BioC experimental data: CHECK report for SomaticCancerAlterations on perceval

Package: SomaticCancerAlterations

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticCancerAlterations_1.5.0.tar.gz

StartedAt: 2015-08-22 10:02:54 -0700 (Sat, 22 Aug 2015)

EndedAt: 2015-08-22 10:06:01 -0700 (Sat, 22 Aug 2015)

EllapsedTime: 187.3 seconds

RetCode: 0

Status:  OK

CheckDir: SomaticCancerAlterations.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SomaticCancerAlterations_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/SomaticCancerAlterations.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.5.0’
* 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 ... [12s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_all.R’ [18s/21s]
 [18s/22s] 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

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-data-experiment/meat/SomaticCancerAlterations.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
all-data	0.048	0.017	0.067
all-functions	0.444	0.029	0.572