Package: BiocInstaller

Version: 1.32.1

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocInstaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocInstaller_1.32.1.tar.gz

StartedAt: 2019-04-13 00:46:16 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:47:57 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 101.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocInstaller.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocInstaller.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocInstaller_1.32.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocInstaller.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.32.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... WARNING
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See 'C:/Users/biocbuild/bbs-3.8-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
* 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 ... 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
* 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
biocValid 5.67   0.53    6.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
biocValid 6.11   0.45     6.8
* 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 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocInstaller.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BiocInstaller_1.32.1.tar.gz && rm -rf BiocInstaller.buildbin-libdir && mkdir BiocInstaller.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocInstaller.buildbin-libdir BiocInstaller_1.32.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BiocInstaller_1.32.1.zip && rm BiocInstaller_1.32.1.tar.gz BiocInstaller_1.32.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 19486  100 19486    0     0   452k      0 --:--:-- --:--:-- --:--:--  487k

install for i386

* installing *source* package 'BiocInstaller' ...
** R
** inst
** byte-compile and prepare 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
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead.
Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help
In R CMD INSTALL

install for x64

* installing *source* package 'BiocInstaller' ...
** testing if installed package can be loaded
Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead.
Bioconductor version 3.8 (BiocInstaller 1.32.1), ?biocLite for help
* MD5 sums
packaged installation of 'BiocInstaller' as BiocInstaller_1.32.1.zip
* DONE (BiocInstaller)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BiocInstaller' successfully unpacked and MD5 sums checked
In R CMD INSTALL

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 3.8 (BiocInstaller 1.32.1), ?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
In addition: Warning message:
'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead. 


RUNIT TEST PROTOCOL -- Sat Apr 13 00:47:52 2019 
*********************************************** 
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 
   0.85    0.03    1.14 

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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 3.8 (BiocInstaller 1.32.1), ?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
In addition: Warning message:
'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
  package instead. 


RUNIT TEST PROTOCOL -- Sat Apr 13 00:47:53 2019 
*********************************************** 
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 
   0.82    0.10    1.14