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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 alpha (2026-04-05 r89794)	4957
kjohnson3	macOS 13.7.7 Ventura	arm64	4.6.0 alpha (2026-04-08 r89818)	4686
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4627
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*

CHECK results for imageFeatureTCGA on kjohnson3

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

Version: 0.99.69

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imageFeatureTCGA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imageFeatureTCGA_0.99.69.tar.gz

StartedAt: 2026-04-17 20:16:52 -0400 (Fri, 17 Apr 2026)

EndedAt: 2026-04-17 20:20:54 -0400 (Fri, 17 Apr 2026)

EllapsedTime: 241.8 seconds

RetCode: 0

Status: OK

CheckDir: imageFeatureTCGA.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:imageFeatureTCGA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings imageFeatureTCGA_0.99.69.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/imageFeatureTCGA.Rcheck’
* using R version 4.6.0 alpha (2026-04-08 r89818)
* 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 Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-18 00:16:52 UTC
* using option ‘--no-vignettes’
* checking for file ‘imageFeatureTCGA/DESCRIPTION’ ... OK
* this is package ‘imageFeatureTCGA’ version ‘0.99.69’
* 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 ‘imageFeatureTCGA’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ProvGigaList 11.462  3.243  55.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/imageFeatureTCGA.Rcheck/00check.log’
for details.

Installation output

imageFeatureTCGA.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘imageFeatureTCGA’ ...
** this is package ‘imageFeatureTCGA’ version ‘0.99.69’
** 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 (imageFeatureTCGA)

Tests output

imageFeatureTCGA.Rcheck/tests/tinytest.Rout


R version 4.6.0 alpha (2026-04-08 r89818)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin23

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.

> if (requireNamespace("tinytest", quietly = TRUE)) {
+   tinytest::test_package("imageFeatureTCGA")
+ }

test-HoverNet.R...............    0 tests    
test-HoverNet.R...............    0 tests    
test-HoverNet.R...............    1 tests OK 
test-HoverNet.R...............    2 tests OK 
Download status: 0 done; 1 in progress (0 b/s). Total size: 1.33 Kb (0%)...
Download status: 1 done; 0 in progress. Total size: 10.24 Mb (100%)... done!             

test-HoverNet.R...............    2 tests OK 
test-HoverNet.R...............    3 tests OK 
test-HoverNet.R...............    4 tests OK 
test-HoverNet.R...............    4 tests OK 
test-HoverNet.R...............    5 tests OK 
test-HoverNet.R...............    5 tests OK 
test-HoverNet.R...............    6 tests OK 
test-HoverNet.R...............    7 tests OK 
test-HoverNet.R...............    7 tests OK 
test-HoverNet.R...............    7 tests OK 
test-HoverNet.R...............    8 tests OK 16.7s

test-ProvGiga.R...............    0 tests    
test-ProvGiga.R...............    0 tests    
test-ProvGiga.R...............    1 tests OK 
test-ProvGiga.R...............    2 tests OK 
Download status: 0 done; 1 in progress (0 b/s). Total size: 1.33 Kb (3%)...
Download status: 1 done; 0 in progress. Total size: 39.07 Kb (100%)... done!             

test-ProvGiga.R...............    2 tests OK 
test-ProvGiga.R...............    3 tests OK 
test-ProvGiga.R...............    4 tests OK 
test-ProvGiga.R...............    5 tests OK 
test-ProvGiga.R...............    5 tests OK 
test-ProvGiga.R...............    6 tests OK 0.4s

Download status: 0 done; 1 in progress (1.00 Mb/s). Total size: 4.62 Mb (15%)...
Download status: 0 done; 1 in progress (1.27 Mb/s). Total size: 12.33 Mb (40%)...
Download status: 0 done; 1 in progress (1.35 Mb/s). Total size: 19.92 Mb (65%)...
Download status: 0 done; 1 in progress (1.39 Mb/s). Total size: 27.44 Mb (90%)...
Download status: 1 done; 0 in progress. Total size: 30.60 Mb (100%)... done!             

test-ProvGigaList.R...........    0 tests    
test-ProvGigaList.R...........    0 tests    
test-ProvGigaList.R...........    1 tests OK 
test-ProvGigaList.R...........    2 tests OK 
test-ProvGigaList.R...........    3 tests OK 
test-ProvGigaList.R...........    4 tests OK 
test-ProvGigaList.R...........    5 tests OK 
test-ProvGigaList.R...........    5 tests OK 
test-ProvGigaList.R...........    6 tests OK 
test-ProvGigaList.R...........    7 tests OK 
test-ProvGigaList.R...........    8 tests OK 
test-ProvGigaList.R...........    8 tests OK 
test-ProvGigaList.R...........    8 tests OK 
Download status: 3 done; 0 in progress. Total size: 120.84 Kb (100%)... done!             

test-ProvGigaList.R...........    8 tests OK 
test-ProvGigaList.R...........    9 tests OK 
test-ProvGigaList.R...........   10 tests OK 
test-ProvGigaList.R...........   11 tests OK 24.3s

Download status: 0 done; 1 in progress (925.54 Kb/s). Total size: 3.03 Mb (10%)...
Download status: 0 done; 1 in progress (1.26 Mb/s). Total size: 10.58 Mb (35%)...
Download status: 0 done; 1 in progress (1.36 Mb/s). Total size: 18.13 Mb (59%)...
Download status: 0 done; 1 in progress (1.39 Mb/s). Total size: 25.61 Mb (84%)...
Download status: 1 done; 0 in progress. Total size: 30.60 Mb (100%)... done!             

test-getCatalog.R.............    0 tests    
test-getCatalog.R.............    1 tests OK 
test-getCatalog.R.............    2 tests OK 
test-getCatalog.R.............    3 tests OK 
Download status: 0 done; 1 in progress (982.49 Kb/s). Total size: 3.98 Mb (13%)...
Download status: 0 done; 1 in progress (1.27 Mb/s). Total size: 11.52 Mb (38%)...
Download status: 0 done; 1 in progress (1.35 Mb/s). Total size: 19.09 Mb (62%)...
Download status: 0 done; 1 in progress (1.40 Mb/s). Total size: 26.70 Mb (87%)...
Download status: 1 done; 0 in progress. Total size: 30.60 Mb (100%)... done!             

test-getCatalog.R.............    3 tests OK 
test-getCatalog.R.............    4 tests OK 
Download status: 0 done; 1 in progress (1.11 Mb/s). Total size: 5.13 Mb (17%)...
Download status: 0 done; 1 in progress (1.33 Mb/s). Total size: 12.74 Mb (42%)...
Download status: 0 done; 1 in progress (1.38 Mb/s). Total size: 20.16 Mb (66%)...
Download status: 0 done; 1 in progress (1.41 Mb/s). Total size: 27.79 Mb (91%)...
Download status: 1 done; 0 in progress. Total size: 30.60 Mb (100%)... done!             

test-getCatalog.R.............    4 tests OK 
test-getCatalog.R.............    5 tests OK 
test-getCatalog.R.............    5 tests OK 
test-getCatalog.R.............    6 tests OK 
test-getCatalog.R.............    7 tests OK 
test-getCatalog.R.............    8 tests OK 1.1s

test-linkTCGA.R...............    1 tests OK 
test-linkTCGA.R...............    2 tests OK 
test-linkTCGA.R...............    3 tests OK 
test-linkTCGA.R...............    4 tests OK 
test-linkTCGA.R...............    5 tests OK 
test-linkTCGA.R...............    5 tests OK 
test-linkTCGA.R...............    5 tests OK 
test-linkTCGA.R...............    6 tests OK 
test-linkTCGA.R...............    7 tests OK 
test-linkTCGA.R...............    8 tests OK 
test-linkTCGA.R...............    9 tests OK 
test-linkTCGA.R...............    9 tests OK 
test-linkTCGA.R...............    9 tests OK 
test-linkTCGA.R...............   10 tests OK 
test-linkTCGA.R...............   11 tests OK 
test-linkTCGA.R...............   12 tests OK 
test-linkTCGA.R...............   13 tests OK 
test-linkTCGA.R...............   14 tests OK 
test-linkTCGA.R...............   15 tests OK 
test-linkTCGA.R...............   16 tests OK 
test-linkTCGA.R...............   17 tests OK 36ms

test-utils.R..................    1 tests OK 
test-utils.R..................    2 tests OK 
test-utils.R..................    3 tests OK 
test-utils.R..................    4 tests OK 
test-utils.R..................    5 tests OK 
test-utils.R..................    6 tests OK 
test-utils.R..................    7 tests OK 
test-utils.R..................    7 tests OK 
test-utils.R..................    7 tests OK 
test-utils.R..................    8 tests OK 
test-utils.R..................    9 tests OK 
test-utils.R..................   10 tests OK 
test-utils.R..................   10 tests OK 
test-utils.R..................   10 tests OK 
test-utils.R..................   10 tests OK 
test-utils.R..................   11 tests OK 
test-utils.R..................   12 tests OK 
test-utils.R..................   13 tests OK 
test-utils.R..................   14 tests OK 
test-utils.R..................   15 tests OK 
test-utils.R..................   16 tests OK 
test-utils.R..................   16 tests OK 
test-utils.R..................   16 tests OK 
test-utils.R..................   16 tests OK 
test-utils.R..................   16 tests OK 
test-utils.R..................   17 tests OK 
test-utils.R..................   18 tests OK 
test-utils.R..................   19 tests OK 
test-utils.R..................   20 tests OK 
test-utils.R..................   21 tests OK 
test-utils.R..................   21 tests OK 
test-utils.R..................   22 tests OK 
test-utils.R..................   23 tests OK 15ms
All ok, 73 results (1m 48.5s)
> 
> proc.time()
   user  system elapsed 
 23.184   1.639 111.310

Example timings

imageFeatureTCGA.Rcheck/imageFeatureTCGA-Ex.timings

name	user	system	elapsed
HoverNet	0.724	0.194	1.346
ProvGiga	0.001	0.000	0.001
ProvGigaList	11.462	3.243	55.115
embeddingStack	0.000	0.000	0.001
getCatalog	0.001	0.001	0.000
linkTCGA	0.000	0.000	0.001