===============================
R CMD BUILD
===============================
* checking for file ‘Rega/DESCRIPTION’ ... OK
* preparing ‘Rega’:
* 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 ‘Rega_0.99.3.tar.gz’
===============================
BiocCheckGitClone('Rega')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3822/07e9461c2fd419f47f3da809e232a7df3a978796/Rega
→ BiocVersion: 3.23
→ Package: Rega
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3822/07e9461c2fd419f47f3da809e232a7df3a978796/Rega.BiocCheck
→ BiocCheckVersion: 1.47.16
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3822/07e9461c2fd419f47f3da809e232a7df3a978796/Rega
→ 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 v1.47.16 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/3822/07e9461c2fd419f47f3da809e232a7df3a978796/Rega.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 ‘Rega/DESCRIPTION’ ... OK
* this is package ‘Rega’ version ‘0.99.3’
* 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 ‘Rega’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [6s/6s] 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 ... WARNING
Documented arguments not in \usage in Rd file 'dot-get_rega_key.Rd':
‘envvar’
Documented arguments not in \usage in Rd file 'parse_text_body.Rd':
‘resource_name’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [3s/5s] ERROR
Running examples in ‘Rega-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: delete_submission_contents
> ### Title: Delete Submission Contents and Log Responses
> ### Aliases: delete_submission_contents
>
> ### ** Examples
>
> mock_client <- list(
+ "delete__submissions__provisional_id__datasets" =
+ function(id) list(status = "deleted")
+ )
> delete_submission_contents(5678901, mock_client)
Error in .validate_character_scalar(method) :
method must be a non-empty character scalar.
Calls: delete_submission_contents -> use_submission -> .validate_character_scalar
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [15s/15s]
[15s/15s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
Step 2/9 - Creating Submission
Step 3/9 - Adding Samples
Step 4/9 - Adding Studies
Step 5/9 - Adding Experiments
Step 6/9 - Adding Runs
Step 7/9 - Retrieving Analysis Files
Step 8/9 - Adding Analyses
Step 9/9 - Adding Datasets
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 1330 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-dot-get_ega_username.R:46:3'): .get_ega_username happy paths: envvar (keyring not set) ──
Expected `.get_ega_username()` to equal "default_user".
Differences:
`actual`: "REGA_EGA_USERNAME"
`expected`: "default_user"
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 1330 ]
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 ... [6s/6s] OK
* DONE
Status: 2 ERRORs, 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3822/07e9461c2fd419f47f3da809e232a7df3a978796/Rega.Rcheck/00check.log’
for details.
===============================
BiocCheck('Rega_0.99.3.tar.gz')
===============================
── Installing Rega ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── Rega session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpEG8ZLO/file3d18c05f7c4bb5/Rega
→ BiocVersion: 3.23
→ Package: Rega
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3822/07e9461c2fd419f47f3da809e232a7df3a978796/Rega.BiocCheck
→ BiocCheckVersion: 1.47.16
→ sourceDir: /tmp/RtmpEG8ZLO/file3d18c05f7c4bb5/Rega
→ installDir: /tmp/RtmpEG8ZLO/file3d18c03fe1dab9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Rega ───────────────────────────────────────────────────
* 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 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Rega...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 20 times)
• <<- in R/workflows.R (line 120, column 33)
• ...
• <<- in R/workflows.R (line 266, column 27)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
The longest 5 functions are:
• new_submission() (R/workflows.R): 200 lines
• ...
• finalise_submission() (R/workflows.R): 59 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...
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/experiment/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/experiment
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/workflows/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/workflows
* 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 v1.47.16 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the Rega.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.