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This page was generated on 2025-12-11 06:35 -0500 (Thu, 11 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.3 LTS)x86_64R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" 926
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Package 224/230HostnameOS / ArchINSTALLBUILDCHECK
VisiumIO 1.7.4  (landing page)
Marcel Ramos
Snapshot Date: 2025-12-11 06:00 -0500 (Thu, 11 Dec 2025)
git_url: https://git.bioconductor.org/packages/VisiumIO
git_branch: devel
git_last_commit: 6fb7dbb
git_last_commit_date: 2025-12-09 14:00:04 -0500 (Tue, 09 Dec 2025)
teran2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    ERROR  


CHECK results for VisiumIO on teran2

To the developers/maintainers of the VisiumIO 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: VisiumIO
Version: 1.7.4
Command: /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:VisiumIO.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings VisiumIO_1.7.4.tar.gz
StartedAt: 2025-12-11 06:31:41 -0500 (Thu, 11 Dec 2025)
EndedAt: 2025-12-11 06:33:16 -0500 (Thu, 11 Dec 2025)
EllapsedTime: 94.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: VisiumIO.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD check --install=check:VisiumIO.install-out.txt --library=/home/rapidbuild/bbs-3.23-bioc-rapid/R/site-library --timings VisiumIO_1.7.4.tar.gz
###
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* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/VisiumIO.Rcheck’
* using R Under development (unstable) (2025-10-28 r88973)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘VisiumIO/DESCRIPTION’ ... OK
* this is package ‘VisiumIO’ version ‘1.7.4’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Marcel Ramos <marcel.ramos@sph.cuny.edu>’

Unknown, possibly misspelled, fields in DESCRIPTION:
  ‘git_url’ ‘git_branch’ ‘git_last_commit’ ‘git_last_commit_date’

The Title field should be in title case. Current version is:
  ‘Import Visium data from the 10X Space Ranger pipeline’
In title case that is:
  ‘Import Visium Data from the 10x Space Ranger Pipeline’

The Description field should not start with the package name,
  'This package' or similar.
* 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 ‘VisiumIO’ 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 use of S3 registration ... 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 ... ERROR
Incorrect (un)loading of package shared object.
Fatal error: cannot create 'R_TempDir'
The system-specific extension for shared objects must not be added.
See ?library.dynam.
 NOTE
Fatal error: cannot create 'R_TempDir'

Found the following possibly unsafe calls:
Fatal error: cannot create 'R_TempDir'

Fatal error: cannot create 'R_TempDir'
* checking Rd files ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking Rd metadata ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Fatal error: cannot create 'R_TempDir'
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 ... WARNING
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
Fatal error: cannot create 'R_TempDir'
* checking Rd \usage sections ... WARNING
Fatal error: cannot create 'R_TempDir'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ...Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Error: inferior call failed
Execution halted

Installation output

VisiumIO.Rcheck/00install.out

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###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL VisiumIO
###
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* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/R/site-library’
* installing *source* package ‘VisiumIO’ ...
** this is package ‘VisiumIO’ version ‘1.7.4’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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 (VisiumIO)

Tests output


Example timings