Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-07-22 12:44 -0400 (Mon, 22 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 210/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomformat 1.33.0  (landing page)
Paul J. McMurdie
Snapshot Date: 2024-07-21 14:00 -0400 (Sun, 21 Jul 2024)
git_url: https://git.bioconductor.org/packages/biomformat
git_branch: devel
git_last_commit: 7eee05a
git_last_commit_date: 2024-04-30 10:47:04 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for biomformat on lconway

To the developers/maintainers of the biomformat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomformat.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: biomformat
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biomformat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biomformat_1.33.0.tar.gz
StartedAt: 2024-07-21 19:47:36 -0400 (Sun, 21 Jul 2024)
EndedAt: 2024-07-21 19:51:31 -0400 (Sun, 21 Jul 2024)
EllapsedTime: 235.5 seconds
RetCode: 0
Status:   OK  
CheckDir: biomformat.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biomformat.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biomformat_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/biomformat.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomformat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomformat’ version ‘1.33.0’
* 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 code 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 ... NOTE
Invalid package aliases in Rd file 'biom-package.Rd':
  ‘biom-package’
* 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 ... 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 ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/biomformat.Rcheck/00check.log’
for details.


Installation output

biomformat.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biomformat
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ]
> 
> proc.time()
   user  system elapsed 
  2.880   0.414  15.081 

Example timings

biomformat.Rcheck/biomformat-Ex.timings

nameusersystemelapsed
biom-class0.0540.0100.251
biom-methods0.0390.0040.119
biom_data-methods0.0570.0090.211
biom_shape-methods0.0030.0020.030
colnames-methods0.0030.0010.078
header-methods0.0030.0020.005
make_biom0.0430.0070.198
matrix_element_type-methods0.0030.0000.004
ncol-methods0.0030.0020.020
nrow-methods0.0020.0010.003
observation_metadata-methods0.0340.0070.068
read_biom0.0050.0010.018
read_hdf5_biom0.0480.0040.277
rownames-methods0.0030.0010.004
sample_metadata-methods0.0210.0050.040
show-methods0.0030.0010.004
write_biom0.0080.0020.011