BioC experimental data: CHECK report for GGdata on zin1

Package: GGdata

Version: 1.11.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GGdata_1.11.0.tar.gz

StartedAt: 2016-09-17 11:43:19 -0700 (Sat, 17 Sep 2016)

EndedAt: 2016-09-17 11:45:35 -0700 (Sat, 17 Sep 2016)

EllapsedTime: 136.1 seconds

RetCode: 0

Status:  OK

CheckDir: GGdata.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GGdata_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-data-experiment/meat/GGdata.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGdata/DESCRIPTION’ ... OK
* this is package ‘GGdata’ version ‘1.11.0’
* 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 ‘GGdata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 71.9Mb
  sub-directories of 1Mb or more:
    data   21.1Mb
    parts  50.8Mb
* checking package 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 ... NOTE
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘GGBase’ ‘illuminaHumanv1.db’ ‘methods’ ‘snpStats’
  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
File ‘GGdata/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste("To get a tailored smlSet, use getSS(\"",     pkgname, "\", [chrvec])", sep = ""), "\n")
    packageStartupMessage("available chromosomes are named ", paste(selectSome(cn),     collapse = ", "), "\n")

See section ‘Good practice’ in '?.onAttach'.
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
hmceuB36-pkg 11.608  2.064  14.015
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-data-experiment/meat/GGdata.Rcheck/00check.log’
for details.

* installing *source* package ‘GGdata’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
* DONE (GGdata)

name	user	system	elapsed
hmceuB36-pkg	11.608	2.064	14.015