Build/check report for BioC 3.24 - CHECK results for imageFeatureTCGA on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4796
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 nebbiolo2

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: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:imageFeatureTCGA.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings imageFeatureTCGA_0.99.69.tar.gz

StartedAt: 2026-04-23 00:36:51 -0400 (Thu, 23 Apr 2026)

EndedAt: 2026-04-23 00:48:12 -0400 (Thu, 23 Apr 2026)

EllapsedTime: 680.8 seconds

RetCode: 0

Status: OK

CheckDir: imageFeatureTCGA.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:imageFeatureTCGA.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings imageFeatureTCGA_0.99.69.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/imageFeatureTCGA.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-23 04:36:52 UTC
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
ProvGigaList 22.742 11.732  88.168
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

imageFeatureTCGA.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL imageFeatureTCGA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-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 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> 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 
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 41.3s

test-ProvGiga.R...............    0 tests    
test-ProvGiga.R...............    0 tests    
test-ProvGiga.R...............    1 tests OK 
test-ProvGiga.R...............    2 tests OK 
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 0.2s

Download status: 0 done; 1 in progress (0 b/s). Total size: 10.58 Kb (0%)...
Download status: 0 done; 1 in progress (1.12 Mb/s). Total size: 6.06 Mb (20%)...
Download status: 0 done; 1 in progress (1.30 Mb/s). Total size: 13.62 Mb (45%)...
Download status: 0 done; 1 in progress (1.37 Mb/s). Total size: 21.07 Mb (69%)...
Download status: 0 done; 1 in progress (1.40 Mb/s). Total size: 28.82 Mb (94%)...
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 
test-ProvGigaList.R...........    8 tests OK 
test-ProvGigaList.R...........    9 tests OK 
test-ProvGigaList.R...........   10 tests OK 
test-ProvGigaList.R...........   11 tests OK 32.3s

Download status: 0 done; 1 in progress (0 b/s). Total size: 1.32 Kb (0%)...
Download status: 0 done; 1 in progress (955.27 Kb/s). Total size: 3.46 Mb (11%)...
Download status: 0 done; 1 in progress (1.08 Mb/s). Total size: 11.89 Mb (39%)...
Download status: 0 done; 1 in progress (1.21 Mb/s). Total size: 19.42 Mb (63%)...
Download status: 0 done; 1 in progress (1.28 Mb/s). Total size: 26.99 Mb (88%)...
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 (652.99 Kb/s). Total size: 2.65 Mb (9%)...
Download status: 0 done; 1 in progress (909.25 Kb/s). Total size: 8.12 Mb (27%)...
Download status: 0 done; 1 in progress (905.41 Kb/s). Total size: 12.56 Mb (41%)...
Download status: 0 done; 1 in progress (935.01 Kb/s). Total size: 17.61 Mb (58%)...
Download status: 0 done; 1 in progress (1.00 Mb/s). Total size: 24.55 Mb (80%)...
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 (773.31 Kb/s). Total size: 3.20 Mb (10%)...
Download status: 0 done; 1 in progress (993.89 Kb/s). Total size: 8.96 Mb (29%)...
Download status: 0 done; 1 in progress (1.01 Mb/s). Total size: 14.32 Mb (47%)...
Download status: 0 done; 1 in progress (1.03 Mb/s). Total size: 19.84 Mb (65%)...
Download status: 0 done; 1 in progress (1.03 Mb/s). Total size: 25.08 Mb (82%)...
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 1.4s

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 35ms

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 26ms
All ok, 73 results (2m 38.2s)
Warning messages:
1: In file.rename(file, dest) :
  cannot rename file '/tmp/Rtmpvr83HS/file3213de5ee72ad2/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content' to '/home/biocbuild/.cache/R/BiocFileCache/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content', reason 'Invalid cross-device link'
2: In file.rename(file, dest) :
  cannot rename file '/tmp/Rtmpvr83HS/file3213de60374948/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content' to '/home/biocbuild/.cache/R/BiocFileCache/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content', reason 'Invalid cross-device link'
3: In file.rename(file, dest) :
  cannot rename file '/tmp/Rtmpvr83HS/file3213de2a5491c5/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content' to '/home/biocbuild/.cache/R/BiocFileCache/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content', reason 'Invalid cross-device link'
4: In file.rename(file, dest) :
  cannot rename file '/tmp/Rtmpvr83HS/file3213de2e2fd541/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content' to '/home/biocbuild/.cache/R/BiocFileCache/api/records/17981132/files/store_cancerdatasci_catalog.tsv/content', reason 'Invalid cross-device link'
> 
> proc.time()
   user  system elapsed 
 62.906   3.987 165.696

Example timings

imageFeatureTCGA.Rcheck/imageFeatureTCGA-Ex.timings

name	user	system	elapsed
HoverNet	2.056	0.223	2.280
ProvGiga	0.001	0.000	0.001
ProvGigaList	22.742	11.732	88.168
embeddingStack	0.001	0.000	0.001
getCatalog	0	0	0
linkTCGA	0	0	0