| Back to Multiple platform build/check report for BioC 3.22: simplified long | 
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This page was generated on 2025-10-24 12:07 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs | 
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 | 
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 | 
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 | 
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 | 
| 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 574/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DESpace 2.1.0  (landing page) Peiying Cai 
 | nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK |  | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
| To the developers/maintainers of the DESpace package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DESpace.git to reflect on this report. See Troubleshooting Build Report for more information. - 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. | 
| Package: DESpace | 
| Version: 2.1.0 | 
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DESpace.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DESpace_2.1.0.tar.gz | 
| StartedAt: 2025-10-21 07:25:56 -0000 (Tue, 21 Oct 2025) | 
| EndedAt: 2025-10-21 07:39:31 -0000 (Tue, 21 Oct 2025) | 
| EllapsedTime: 814.5 seconds | 
| RetCode: 1 | 
| Status: ERROR | 
| CheckDir: DESpace.Rcheck | 
| Warnings: NA | 
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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:DESpace.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DESpace_2.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DESpace.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESpace’ version ‘2.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘DESpace’ 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
individual_dsp 19.566  0.642  23.277
dsp_test       16.948  0.626 401.554
svg_test       11.139  0.167  11.346
* checking for unstated dependencies in ‘tests’ ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking tests ...Warning in file.copy(Sys.glob(paste0(testsrcdir, "/*")), testdir, recursive = TRUE) :
  problem creating directory /home/biocbuild/bbs-3.22-bioc/meat/DESpace.Rcheck/00_pkg_src/DESpace/tests/testthat: No space left on device
Fatal error: cannot create 'R_TempDir'
 ERROR
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/DESpace.Rcheck/00check.log’
for details.
DESpace.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DESpace ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘DESpace’ ... ** this is package ‘DESpace’ version ‘2.1.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (DESpace)
DESpace.Rcheck/DESpace-Ex.timings
| name | user | system | elapsed | |
| FeaturePlot | 2.373 | 0.107 | 2.488 | |
| LIBD_subset | 0.001 | 0.000 | 0.000 | |
| dsp_test | 16.948 | 0.626 | 401.554 | |
| individual_dsp | 19.566 | 0.642 | 23.277 | |
| individual_svg | 4.482 | 0.046 | 4.547 | |
| results_individual_svg | 0.000 | 0.001 | 0.001 | |
| results_svg_test | 0.001 | 0.000 | 0.000 | |
| svg_test | 11.139 | 0.167 | 11.346 | |
| top_results | 0.497 | 0.000 | 0.498 | |