===============================
R CMD BUILD
===============================
* checking for file ‘imageFeatureTCGA/DESCRIPTION’ ... OK
* preparing ‘imageFeatureTCGA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘imageFeatureTCGA_0.99.66.tar.gz’
===============================
BiocCheckGitClone('imageFeatureTCGA')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4149/749664ac924029d47cf1be5b9d8bda16f3297501/imageFeatureTCGA
→ BiocVersion: 3.23
→ Package: imageFeatureTCGA
→ PackageVersion: 0.99.66
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4149/749664ac924029d47cf1be5b9d8bda16f3297501/imageFeatureTCGA.BiocCheck
→ BiocCheckVersion: 1.47.25
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4149/749664ac924029d47cf1be5b9d8bda16f3297501/imageFeatureTCGA
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.47.25 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4149/749664ac924029d47cf1be5b9d8bda16f3297501/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: 2026-04-14 18:39:13 UTC
* using option ‘--no-vignettes’
* checking for file ‘imageFeatureTCGA/DESCRIPTION’ ... OK
* this is package ‘imageFeatureTCGA’ version ‘0.99.66’
* 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 for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... 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 ... [22s/22s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [13s/14s] ERROR
Running examples in ‘imageFeatureTCGA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ProvGigaList
> ### Title: ProvGigaList class for handling lists of ProvGiga objects
> ### Aliases: ProvGigaList .ProvGigaList ProvGigaList-class
> ### path,ProvGigaList-method import,ProvGigaList,ANY,ANY-method
>
> ### ** Examples
>
> ## slide level imports
> slide_urls <- getCatalog("provgigapath") |>
+ dplyr::filter(level == "slide_level", Project.ID == "TCGA-UVM") |>
+ dplyr::slice(1:3) |>
+ getFileURLs()
>
> ## set a temporary BiocFileCache cache location
> old <- options(BiocFileCache.cache = tempdir())
> on.exit(options(BiocFileCache.cache = old))
>
> ProvGigaList(slide_urls) |>
+ import(redownload = FALSE)
Download status: 0 done; 3 in progress (0 b/s). Total size: 8.95 Kb (??%)...
Download status: 3 done; 0 in progress. Total size: 120.84 Kb (100%)... done!
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘yaml’
Calls: import ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tinytest.R’ [55s/54s]
[55s/55s] 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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4149/749664ac924029d47cf1be5b9d8bda16f3297501/imageFeatureTCGA.Rcheck/00check.log’
for details.
===============================
BiocCheck('imageFeatureTCGA_0.99.66.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
── Installing imageFeatureTCGA ─────────────────────────────────────────────────
✔ Package installed successfully
── imageFeatureTCGA session metadata ───────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9hbbnh/file2c3bf01af97fad/imageFeatureTCGA
→ BiocVersion: 3.23
→ Package: imageFeatureTCGA
→ PackageVersion: 0.99.66
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4149/749664ac924029d47cf1be5b9d8bda16f3297501/imageFeatureTCGA.BiocCheck
→ BiocCheckVersion: 1.47.25
→ sourceDir: /tmp/Rtmp9hbbnh/file2c3bf01af97fad/imageFeatureTCGA
→ installDir: /tmp/Rtmp9hbbnh/file2c3bf0112fbb0a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on imageFeatureTCGA ───────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.5.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (61%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• imageFeatureTCGA.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of imageFeatureTCGA...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/utils.R (line 147, column 38)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
The longest 5 functions are:
• .cache_url_files() (R/utils.R): 73 lines
• _anonymous_.215() (R/HoverNet.R): 56 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
First few lines:
• vignettes/imageFeatureTCGA.Rmd#L103 position on the slide ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Unable to find your email in the Support Site: HTTP 502 Bad Gateway.
── BiocCheck v1.47.25 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 6 NOTES
i See the imageFeatureTCGA.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.