BioC 3.5: CHECK report for BiocInstaller on malbec2

Package: BiocInstaller

Version: 1.26.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BiocInstaller_1.26.1.tar.gz

StartedAt: 2017-10-17 21:32:54 -0400 (Tue, 17 Oct 2017)

EndedAt: 2017-10-17 21:33:50 -0400 (Tue, 17 Oct 2017)

EllapsedTime: 55.9 seconds

RetCode: 0

Status:  OK

CheckDir: BiocInstaller.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BiocInstaller_1.26.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/BiocInstaller.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocInstaller/DESCRIPTION’ ... OK
* this is package ‘BiocInstaller’ version ‘1.26.1’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
biocValid 4.444  0.224  26.801
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘BiocInstaller_unit_tests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.5-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 3.5 (BiocInstaller 1.26.1), ?biocLite for help
* DONE (BiocInstaller)

name	user	system	elapsed
BiocUpgrade	0.000	0.000	0.001
biocLite	0.024	0.008	0.031
biocUpdatePackages	0.000	0.000	0.001
biocValid	4.444	0.224	26.801
biocVersion	0.004	0.000	0.002
biocinstallRepos	0.000	0.000	0.002
packageGroups	0.072	0.012	0.086
useDevel	0	0	0