

This page was generated on 2015-04-10 09:40:02 -0700 (Fri, 10 Apr 2015).

Package 114/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.2.0
Kasper Daniel Hansen
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/bsseq
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: bsseq
Version: 1.2.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_1.2.0.tar.gz
StartedAt: 2015-04-09 22:08:20 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:10:56 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 155.8 seconds
RetCode: 0
Status:  OK 
CheckDir: bsseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings bsseq_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/bsseq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.2.0’
* 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 ... [15s/15s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
BSmooth.tstat : smoothSd: no visible global function definition for
  ‘Rle’
BSseq: no visible global function definition for ‘SimpleList’
chrSelectBSseq: no visible global function definition for ‘seqlevels<-’
makeClusters: no visible global function definition for ‘runValue’
orderBSseq: no visible global function definition for ‘seqlevels<-’
parsingPipeline : oneDir: no visible global function definition for
  ‘seqlevels’
parsingPipeline : oneDir: no visible global function definition for
  ‘seqlevels<-’
read.bismarkFileRaw: no visible global function definition for
  ‘DataFrame’
read.bsmoothDirRaw: no visible global function definition for
  ‘DataFrame’
seqlengths,hasGRanges: no visible global function definition for
  ‘seqlengths’
seqlengths<-,hasGRanges: no visible global function definition for
  ‘seqlengths<-’
seqlevels,hasGRanges: no visible global function definition for
  ‘seqlevels’
* 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 ... [21s/22s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
BSmooth.tstat 6.352  0.392   7.292
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-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.chr220.9320.0200.956
BSmooth0.0000.0000.001
BSmooth.tstat6.3520.3927.292
BSseq-class0.2160.0000.217
BSseq0.1920.0000.190
data.frame2GRanges0.0160.0000.017
dmrFinder1.9200.0562.101
fisherTests0.1120.0000.112
getCoverage0.8530.0000.857
getMeth1.0640.4681.562
getStats0.5080.0080.551
goodnessOfFit1.7080.0561.888
hasGRanges-class0.0000.0000.002
read.bismark000
read.umtab000