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BioC experimental data: CHECK report for SomaticCancerAlterations on zin1

This page was generated on 2015-04-08 17:40:48 -0700 (Wed, 08 Apr 2015).

Package 196/219HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SomaticCancerAlterations 1.1.1
Julian Gehring
Snapshot Date: 2015-04-08 06:15:26 -0700 (Wed, 08 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioc-data/branches/RELEASE_3_0/experiment/pkgs/SomaticCancerAlterations
Last Changed Rev: 3075 / Revision: 3266
Last Changed Date: 2014-10-13 14:52:40 -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 

Summary

Package: SomaticCancerAlterations
Version: 1.1.1
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SomaticCancerAlterations_1.1.1.tar.gz
StartedAt: 2015-04-08 08:58:26 -0700 (Wed, 08 Apr 2015)
EndedAt: 2015-04-08 09:00:37 -0700 (Wed, 08 Apr 2015)
EllapsedTime: 130.9 seconds
RetCode: 0
Status:  OK 
CheckDir: SomaticCancerAlterations.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings SomaticCancerAlterations_1.1.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.0-data-experiment/meat/SomaticCancerAlterations.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 ‘SomaticCancerAlterations/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SomaticCancerAlterations’ version ‘1.1.1’
* package encoding: UTF-8
* 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 ‘SomaticCancerAlterations’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* 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
hg2ncbi: no visible global function definition for ‘seqnameStyle<-’
hg2ncbi: no visible global function definition for ‘genome<-’
mutationDensity: no visible global function definition for
  ‘keepSeqlevels’
ncbi2hg: no visible global function definition for ‘seqnameStyle<-’
ncbi2hg: no visible global function definition for ‘genome<-’
* 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 ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test_all.R’ [18s/18s]
 [18s/18s] 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 was 1 note.
See
  ‘/home/biocbuild/bbs-3.0-data-experiment/meat/SomaticCancerAlterations.Rcheck/00check.log’
for details.

SomaticCancerAlterations.Rcheck/00install.out:

* installing *source* package ‘SomaticCancerAlterations’ ...
** 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 (SomaticCancerAlterations)

SomaticCancerAlterations.Rcheck/SomaticCancerAlterations-Ex.timings:

nameusersystemelapsed
all-data0.0560.0080.064
all-functions0.2880.0040.292