===============================
R CMD BUILD
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* checking for file CrcBiomeScreen/DESCRIPTION ... OK
* preparing CrcBiomeScreen:
* 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
* looking to see if a data/datalist file should be added
* building CrcBiomeScreen_0.99.3.tar.gz
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BiocCheckGitClone('CrcBiomeScreen')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen
BiocVersion: 3.23
Package: CrcBiomeScreen
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
/home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen/tests/testthat/CrcBiomeScreenObject_TestTask_XGBoost.rds
* 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 v1.47.1 results
0 ERRORS | 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen.Rcheck
* using R Under development (unstable) (2025-10-20 r88955)
* 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 CrcBiomeScreen/DESCRIPTION ... OK
* this is package CrcBiomeScreen version 0.99.3
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: methods
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen.Rcheck/00check.log
for details.
===============================
BiocCheck('CrcBiomeScreen_0.99.3.tar.gz')
===============================
Installing CrcBiomeScreen
Package installed successfully
CrcBiomeScreen session metadata
sourceDir: /tmp/RtmpyfXSQ3/filef57592f9749e9/CrcBiomeScreen
BiocVersion: 3.23
Package: CrcBiomeScreen
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e37201fd7dff4e3ed80584801b96a510694b40d2/CrcBiomeScreen.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/RtmpyfXSQ3/filef57592f9749e9/CrcBiomeScreen
installDir: /tmp/RtmpyfXSQ3/filef5759782fb044
isTarBall: TRUE
platform: unix
Running BiocCheck on CrcBiomeScreen
* 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 4.3.0 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 (10%).
* 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:
CrcBiomeScreen.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CrcBiomeScreen...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/KeepTaxonomicLevel.R (line 40, column 10)
* 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 11
functions greater than 50 lines.
The longest 5 functions are:
SplitTaxas() (R/SplitTaxas.R): 94 lines
...
ModelingXGBoost_noweights() (R/ModelingXGBoost_noweights.R): 74 lines
* Checking man page documentation...
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
checkClassBalance.Rd
...
ValidateModelOnData.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 78% of man
pages use at least one of these tags.
Found in files:
checkClassBalance.Rd
...
ValidateModelOnData.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
checkClassBalance.Rd
...
ValidateModelOnData.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
i NOTE: skip_on_bioc() found in testthat files: test-checkClassBalance.R
test-CreateCrcBiomeScreenObject.R test-SplitDataSet.R test-SplitTaxas.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 260 lines (10%) are > 80 characters long.
First few lines:
R/checkClassBalance.R#L14 #' @examples \dontrun{checkClassBalance ...
...
vignettes/CrcBiomeScreen.Rmd#L585 **Note**: This vignette demonstrates the
...
i NOTE: Consider multiples of 4 spaces for line indents; 753 lines (29%) are
not.
First few lines:
R/checkClassBalance.R#L18 labels <- as.factor(labels) ...
...
vignettes/CrcBiomeScreen.Rmd#L532 ...
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.
ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
BiocCheck v1.47.1 results
2 ERRORS | 0 WARNINGS | i 10 NOTES
i See the CrcBiomeScreen.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.