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CHECK report for biomformat on malbec1

This page was generated on 2020-08-10 11:41:42 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biomformat PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 168/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomformat 1.17.0
Paul J. McMurdie
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/biomformat
Branch: master
Last Commit: 8291a5b
Last Changed Date: 2020-04-27 14:53:04 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: biomformat
Version: 1.17.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biomformat.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biomformat_1.17.0.tar.gz
StartedAt: 2020-08-10 01:52:07 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 01:53:01 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 54.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: biomformat.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:biomformat.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings biomformat_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/biomformat.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomformat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomformat’ version ‘1.17.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘biomformat’ 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
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.12-bioc/meat/biomformat.Rcheck/00check.log’
for details.



Installation output

biomformat.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL biomformat
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* 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
** 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
* DONE (biomformat)

Tests output

biomformat.Rcheck/tests/testthat-biomformat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  4.436   0.132   4.577 

Example timings

biomformat.Rcheck/biomformat-Ex.timings

nameusersystemelapsed
biom-class0.1440.0000.156
biom-methods0.0280.0000.025
biom_data-methods0.0960.0000.104
biom_shape-methods0.0080.0000.006
colnames-methods0.0080.0000.006
header-methods0.0040.0000.005
make_biom0.0960.0040.098
matrix_element_type-methods0.0080.0000.005
ncol-methods0.0040.0000.006
nrow-methods0.0040.0000.006
observation_metadata-methods0.0560.0000.056
read_biom0.0120.0000.010
read_hdf5_biom0.0920.0000.089
rownames-methods0.0040.0000.005
sample_metadata-methods0.0440.0000.041
show-methods0.0040.0000.006
write_biom0.0120.0040.016