Package: BiocPkgTools

Version: 1.0.3

Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocPkgTools_1.0.3.tar.gz

StartedAt: 2019-04-13 00:47:40 -0400 (Sat, 13 Apr 2019)

EndedAt: 2019-04-13 00:54:27 -0400 (Sat, 13 Apr 2019)

EllapsedTime: 406.9 seconds

RetCode: 0

Status:  OK

CheckDir: BiocPkgTools.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocPkgTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings BiocPkgTools_1.0.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocPkgTools.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 'BiocPkgTools/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocPkgTools' version '1.0.3'
* package encoding: UTF-8
* 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 'BiocPkgTools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
Namespace in Imports field not imported from: 'gh'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
inducedSubgraphByPkgs: warning in induced_subgraph(g, v = pkgs):
  partial argument match of 'v' to 'vids'
subgraphByDegree: warning in induced_subgraph(g, v = names(d2)):
  partial argument match of 'v' to 'vids'
.gh_pkg_info: no visible global function definition for 'gh'
biocBuildReport: no visible binding for global variable 'start'
biocBuildReport: no visible global function definition for 'capture'
biocBuildReport: no visible global function definition for
  'except_any_of'
biocBuildReport: no visible binding for global variable 'blank'
biocBuildReport: no visible binding for global variable 'anything'
biocBuildReport: no visible binding for global variable 'any_alnums'
biocBuildReport: no visible global function definition for 'maybe'
biocBuildReport: no visible binding for global variable 'any_blanks'
biocBuildReport: no visible binding for global variable 'any_alphas'
biocBuildReport: no visible binding for global variable
  'any_non_alnums'
biocBuildReport: no visible global function definition for 'any_of'
biocBuildReport: no visible binding for global variable 'digit'
get_bioc_data: no visible binding for global variable 'tags'
inducedSubgraphByPkgs: no visible global function definition for 'V<-'
process_data: no visible binding for global variable 'Author'
process_data: no visible binding for global variable 'Package'
process_data: no visible binding for global variable 'License'
process_data: no visible binding for global variable 'biocViews'
process_data: no visible binding for global variable 'Description'
process_data: no visible binding for global variable 'downloads_month'
process_data: no visible binding for global variable 'downloads_total'
summarise_dl_stats: no visible binding for global variable 'Package'
summarise_dl_stats: no visible binding for global variable
  'Nb_of_downloads'
Undefined global functions or variables:
  Author Description License Nb_of_downloads Package V<- any_alnums
  any_alphas any_blanks any_non_alnums any_of anything biocViews blank
  capture digit downloads_month downloads_total except_any_of gh maybe
  start tags
Consider adding
  importFrom("stats", "start")
to your NAMESPACE file.
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
get_bioc_data               42.36  11.47   53.89
biocDownloadStats           38.35   9.93   48.43
buildPkgDependencyDataFrame 10.70   0.04   10.77
buildPkgDependencyIgraph     5.21   0.00    5.23
subgraphByDegree             5.08   0.00    5.10
getBiocVignette              5.02   0.01    5.06
biocPkgList                  4.97   0.03    5.11
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
biocDownloadStats           27.52  16.90   44.51
get_bioc_data               33.15  10.97   44.26
buildPkgDependencyDataFrame  7.53   0.04    7.61
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/BiocPkgTools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BiocPkgTools_1.0.3.tar.gz && rm -rf BiocPkgTools.buildbin-libdir && mkdir BiocPkgTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocPkgTools.buildbin-libdir BiocPkgTools_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BiocPkgTools_1.0.3.zip && rm BiocPkgTools_1.0.3.tar.gz BiocPkgTools_1.0.3.zip
###
##############################################################################
##############################################################################


  % 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  254k  100  254k    0     0  6181k      0 --:--:-- --:--:-- --:--:-- 6882k

install for i386

* installing *source* package 'BiocPkgTools' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocPkgTools'
    finding HTML links ... done
    BiocPkgTools                            html  
    biocBuildReport                         html  
    biocDownloadStats                       html  
    biocExplore                             html  
    biocPkgList                             html  
    buildPkgDependencyDataFrame             html  
    buildPkgDependencyIgraph                html  
    dataciteXMLGenerate                     html  
    generateBiocPkgDOI                      html  
    getBiocVignette                         html  
    getPackageInfo                          html  
    get_bioc_data                           html  
    githubURLParts                          html  
    inducedSubgraphByPkgs                   html  
    problemPage                             html  
    subgraphByDegree                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BiocPkgTools' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocPkgTools' as BiocPkgTools_1.0.3.zip
* DONE (BiocPkgTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BiocPkgTools' 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.

> library(testthat)
> library(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.8/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1089479 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

== testthat results  ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  19.03    0.89   20.67 

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.

> library(testthat)
> library(BiocPkgTools)
Loading required package: htmlwidgets
> 
> test_check("BiocPkgTools")
trying URL 'https://bioconductor.org/packages/3.8/bioc/vignettes/a4/inst/doc/a4vignette.pdf'
Content type 'application/pdf' length 1089479 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

== testthat results  ===========================================================
OK: 17 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  14.01    1.03   15.60