Back to Build/check report for BioC 3.21 experimental data |
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This page was generated on 2025-06-10 15:01 -0400 (Tue, 10 Jun 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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: 2025-06-10 12:58:50 -0400 (Tue, 10 Jun 2025) |
EndedAt: 2025-06-10 13:20:22 -0400 (Tue, 10 Jun 2025) |
EllapsedTime: 1291.8 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: SpatialDatasets.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running 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 ### ############################################################################## ############################################################################## * 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)