| Back to Build/check report for BioC 3.21 experimental data |
|
This page was generated on 2025-06-12 15:01 -0400 (Thu, 12 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4838 |
| 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 377/432 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| SpatialDatasets 1.6.3 (landing page) Ellis Patrick
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | |||||||
|
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. |
| Package: SpatialDatasets |
| Version: 1.6.3 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SpatialDatasets.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SpatialDatasets_1.6.3.tar.gz |
| StartedAt: 2025-06-12 12:57:41 -0400 (Thu, 12 Jun 2025) |
| EndedAt: 2025-06-12 13:18:31 -0400 (Thu, 12 Jun 2025) |
| EllapsedTime: 1250.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SpatialDatasets.Rcheck |
| Warnings: 3 |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:SpatialDatasets.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings SpatialDatasets_1.6.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* 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 ‘1.6.3’
* 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-3.21-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
Warning: /home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
Warning: /home/biocbuild/bbs-3.21-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-3.21-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-3.21-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
Warning: /home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
Warning: /home/biocbuild/bbs-3.21-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-3.21-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value'
Warning: /home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets.Rcheck/00_pkg_src/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples'
Warning: /home/biocbuild/bbs-3.21-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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets.Rcheck/00check.log’
for details.
SpatialDatasets.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL SpatialDatasets ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘SpatialDatasets’ ... ** this is package ‘SpatialDatasets’ version ‘1.6.3’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help Warning: /home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:52: unexpected section header '\value' Warning: /home/biocbuild/bbs-3.21-data-experiment/meat/SpatialDatasets/man/SpatialDatasets.Rd:55: unexpected section header '\examples' Warning: /home/biocbuild/bbs-3.21-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)