BioC 3.3: CHECK report for BiocInstaller on morelia

Package: BiocInstaller

Version: 1.21.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocInstaller_1.21.1.tar.gz

StartedAt: 2015-10-22 03:49:55 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 03:50:33 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 37.3 seconds

RetCode: 0

Status:  OK

CheckDir: BiocInstaller.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 BiocInstaller_1.21.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BiocInstaller.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocInstaller/DESCRIPTION’ ... OK
* this is package ‘BiocInstaller’ version ‘1.21.1’
* 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 ‘BiocInstaller’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* 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
'library' or 'require' call to ‘utils’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘utils:::.clean_up_dependencies’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.updateBiocInstallerFinish’ ‘.updateFinish’
* 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 ... 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 examples ... [4s/19s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
biocValid 3.296   0.15  18.491
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘BiocInstaller_unit_tests.R’ [1s/2s]
 [1s/2s] OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/BiocInstaller.Rcheck/00check.log’
for details.

* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.3 (BiocInstaller 1.21.1), ?biocLite for help
* DONE (BiocInstaller)

name	user	system	elapsed
BiocUpgrade	0	0	0
biocLite	0.019	0.003	0.021
biocUpdatePackages	0	0	0
biocValid	3.296	0.150	18.491
biocVersion	0.001	0.000	0.001
biocinstallRepos	0.004	0.000	0.004
packageGroups	0.052	0.000	0.054
useDevel	0.001	0.000	0.000