Package: biomformat

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomformat.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings biomformat_1.14.0.tar.gz

StartedAt: 2020-04-15 01:36:37 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:37:49 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 71.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: biomformat.Rcheck

Warnings: 2

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biomformat.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings biomformat_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/biomformat.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biomformat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biomformat' version '1.14.0'
* 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 'biomformat' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/biom_data-methods.Rd:46: missing link 'plyr-package'
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/ncol-methods.Rd:6: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/ncol-methods.Rd:19: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/ncol-methods.Rd:31: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/observation_metadata-methods.Rd:30: missing link 'plyr-package'
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/rownames-methods.Rd:6: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/rownames-methods.Rd:19: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/rownames-methods.Rd:31: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/sample_metadata-methods.Rd:30: missing link 'plyr-package'
See 'C:/Users/biocbuild/bbs-3.10-bioc/meat/biomformat.Rcheck/00install.out' for details.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
make_biom: no visible global function definition for 'packageVersion'
namedList: no visible global function definition for 'setNames'
Undefined global functions or variables:
  packageVersion setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'biom_data-methods.Rd':
  'plyr-package'

Missing link or links in documentation object 'observation_metadata-methods.Rd':
  'plyr-package'

Missing link or links in documentation object 'sample_metadata-methods.Rd':
  'plyr-package'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat-biomformat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat-biomformat.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 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/biomformat.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/biomformat_1.14.0.tar.gz && rm -rf biomformat.buildbin-libdir && mkdir biomformat.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biomformat.buildbin-libdir biomformat_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL biomformat_1.14.0.zip && rm biomformat_1.14.0.tar.gz biomformat_1.14.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 30091  100 30091    0     0   898k      0 --:--:-- --:--:-- --:--:-- 1013k

install for i386

* installing *source* package 'biomformat' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'nrow' from package 'base' in package 'biomformat'
Creating a generic function for 'ncol' from package 'base' in package 'biomformat'
Creating a generic function for 'rownames' from package 'base' in package 'biomformat'
Creating a generic function for 'colnames' from package 'base' in package 'biomformat'
** help
*** installing help indices
  converting help for package 'biomformat'
    finding HTML links ... done
    biom-class                              html  
    biom-methods                            html  
    finding level-2 HTML links ... done

    biom-package                            html  
    biom_data-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/biom_data-methods.Rd:46: missing link 'plyr-package'
    biom_shape-methods                      html  
    colnames-methods                        html  
    header-methods                          html  
    make_biom                               html  
    matrix_element_type-methods             html  
    ncol-methods                            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/ncol-methods.Rd:6: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/ncol-methods.Rd:19: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/ncol-methods.Rd:31: file link 'ncol' in package 'base' does not exist and so has been treated as a topic
    nrow-methods                            html  
    observation_metadata-methods            html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/observation_metadata-methods.Rd:30: missing link 'plyr-package'
    read_biom                               html  
    read_hdf5_biom                          html  
    rownames-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/rownames-methods.Rd:6: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/rownames-methods.Rd:19: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/rownames-methods.Rd:31: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
    sample_metadata-methods                 html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/Rtmpay3ANR/R.INSTALL10ec5c847f6/biomformat/man/sample_metadata-methods.Rd:30: missing link 'plyr-package'
    show-methods                            html  
    write_biom                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'biomformat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomformat' as biomformat_1.14.0.zip
* DONE (biomformat)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'biomformat' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("biomformat")
Loading required package: biomformat
== testthat results  ===========================================================
[ OK: 136 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.95    0.23    4.21 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("biomformat")
Loading required package: biomformat
== testthat results  ===========================================================
[ OK: 136 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   3.12    0.14    3.25