Multiple platform build/check report for BioC 3.23 - CHECK results for DESpace on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4837
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"	4050
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CHECK results for DESpace on kjohnson3

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.

raw results

Summary

Package: DESpace

Version: 2.3.2

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DESpace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DESpace_2.3.2.tar.gz

StartedAt: 2026-03-13 18:23:11 -0400 (Fri, 13 Mar 2026)

EndedAt: 2026-03-13 18:26:03 -0400 (Fri, 13 Mar 2026)

EllapsedTime: 172.1 seconds

RetCode: 0

Status: WARNINGS

CheckDir: DESpace.Rcheck

Warnings: 4

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DESpace.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DESpace_2.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/DESpace.Rcheck’
* using R Under development (unstable) (2026-03-01 r89506)
* using platform: aarch64-apple-darwin23
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.3.19.1)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* current time: 2026-03-13 22:23:12 UTC
* using option ‘--no-vignettes’
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESpace’ version ‘2.3.2’
* 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 dependencies in R code ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking S3 generic/method consistency ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
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
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
* checking Rd \usage sections ... NOTE
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 6.498  0.656   7.785
dsp_test       6.410  0.314   7.682
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testhat.R’
 OK
* 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: 4 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/DESpace.Rcheck/00check.log’
for details.

Installation output

DESpace.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DESpace
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘DESpace’ ...
** this is package ‘DESpace’ version ‘2.3.2’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package can be loaded from final location
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
** testing if installed package keeps a record of temporary installation path
* DONE (DESpace)

Tests output

DESpace.Rcheck/tests/testhat.Rout


R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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> library(testthat)
> library(DESpace)
proj_create: /opt/R/arm64/share/proj/proj.db contains DATABASE.LAYOUT.VERSION.MINOR = 2 whereas a number >= 4 is expected. It comes from another PROJ installation.
proj_create: no database context specified
There appears to be a problem with the PROJ installation
> test_check("DESpace")
         (Intercept) condition20DPI condition2DPI cluster_id1 cluster_id2
2DPI_1_0           1              0             1           0           0
2DPI_2_0           1              0             1           0           0
         cluster_id3 cluster_id4 condition20DPI:cluster_id1
2DPI_1_0           0           0                          0
2DPI_2_0           0           0                          0
         condition2DPI:cluster_id1 condition20DPI:cluster_id2
2DPI_1_0                         0                          0
2DPI_2_0                         0                          0
         condition2DPI:cluster_id2 condition20DPI:cluster_id3
2DPI_1_0                         0                          0
2DPI_2_0                         0                          0
         condition2DPI:cluster_id3 condition20DPI:cluster_id4
2DPI_1_0                         0                          0
2DPI_2_0                         0                          0
         condition2DPI:cluster_id4
2DPI_1_0                         0
2DPI_2_0                         0
             (Intercept) condition20DPI condition2DPI cluster_id0
2DPI_1_Other           1              0             1           0
2DPI_2_Other           1              0             1           0
             condition20DPI:cluster_id0 condition2DPI:cluster_id0
2DPI_1_Other                          0                         0
2DPI_2_Other                          0                         0
             (Intercept) condition20DPI condition2DPI cluster_id1
2DPI_1_Other           1              0             1           0
2DPI_2_Other           1              0             1           0
             condition20DPI:cluster_id1 condition2DPI:cluster_id1
2DPI_1_Other                          0                         0
2DPI_2_Other                          0                         0
             (Intercept) condition20DPI condition2DPI cluster_id2
2DPI_1_Other           1              0             1           0
2DPI_2_Other           1              0             1           0
             condition20DPI:cluster_id2 condition2DPI:cluster_id2
2DPI_1_Other                          0                         0
2DPI_2_Other                          0                         0
             (Intercept) condition20DPI condition2DPI cluster_id3
2DPI_1_Other           1              0             1           0
2DPI_2_Other           1              0             1           0
             condition20DPI:cluster_id3 condition2DPI:cluster_id3
2DPI_1_Other                          0                         0
2DPI_2_Other                          0                         0
             (Intercept) condition20DPI condition2DPI cluster_id4
2DPI_1_Other           1              0             1           0
2DPI_2_Other           1              0             1           0
             condition20DPI:cluster_id4 condition2DPI:cluster_id4
2DPI_1_Other                          0                         0
2DPI_2_Other                          0                         0
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
 23.460   1.296  26.707

Example timings

DESpace.Rcheck/DESpace-Ex.timings

name	user	system	elapsed
FeaturePlot	0.879	0.015	0.932
LIBD_subset	0	0	0
dsp_test	6.410	0.314	7.682
individual_dsp	6.498	0.656	7.785
individual_svg	1.034	0.083	1.138
results_individual_svg	0.000	0.000	0.001
results_svg_test	0	0	0
svg_test	2.989	0.144	3.264
top_results	0.103	0.002	0.108