Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-03-27 11:40:29 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
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 194/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biocthis 1.13.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/biocthis
git_branch: devel
git_last_commit: 2f8bc84
git_last_commit_date: 2023-12-02 13:55:46 -0400 (Sat, 02 Dec 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for biocthis on kunpeng2


To the developers/maintainers of the biocthis package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocthis.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: biocthis
Version: 1.13.0
Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:biocthis.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings biocthis_1.13.0.tar.gz
StartedAt: 2024-03-27 02:56:12 -0000 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 02:56:56 -0000 (Wed, 27 Mar 2024)
EllapsedTime: 44.1 seconds
RetCode: 0
Status:   OK  
CheckDir: biocthis.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD check --install=check:biocthis.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library --no-vignettes --timings biocthis_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/biocthis.Rcheck’
* using R Under development (unstable) (2024-03-19 r86153)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocthis/DESCRIPTION’ ... OK
* this is package ‘biocthis’ version ‘1.13.0’
* package encoding: UTF-8
* 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 ‘biocthis’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Missing object imported by a ':::' call: ‘usethis:::get_active_r_file’
Unexported objects imported by ':::' calls:
  ‘BiocManager:::.version_map_get_online’ ‘BiocManager:::isDevel’
  ‘usethis:::asciify’ ‘usethis:::check_is_package’
  ‘usethis:::check_vignette_name’ ‘usethis:::create_directory’
  ‘usethis:::is_package’ ‘usethis:::proj_desc_field_update’
  ‘usethis:::proj_version’ ‘usethis:::project_name’
  ‘usethis:::render_template’ ‘usethis:::target_repo_spec’
  ‘usethis:::use_dot_github’ ‘usethis:::uses_git’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
use_bioc_github_action: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/biocthis.Rcheck/00check.log’
for details.


Installation output

biocthis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD INSTALL biocthis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2024.03.20/site-library’
* installing *source* package ‘biocthis’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
** testing if installed package can be loaded from final location
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
Warning in normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
** testing if installed package keeps a record of temporary installation path
* DONE (biocthis)

Tests output

biocthis.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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(biocthis)
Warning messages:
1: In normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
2: In normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
3: In normalizePath(tools::R_user_dir("R.cache", which = "cache")) :
  path[1]="/home/biocbuild/.cache/R/R.cache": No such file or directory
> 
> test_check("biocthis")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  1.236   0.113   1.387 

Example timings

biocthis.Rcheck/biocthis-Ex.timings

nameusersystemelapsed
bioc_badges000
bioc_style0.5030.0200.525
biocthis_example_pkg0.0430.0080.052
use_bioc_citation0.1770.0320.211
use_bioc_coc0.1440.0080.153
use_bioc_description0.1710.0120.189
use_bioc_feature_request_template0.1020.0080.112
use_bioc_github_action000
use_bioc_issue_template0.0930.0000.095
use_bioc_news_md0.0900.0070.099
use_bioc_pkg_templates0.1980.0120.215
use_bioc_pkgdown_css0.0770.0150.095
use_bioc_readme_rmd0.2020.0000.205
use_bioc_support0.1170.0000.119
use_bioc_vignette0.9030.0410.959