Ilaria Billato
| Snapshot Date: 2026-04-21 14:59 -0400 (Tue, 21 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) |
| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-22 11:57 -0400 (Wed, 22 Apr 2026).
| 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 | ||||
| Package 1040/2351 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| imageFeatureTCGA 0.99.69 (landing page) Ilaria Billato
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for imageFeatureTCGA in R Universe. | ||||||||||||||
|
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. |
| 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: 2026-04-22 01:20:37 -0400 (Wed, 22 Apr 2026) |
| EndedAt: 2026-04-22 01:51:18 -0400 (Wed, 22 Apr 2026) |
| EllapsedTime: 1841.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: imageFeatureTCGA.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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: 2026-04-22 05:20:37 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 24.028 13.102 735.975
* 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
imageFeatureTCGA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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 46.2s
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
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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 4.4s
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test-getCatalog.R............. 0 tests
test-getCatalog.R............. 1 tests OK
test-getCatalog.R............. 2 tests OK
test-getCatalog.R............. 3 tests OK
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test-getCatalog.R............. 3 tests OK
test-getCatalog.R............. 4 tests OK
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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 2.3s
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 47ms
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 28ms
All ok, 73 results (7m 25.8s)
Warning messages:
1: In file.rename(file, dest) :
cannot rename file '/tmp/Rtmp1euCZF/file2953642f8df6d3/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/Rtmp1euCZF/file29536423f133fa/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/Rtmp1euCZF/file29536418a0e62c/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/Rtmp1euCZF/file2953646067e48b/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
63.654 4.329 453.851
imageFeatureTCGA.Rcheck/imageFeatureTCGA-Ex.timings
| name | user | system | elapsed | |
| HoverNet | 1.937 | 0.175 | 2.112 | |
| ProvGiga | 0.001 | 0.000 | 0.000 | |
| ProvGigaList | 24.028 | 13.102 | 735.975 | |
| embeddingStack | 0.001 | 0.000 | 0.001 | |
| getCatalog | 0.000 | 0.001 | 0.000 | |
| linkTCGA | 0.000 | 0.000 | 0.001 | |