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CHECK report for biomformat on tokay1

This page was generated on 2018-04-12 13:27:12 -0400 (Thu, 12 Apr 2018).

Package 135/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomformat 1.6.0
Paul J. McMurdie
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/biomformat
Branch: RELEASE_3_6
Last Commit: 61fb8c7
Last Changed Date: 2017-10-30 12:41:10 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomformat
Version: 1.6.0
Command: rm -rf biomformat.buildbin-libdir biomformat.Rcheck && mkdir biomformat.buildbin-libdir biomformat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomformat.buildbin-libdir biomformat_1.6.0.tar.gz >biomformat.Rcheck\00install.out 2>&1 && cp biomformat.Rcheck\00install.out biomformat-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biomformat.buildbin-libdir --install="check:biomformat-install.out" --force-multiarch --no-vignettes --timings biomformat_1.6.0.tar.gz
StartedAt: 2018-04-11 22:31:23 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:32:52 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 88.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: biomformat.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf biomformat.buildbin-libdir biomformat.Rcheck && mkdir biomformat.buildbin-libdir biomformat.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=biomformat.buildbin-libdir biomformat_1.6.0.tar.gz >biomformat.Rcheck\00install.out 2>&1 && cp biomformat.Rcheck\00install.out biomformat-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=biomformat.buildbin-libdir --install="check:biomformat-install.out" --force-multiarch --no-vignettes --timings biomformat_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/biomformat.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 'biomformat/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biomformat' version '1.6.0'
* 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-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/ncol-methods.Rd:6: missing file link 'ncol'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/ncol-methods.Rd:19: missing file link 'ncol'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/ncol-methods.Rd:31: missing file link 'ncol'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/rownames-methods.Rd:6: missing file link 'rownames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/rownames-methods.Rd:19: missing file link 'rownames'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/rownames-methods.Rd:31: missing file link 'rownames'
See 'C:/Users/biocbuild/bbs-3.6-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 ... 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 installed files from 'inst/doc' ... 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: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/biomformat.Rcheck/00check.log'
for details.

Installation output

biomformat.Rcheck/00install.out


install for i386

* installing *source* package 'biomformat' ...
** R
** inst
** preparing 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  
    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-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/ncol-methods.Rd:6: missing file link 'ncol'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/ncol-methods.Rd:19: missing file link 'ncol'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/ncol-methods.Rd:31: missing file link 'ncol'
    nrow-methods                            html  
    observation_metadata-methods            html  
    read_biom                               html  
    read_hdf5_biom                          html  
    rownames-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/rownames-methods.Rd:6: missing file link 'rownames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/rownames-methods.Rd:19: missing file link 'rownames'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpi66Moe/R.INSTALLa2c70f56b6c/biomformat/man/rownames-methods.Rd:31: missing file link 'rownames'
    sample_metadata-methods                 html  
    show-methods                            html  
    write_biom                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'biomformat' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biomformat' as biomformat_1.6.0.zip
* DONE (biomformat)
In R CMD INSTALL
In R CMD INSTALL

Tests output

biomformat.Rcheck/tests_i386/testthat-biomformat.Rout


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.

> 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   2.87    0.12    3.00

biomformat.Rcheck/tests_x64/testthat-biomformat.Rout


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.

> 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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.09    0.07    4.20

Example timings

biomformat.Rcheck/examples_i386/biomformat-Ex.timings

nameusersystemelapsed
biom-class0.320.000.33
biom-methods0.430.010.44
biom_data-methods0.150.000.16
biom_shape-methods000
colnames-methods000
header-methods0.020.000.01
make_biom0.090.000.10
matrix_element_type-methods000
ncol-methods0.020.000.01
nrow-methods000
observation_metadata-methods0.030.000.03
read_biom0.010.000.02
read_hdf5_biom0.290.000.53
rownames-methods0.010.000.01
sample_metadata-methods0.050.000.05
show-methods000
write_biom0.010.000.02

biomformat.Rcheck/examples_x64/biomformat-Ex.timings

nameusersystemelapsed
biom-class0.360.000.36
biom-methods0.530.000.53
biom_data-methods0.210.000.20
biom_shape-methods000
colnames-methods0.010.000.02
header-methods000
make_biom0.130.000.12
matrix_element_type-methods000
ncol-methods000
nrow-methods0.010.000.02
observation_metadata-methods0.030.000.03
read_biom0.020.000.01
read_hdf5_biom0.230.001.58
rownames-methods000
sample_metadata-methods0.030.000.03
show-methods000
write_biom0.020.000.02