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This page was generated on 2026-04-18 11:36 -0400 (Sat, 18 Apr 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 alpha (2026-04-05 r89794) 4957
kjohnson3macOS 13.7.7 Venturaarm644.6.0 alpha (2026-04-08 r89818) 4686
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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

Package 1063/2404HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
imageFeatureTCGA 0.99.69  (landing page)
Ilaria Billato
Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026)
git_url: https://git.bioconductor.org/packages/imageFeatureTCGA
git_branch: devel
git_last_commit: 6fb8e9f
git_last_commit_date: 2026-04-14 16:08:37 -0400 (Tue, 14 Apr 2026)
nebbiolo1Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    OK    OK  YES
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  NA    NA    NA  
See other builds for imageFeatureTCGA in R Universe.

CHECK results for imageFeatureTCGA on nebbiolo1

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-3.23-bioc/R/bin/R CMD check --install=check:imageFeatureTCGA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings imageFeatureTCGA_0.99.69.tar.gz
StartedAt: 2026-04-18 00:59:56 -0400 (Sat, 18 Apr 2026)
EndedAt: 2026-04-18 01:06:11 -0400 (Sat, 18 Apr 2026)
EllapsedTime: 374.5 seconds
RetCode: 0
Status:   OK  
CheckDir: imageFeatureTCGA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:imageFeatureTCGA.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings imageFeatureTCGA_0.99.69.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/imageFeatureTCGA.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* 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: 2026-04-18 04:59:57 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 21.846 12.446  53.141
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL imageFeatureTCGA
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-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 alpha (2026-04-05 r89794)
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 
Download status: 0 done; 1 in progress (0 b/s). Total size: 15.28 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 46.8s

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: 4.00 Kb (10%)...
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 0.5s

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 5.7s

test-getCatalog.R.............    0 tests    
test-getCatalog.R.............    1 tests OK 
test-getCatalog.R.............    2 tests OK 
test-getCatalog.R.............    3 tests OK 
test-getCatalog.R.............    3 tests OK 
test-getCatalog.R.............    4 tests OK 
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 2.7s

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 37ms

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 29ms
All ok, 73 results (55.8s)
Warning messages:
1: In file.rename(file, dest) :
  cannot rename file '/tmp/RtmpYEhVU7/file2ecf5e20782a82/https:/store.cancerdatasci.org/hovernet/json/TCGA-VG-A8LO-01A-01-DX1.B39A4D64-82A1-4A04-8AB6-918F3058B83B.json.gz' to '/home/biocbuild/.cache/R/BiocFileCache/https://store.cancerdatasci.org/hovernet/json/TCGA-VG-A8LO-01A-01-DX1.B39A4D64-82A1-4A04-8AB6-918F3058B83B.json.gz', reason 'Invalid cross-device link'
2: In file.rename(file, dest) :
  cannot rename file '/tmp/RtmpYEhVU7/file2ecf5e42a2bf00/https:/store.cancerdatasci.org/provgigapath/slide_level/TCGA-OR-A5JJ-01Z-00-DX1.459B5DFE-47B1-426F-B009-7664C1B6FEEC.csv.gz' to '/home/biocbuild/.cache/R/BiocFileCache/https://store.cancerdatasci.org/provgigapath/slide_level/TCGA-OR-A5JJ-01Z-00-DX1.459B5DFE-47B1-426F-B009-7664C1B6FEEC.csv.gz', reason 'Invalid cross-device link'
3: In file.rename(file, dest) :
  cannot rename file '/tmp/RtmpYEhVU7/file2ecf5e8426c87/waldronlab-image-features/provgigapath/slide_level/TCGA-RZ-AB0B-01Z-00-DX1.0DF1A3A6-3030-4988-AC2C-CAA0F2EBAEB2.csv.gz' to '/home/biocbuild/.cache/R/BiocFileCache/waldronlab-image-features/provgigapath/slide_level/TCGA-RZ-AB0B-01Z-00-DX1.0DF1A3A6-3030-4988-AC2C-CAA0F2EBAEB2.csv.gz', reason 'Invalid cross-device link'
4: In file.rename(file, dest) :
  cannot rename file '/tmp/RtmpYEhVU7/file2ecf5e8426c87/waldronlab-image-features/provgigapath/slide_level/TCGA-V3-A9ZX-01Z-00-DX1.B4A9BC5E-3AFA-4765-BB79-25F3B0497B09.csv.gz' to '/home/biocbuild/.cache/R/BiocFileCache/waldronlab-image-features/provgigapath/slide_level/TCGA-V3-A9ZX-01Z-00-DX1.B4A9BC5E-3AFA-4765-BB79-25F3B0497B09.csv.gz', reason 'Invalid cross-device link'
5: In file.rename(file, dest) :
  cannot rename file '/tmp/RtmpYEhVU7/file2ecf5e8426c87/waldronlab-image-features/provgigapath/slide_level/TCGA-V3-A9ZY-01Z-00-DX1.4A7D770A-0F63-453C-A7F9-966F8EE9D64F.csv.gz' to '/home/biocbuild/.cache/R/BiocFileCache/waldronlab-image-features/provgigapath/slide_level/TCGA-V3-A9ZY-01Z-00-DX1.4A7D770A-0F63-453C-A7F9-966F8EE9D64F.csv.gz', reason 'Invalid cross-device link'
> 
> proc.time()
   user  system elapsed 
 58.187   4.703  63.941

Example timings

imageFeatureTCGA.Rcheck/imageFeatureTCGA-Ex.timings

nameusersystemelapsed
HoverNet2.4510.7293.395
ProvGiga0.0000.0010.001
ProvGigaList21.84612.44653.141
embeddingStack0.0010.0000.000
getCatalog0.0010.0000.000
linkTCGA0.0010.0000.000