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This page was generated on 2025-08-04 12:13 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 2035/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpatialDecon 1.19.0  (landing page)
Maddy Griswold
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/SpatialDecon
git_branch: devel
git_last_commit: eba6c2d
git_last_commit_date: 2025-04-15 12:11:46 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for SpatialDecon on taishan

To the developers/maintainers of the SpatialDecon package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpatialDecon.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.

raw results


Summary

Package: SpatialDecon
Version: 1.19.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SpatialDecon_1.19.0.tar.gz
StartedAt: 2025-08-01 11:37:55 -0000 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:56:10 -0000 (Fri, 01 Aug 2025)
EllapsedTime: 1094.3 seconds
RetCode: 1
Status:   ERROR  
CheckDir: SpatialDecon.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:SpatialDecon.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SpatialDecon_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpatialDecon.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 ‘SpatialDecon/DESCRIPTION’ ... OK
* this is package ‘SpatialDecon’ version ‘1.19.0’
* 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 ‘SpatialDecon’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
download_profile_matrix: no visible binding for global variable
  ‘profile_matrix’
Undefined global functions or variables:
  profile_matrix
* 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 LazyData ... 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
runCollapseCellTypes 119.557  0.837 161.791
runReverseDecon      118.061  0.263 155.113
runspatialdecon       57.256  0.976  79.355
runMergeTumorIntoX    20.905  0.108  28.203
runErrorModel         20.613  0.099  29.433
reverseDecon           9.567  0.275  15.062
spatialdecon           4.381  0.290   6.066
SpatialDecon-package   4.481  0.120   6.033
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "2 / 4 : C"
  [1] "3 / 4 : A"
  [1] "4 / 4 : D"
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-integration-testing.R:105:3'): spatialdeconTILs is as expected: beta ──
  all(abs(res.test$beta - res$beta) < 0.01) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
  Error: Test failures
  Execution halted
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SpatialDecon.Rcheck/00check.log’
for details.


Installation output

SpatialDecon.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL SpatialDecon
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘SpatialDecon’ ...
** this is package ‘SpatialDecon’ version ‘1.19.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (SpatialDecon)

Tests output

SpatialDecon.Rcheck/tests/testthat.Rout.fail


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SpatialDecon)
> 
> test_check("SpatialDecon")
[1] "Creating Atlas"
[1] "1 / 4 : B"
[1] "2 / 4 : C"
[1] "3 / 4 : A"
[1] "4 / 4 : D"
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-integration-testing.R:105:3'): spatialdeconTILs is as expected: beta ──
all(abs(res.test$beta - res$beta) < 0.01) is not TRUE

`actual`:   FALSE
`expected`: TRUE 

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 95 ]
Error: Test failures
Execution halted

Example timings

SpatialDecon.Rcheck/SpatialDecon-Ex.timings

nameusersystemelapsed
SpatialDecon-package4.4810.1206.033
TIL_barplot1.4780.0042.155
collapseCellTypes1.4900.0162.350
create_profile_matrix0.5670.0521.064
derive_GeoMx_background0.0040.0000.004
download_profile_matrix0.2460.1543.149
florets1.5060.0362.878
mergeTumorIntoX0.0110.0040.038
reverseDecon 9.567 0.27515.062
runCollapseCellTypes119.557 0.837161.791
runErrorModel20.613 0.09929.433
runMergeTumorIntoX20.905 0.10828.203
runReverseDecon118.061 0.263155.113
runspatialdecon57.256 0.97679.355
spatialdecon4.3810.2906.066