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CHECK report for BiocInstaller on veracruz1

This page was generated on 2018-04-12 13:34:19 -0400 (Thu, 12 Apr 2018).

Package 125/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocInstaller 1.28.0
Bioconductor Package Maintainer
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/BiocInstaller
Branch: RELEASE_3_6
Last Commit: 7261763
Last Changed Date: 2017-10-30 12:39:34 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocInstaller
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocInstaller_1.28.0.tar.gz
StartedAt: 2018-04-12 00:56:17 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:56:49 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 31.6 seconds
RetCode: 0
Status:  OK 
CheckDir: BiocInstaller.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BiocInstaller_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiocInstaller.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.28.0’
* 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 ... 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 4.65   0.21   5.563
* 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
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/BiocInstaller.Rcheck/00check.log’
for details.



Installation output

BiocInstaller.Rcheck/00install.out

* 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 3.6 (BiocInstaller 1.28.0), ?biocLite for help
* DONE (BiocInstaller)

Tests output

BiocInstaller.Rcheck/tests/BiocInstaller_unit_tests.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 3.6 (BiocInstaller 1.28.0), ?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 -- Thu Apr 12 00:56:45 2018 
*********************************************** 
Number of test functions: 9 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocInstaller RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of deactivated test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  1.476   0.080   2.204 

Example timings

BiocInstaller.Rcheck/BiocInstaller-Ex.timings

nameusersystemelapsed
BiocUpgrade0.0000.0000.001
biocLite0.0220.0040.026
biocUpdatePackages0.0000.0000.001
biocValid4.6500.2105.563
biocVersion0.0010.0000.002
biocinstallRepos0.0020.0010.002
packageGroups0.0960.0090.105
useDevel0.0010.0000.001