BioC experimental data: CHECK report for dsQTL on perceval

Package: dsQTL

Version: 0.3.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch dsQTL_0.3.1.tar.gz

StartedAt: 2015-04-08 09:31:14 -0700 (Wed, 08 Apr 2015)

EndedAt: 2015-04-08 09:57:53 -0700 (Wed, 08 Apr 2015)

EllapsedTime: 1599.0 seconds

RetCode: 0

Status:  OK

CheckDir: dsQTL.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 --no-multiarch dsQTL_0.3.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/dsQTL.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dsQTL/DESCRIPTION’ ... OK
* this is package ‘dsQTL’ version ‘0.3.1’
* 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 ‘dsQTL’ can be installed ... [53s/184s] OK
* checking installed package size ... NOTE
  installed size is 988.9Mb
  sub-directories of 1Mb or more:
    data   975.0Mb
    parts   13.7Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘GenomicRanges’ ‘GGBase’
  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
getSNPlocs: no visible binding for global variable ‘ch2locs’
getSNPlocs: no visible binding for global variable ‘ch17locs’
SE2ES: no visible global function definition for ‘assays’
SE2ES: no visible global function definition for ‘colData’
SE2ES: no visible global function definition for ‘sampleNames<-’
SE2ES: no visible global function definition for ‘experimentData<-’
SE2ES: no visible global function definition for ‘exptData’
SE2ES: no visible global function definition for ‘annotation<-’
* checking Rd files ... NOTE
prepare_Rd: dsQTL-package.Rd:60-61: Dropping empty section \seealso
* 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 ... [34s/59s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  ‘GGtools’ ‘rtracklayer’
* 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
  ‘/Users/biocbuild/bbs-3.0-data-experiment/meat/dsQTL.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
dsQTL-package	0.003	0.000	0.073