Back to Build/check report for BioC 3.22 experimental data
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-05-15 15:41 -0400 (Thu, 15 May 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4749
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 375/429HostnameOS / ArchINSTALLBUILDCHECK
SpatialDatasets 1.7.1  (landing page)
Ellis Patrick
Snapshot Date: 2025-05-15 07:30 -0400 (Thu, 15 May 2025)
git_url: https://git.bioconductor.org/packages/SpatialDatasets
git_branch: devel
git_last_commit: e4d7cda
git_last_commit_date: 2025-05-14 03:22:57 -0400 (Wed, 14 May 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    ERROR  

CHECK results for SpatialDatasets on nebbiolo2

To the developers/maintainers of the SpatialDatasets package:
- 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: SpatialDatasets
Version: 1.7.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpatialDatasets.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpatialDatasets_1.7.1.tar.gz
StartedAt: 2025-05-15 12:59:35 -0400 (Thu, 15 May 2025)
EndedAt: 2025-05-15 13:03:16 -0400 (Thu, 15 May 2025)
EllapsedTime: 220.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SpatialDatasets.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpatialDatasets.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpatialDatasets_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SpatialDatasets/DESCRIPTION’ ... OK
* this is package ‘SpatialDatasets’ version ‘1.7.1’
* 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 ‘SpatialDatasets’ can be installed ... WARNING
Found the following significant warnings:
  Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
  Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
  Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:60: unexpected END_OF_INPUT '
  Warning: previous export '‘Ferguson_Images’' is being replaced
  Warning: previous export '‘spe_Ferguson_2022’' is being replaced
  Warning: previous export '‘fergusonClinical’' is being replaced
  Warning: previous export '‘spe_Schurch_2020’' is being replaced
  Warning: previous export '‘spe_Ali_2020’' is being replaced
See ‘/home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ...Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:60: unexpected END_OF_INPUT '
'
 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 ... NOTE
Warning: previous export '‘Ferguson_Images’' is being replaced
Warning: previous export '‘spe_Ferguson_2022’' is being replaced
Warning: previous export '‘fergusonClinical’' is being replaced
Warning: previous export '‘spe_Schurch_2020’' is being replaced
Warning: previous export '‘spe_Ali_2020’' is being replaced

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... WARNING
prepare_Rd: ./man/SpatialDatasets.Rd:52: unexpected section header '\value'
prepare_Rd: ./man/SpatialDatasets.Rd:55: unexpected section header '\examples'
prepare_Rd: ./man/SpatialDatasets.Rd:60: unexpected END_OF_INPUT '
'
checkRd: (-1) SpatialDatasets.Rd:52-54: Lost braces
    52 | \value{
       |       ^
checkRd: (-1) SpatialDatasets.Rd:55-59: Lost braces
    55 | \examples{
       |          ^
* checking Rd metadata ... OK
* checking Rd cross-references ...Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:60: unexpected END_OF_INPUT '
'
 OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘fergusonClinical’ ‘spe_Amancherla_2025’ ‘spe_Vannan_2025’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘SpatialDatasets_overview.Rmd’ using rmarkdown

Quitting from SpatialDatasets_overview.Rmd:102-117 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `loadNamespace()`:
! there is no package called 'cytomapper'
---
Backtrace:
    ▆
 1. └─base::loadNamespace(x)
 2.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
 3.     └─base (local) withOneRestart(expr, restarts[[1L]])
 4.       └─base (local) doWithOneRestart(return(expr), restart)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'SpatialDatasets_overview.Rmd' failed with diagnostics:
there is no package called 'cytomapper'
--- failed re-building ‘SpatialDatasets_overview.Rmd’

SUMMARY: processing the following file failed:
  ‘SpatialDatasets_overview.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets.Rcheck/00check.log’
for details.

Installation output

SpatialDatasets.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SpatialDatasets
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SpatialDatasets’ ...
** this is package ‘SpatialDatasets’ version ‘1.7.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
Warning: /home/biocbuild/bbs-3.22-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:60: unexpected END_OF_INPUT '
'
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: previous export '‘Ferguson_Images’' is being replaced
Warning: previous export '‘spe_Ferguson_2022’' is being replaced
Warning: previous export '‘fergusonClinical’' is being replaced
Warning: previous export '‘spe_Schurch_2020’' is being replaced
Warning: previous export '‘spe_Ali_2020’' is being replaced
** testing if installed package can be loaded from final location
Warning: previous export '‘Ferguson_Images’' is being replaced
Warning: previous export '‘spe_Ferguson_2022’' is being replaced
Warning: previous export '‘fergusonClinical’' is being replaced
Warning: previous export '‘spe_Schurch_2020’' is being replaced
Warning: previous export '‘spe_Ali_2020’' is being replaced
** testing if installed package keeps a record of temporary installation path
* DONE (SpatialDatasets)

Tests output


Example timings