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BioC 3.0: CHECK report for nucleR on zin1

This page was generated on 2015-04-10 09:39:29 -0700 (Fri, 10 Apr 2015).

Package 612/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 1.14.0
Oscar Flores
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/nucleR
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  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: nucleR
Version: 1.14.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings nucleR_1.14.0.tar.gz
StartedAt: 2015-04-10 02:37:03 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:40:54 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 230.6 seconds
RetCode: 0
Status:  OK 
CheckDir: nucleR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings nucleR_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/nucleR.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 ‘nucleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nucleR’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘htSeqTools’
* 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 ‘nucleR’ can be installed ... [19s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘BiocGenerics’ ‘IRanges’ ‘Biobase’ ‘ShortRead’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘Biobase’ ‘ShortRead’ ‘parallel’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.mergeSpace: no visible global function definition for ‘findOverlaps’
.mergeSpace: no visible global function definition for ‘reduce’
.mergeSpace: no visible global function definition for ‘mclapply’
processTilingArray: no visible global function definition for
  ‘mclapply’
fragmentLenDetect,AlignedRead: no visible global function definition
  for ‘mclapply’
fragmentLenDetect,RangedData: no visible global function definition for
  ‘mclapply’
peakDetection,list: no visible global function definition for
  ‘mclapply’
peakDetection,numeric: no visible global function definition for
  ‘mclapply’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘Starr’
* 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 ... [14s/15s] 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 5 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/nucleR.Rcheck/00check.log’
for details.

nucleR.Rcheck/00install.out:

* installing *source* package ‘nucleR’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nucleR)

nucleR.Rcheck/nucleR-Ex.timings:

nameusersystemelapsed
controlCorrection0.0240.0000.027
coverage.rpm0.0920.0040.096
export.bed0.0040.0000.001
export.wig0.0000.0000.001
filterFFT0.1760.0000.190
fragmentLenDetect1.4720.0001.686
mergeCalls0.4720.0000.587
nucleR-package0.4040.0000.404
pcKeepCompDetect0.2280.0000.227
peakDetection0.6800.0120.691
peakScoring0.1600.0040.163
plotPeaks0.3560.0000.356
processReads0.1200.0000.118
processTilingArray0.0040.0000.001
syntheticNucMap0.2440.0040.249