Package: BiocInstaller

Version: 1.31.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocInstaller.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocInstaller_1.31.3.tar.gz

StartedAt: 2018-10-29 00:56:57 -0400 (Mon, 29 Oct 2018)

EndedAt: 2018-10-29 00:57:32 -0400 (Mon, 29 Oct 2018)

EllapsedTime: 35.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocInstaller.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BiocInstaller.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BiocInstaller_1.31.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocInstaller.Rcheck’
* using R Under development (unstable) (2018-10-16 r75448)
* 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 ‘1.31.3’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocInstaller.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead.

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 6.449  0.103   7.558
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/BiocInstaller.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BiocInstaller
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead.
Bioconductor version 3.8 (BiocInstaller 1.31.3), ?biocLite for help
Bioconductor does not yet support R version 3.6.0
* DONE (BiocInstaller)

R Under development (unstable) (2018-10-16 r75448) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 3.8 (BiocInstaller 1.31.3), ?biocLite for help
Bioconductor does not yet support R version 3.6.0
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
In addition: Warning message:
'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead. 


RUNIT TEST PROTOCOL -- Mon Oct 29 00:57:28 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 
  1.125   0.107   2.023 

name	user	system	elapsed
BiocUpgrade	0.000	0.000	0.001
biocLite	0.026	0.004	0.031
biocUpdatePackages	0	0	0
biocValid	6.449	0.103	7.558
biocVersion	0.001	0.000	0.000
biocinstallRepos	0.003	0.000	0.002
packageGroups	0.167	0.008	0.176
useDevel	0	0	0