===============================
R CMD BUILD
===============================
* checking for file ImageArray/DESCRIPTION ... OK
* preparing ImageArray:
* 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
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
ImageArray.R
* building ImageArray_0.99.5.tar.gz
===============================
BiocCheckGitClone('ImageArray')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3946/6bc6923576618eb2ccf81c945a903e6fc67c6113/ImageArray
BiocVersion: 3.23
Package: ImageArray
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3946/6bc6923576618eb2ccf81c945a903e6fc67c6113/ImageArray.BiocCheck
BiocCheckVersion: 1.47.12
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3946/6bc6923576618eb2ccf81c945a903e6fc67c6113/ImageArray
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 v1.47.12 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/3946/6bc6923576618eb2ccf81c945a903e6fc67c6113/ImageArray.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file ImageArray/DESCRIPTION ... OK
* checking extension type ... Package
* this is package ImageArray version 0.99.5
* 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 ImageArray 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: DelayedArray:::normarg_verbose
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [19s/19s] 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 ... [21s/15s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
BFArray-methods 7.536 0.545 2.504
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [192s/174s]
[192s/174s] ERROR
Running the tests in tests/testthat.R failed.
Last 20 lines of output:
Error in `read_chunk(zarr_array_path = path, chunk_name = chunk_id, metadata = metadata_v3, fill = TRUE)`: object 'converted_chunk' not found
Backtrace:
1. ImageArray::writeImageArray(...) at test-manipulation.R:145:3
2. Rarr::writeZarrArray(...)
3. DelayedArray::BLOCK_write_to_sink(sink, x)
4. DelayedArray::sinkApply(...)
5. DelayedArray::gridReduce(FUN_WRAPPER, grid, sink, FUN, ..., verbose = verbose)
6. DelayedArray (local) FUN(viewport, init, ...)
7. DelayedArray (local) FUN(init, viewport, ...)
8. S4Arrays::write_block(sink, viewport, block)
9. Rarr (local) write_block(sink, viewport, block)
10. Rarr::update_zarr_array(sink@zarr_array_path, x = block, index = index)
11. BiocGenerics::lapply(...)
12. base::lapply(...)
13. Rarr (local) FUN(X[[i]], ...)
14. Rarr:::read_chunk(...)
[ FAIL 1 | WARN 2 | SKIP 0 | PASS 87 ]
Error:
! Test failures.
Execution halted
* 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, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3946/6bc6923576618eb2ccf81c945a903e6fc67c6113/ImageArray.Rcheck/00check.log
for details.
===============================
BiocCheck('ImageArray_0.99.5.tar.gz')
===============================
Installing ImageArray
Package installed successfully
ImageArray session metadata
sourceDir: /tmp/RtmpwmNYvA/file3087da31061dfd/ImageArray
BiocVersion: 3.23
Package: ImageArray
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3946/6bc6923576618eb2ccf81c945a903e6fc67c6113/ImageArray.BiocCheck
BiocCheckVersion: 1.47.12
sourceDir: /tmp/RtmpwmNYvA/file3087da31061dfd/ImageArray
installDir: /tmp/RtmpwmNYvA/file3087da2e45b7c5
isTarBall: TRUE
platform: unix
Running BiocCheck on ImageArray
* 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 4.1.0 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 (70%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ImageArray...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/ImageArray.R (line 606, column 3)
* 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 8
functions greater than 50 lines.
The longest 5 functions are:
writeImageArray() (R/ImageArray.R): 104 lines
...
BFArray() (R/BFArray.R): 57 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; 484 lines (27%) are
not.
First few lines:
R/AllClasses.R#L2 Class = "ImageArray", ...
...
vignettes/ImageArray.Rmd#L318 shinyApp(ui = ui, server = server) ...
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 Package is in the Support Site Watched Tags.
BiocCheck v1.47.12 results
0 ERRORS | 0 WARNINGS | i 4 NOTES
i See the ImageArray.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.