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BioC 2.14: CHECK report for nucleR on zin2

This page was generated on 2014-10-08 08:49:12 -0700 (Wed, 08 Oct 2014).

Package 541/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nucleR 1.12.0
Oscar Flores
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/nucleR
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: nucleR
Version: 1.12.0
Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings nucleR_1.12.0.tar.gz
StartedAt: 2014-10-08 01:30:00 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:33:13 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 193.3 seconds
RetCode: 0
Status:  OK 
CheckDir: nucleR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings nucleR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/nucleR.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.12.0’
* 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 ... [18s/18s] 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.
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 ... 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 ... [13s/14s] 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 4 notes.
See
  ‘/home/biocbuild/bbs-2.14-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
controlCorrection0.0320.0000.032
coverage.rpm0.1120.0000.110
export.bed0.0000.0000.001
export.wig0.0000.0000.001
filterFFT0.1920.0000.198
fragmentLenDetect1.5320.0001.534
mergeCalls0.4280.0040.431
nucleR-package0.4800.0080.490
pcKeepCompDetect0.2480.0000.246
peakDetection0.5920.0000.603
peakScoring0.1800.0080.188
plotPeaks0.4600.0040.471
processReads0.1520.0040.154
processTilingArray0.0000.0000.001
syntheticNucMap0.2680.0120.286