Package: BiocInstaller

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocInstaller.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocInstaller_1.30.0.tar.gz

StartedAt: 2018-10-16 20:06:23 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:07:06 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 43.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocInstaller.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BiocInstaller.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BiocInstaller_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/BiocInstaller.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocInstaller/DESCRIPTION’ ... OK
* this is package ‘BiocInstaller’ version ‘1.30.0’
* 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 ‘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 ... WARNING
Missing link or links in documentation object 'biocLite.Rd':
  ‘[remotes]{install}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 9.303  0.503  11.564
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘BiocInstaller_unit_tests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/BiocInstaller.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BiocInstaller
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
* DONE (BiocInstaller)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("BiocInstaller")
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Bar
installation path not writeable, unable to update packages: Foo, Bar, Baz
installation path not writeable, unable to update packages: Foo
installation path not writeable, unable to update packages: Bar
installation path not writeable, unable to update packages: Foo, Bar, Baz
Timing stopped at: 0 0 0
Error in DEACTIVATED("too idiosyncratic for standardized testing") : 
  too idiosyncratic for standardized testing


RUNIT TEST PROTOCOL -- Tue Oct 16 20:07:02 2018 
*********************************************** 
Number of test functions: 10 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocInstaller RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.956   0.108   2.541 

name	user	system	elapsed
BiocUpgrade	0.001	0.000	0.001
biocLite	0.019	0.002	0.021
biocUpdatePackages	0.001	0.000	0.001
biocValid	9.303	0.503	11.564
biocVersion	0.002	0.000	0.002
biocinstallRepos	0.005	0.001	0.005
packageGroups	0.153	0.014	0.167
useDevel	0.001	0.001	0.002