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This page was generated on 2025-12-11 06:35 -0500 (Thu, 11 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-28 r88973) -- "Unsuffered Consequences" | 926 |
| 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 224/230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
| VisiumIO 1.7.4 (landing page) Marcel Ramos
| teran2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||
|
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. |
| 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 |
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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
VisiumIO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/R CMD INSTALL VisiumIO ### ############################################################################## ############################################################################## * 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)