Package: BiocInstaller

Version: 1.28.0

Command: rm -rf BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && mkdir BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocInstaller.buildbin-libdir BiocInstaller_1.28.0.tar.gz >BiocInstaller.Rcheck\00install.out 2>&1 && cp BiocInstaller.Rcheck\00install.out BiocInstaller-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocInstaller.buildbin-libdir --install="check:BiocInstaller-install.out" --force-multiarch --no-vignettes --timings BiocInstaller_1.28.0.tar.gz

StartedAt: 2018-04-11 22:29:24 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:30:06 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 41.7 seconds

RetCode: 0

Status:  OK

CheckDir: BiocInstaller.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && mkdir BiocInstaller.buildbin-libdir BiocInstaller.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiocInstaller.buildbin-libdir BiocInstaller_1.28.0.tar.gz >BiocInstaller.Rcheck\00install.out 2>&1 && cp BiocInstaller.Rcheck\00install.out BiocInstaller-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BiocInstaller.buildbin-libdir --install="check:BiocInstaller-install.out" --force-multiarch --no-vignettes --timings BiocInstaller_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocInstaller.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
biocValid 4.02   0.33    5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'BiocInstaller_unit_tests.R'
 OK
** running tests for arch 'x64' ...
  Running 'BiocInstaller_unit_tests.R'
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/BiocInstaller.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BiocInstaller' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocInstaller'
    finding HTML links ... done
    BiocUpgrade                             html  
    biocLite                                html  
    biocUpdatePackages                      html  
    biocValid                               html  
    biocVersion                             html  
    biocinstallRepos                        html  
    packageGroups                           html  
    useDevel                                html  
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
In R CMD INSTALL

install for x64

* installing *source* package 'BiocInstaller' ...
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
* MD5 sums
packaged installation of 'BiocInstaller' as BiocInstaller_1.28.0.zip
* DONE (BiocInstaller)
In R CMD INSTALL
In R CMD INSTALL

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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
Timing stopped at: 0 0 0
Error in DEACTIVATED("too idiosyncratic for standardized testing") : 
  too idiosyncratic for standardized testing


RUNIT TEST PROTOCOL -- Wed Apr 11 22:30:00 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 
   1.23    0.04    1.62 

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
Timing stopped at: 0 0 0
Error in DEACTIVATED("too idiosyncratic for standardized testing") : 
  too idiosyncratic for standardized testing


RUNIT TEST PROTOCOL -- Wed Apr 11 22:30:02 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 
   1.39    0.09    1.70