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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_0.99.2.tar.gz
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BiocCheckGitClone('CrcBiomeScreen')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/CrcBiomeScreen
BiocVersion: 3.23
Package: CrcBiomeScreen
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/CrcBiomeScreen.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/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/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/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/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/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 0.99.2
* 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 CrcBiomeScreen 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: rlang
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [30s/30s] NOTE
CreateCrcBiomeScreenObject: no visible global function definition for
new
ModelingRF: no visible binding for global variable n_cv
ModelingRF : <anonymous>: no visible binding for global variable i
ModelingRF_noweights: no visible binding for global variable n_cv
ModelingRF_noweights : <anonymous>: no visible binding for global
variable i
SplitTaxas: no visible binding for global variable tmp
SplitTaxas: no visible binding for global variable Kingdom
SplitTaxas: no visible binding for global variable Species
qcByCmdscale: no visible binding for global variable Dim1
qcByCmdscale: no visible binding for global variable Dim2
qcByCmdscale: no visible binding for global variable IsOutlier
qcByCmdscale: no visible binding for global variable SampleID
setNormalizedData<-,CrcBiomeScreen: no visible global function
definition for validObject
setTaxaData<-,CrcBiomeScreen: no visible global function definition for
validObject
Undefined global functions or variables:
Dim1 Dim2 IsOutlier Kingdom SampleID Species i n_cv new tmp
validObject
Consider adding
importFrom("methods", "new", "validObject")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'EvaluateCrcBiomeScreen.Rd':
\examples lines wider than 100 characters:
# EvaluateCrcBiomeScreen(predictions, true_labels, TrueLabel = "CRC", TaskName = "MyEvaluation", PlotAUC = TRUE)
Rd file 'PredictCrcBiomeScreen.Rd':
\examples lines wider than 100 characters:
newdata = getNormalizedData(ValidationData_filtered_qc), # Use the appropriate data slot from your new data
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
NHSBCSP_screeningData Thomas_2018_RelativeAbundance
ZellerG_2014_RelativeAbundance
All user-level objects in a package should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'NormalizeData.Rd'
level
Documented arguments not in \usage in Rd file 'RunScreening.Rd':
normalize_method
Undocumented arguments in Rd file 'qcByCmdscale.Rd'
plot
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 ... NOTE
Argument items with no description in Rd file 'SplitTaxas.Rd':
CrcBiomeScreenObject
* checking for unstated dependencies in examples ... OK
* checking contents of data directory ... OK
* checking data for non-ASCII characters ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [20s/20s] ERROR
Running examples in CrcBiomeScreen-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getModelResult
> ### Title: Accessor for ModelResult slot of CrcBiomeScreen object
> ### Aliases: getModelResult getModelResult,CrcBiomeScreen-method
>
> ### ** Examples
>
> getModelResult(CrcBiomeScreenObject)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'getModelResult': object 'CrcBiomeScreenObject' not found
Calls: getModelResult -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in tests ... WARNING
'library' or 'require' call not declared from: curatedMetagenomicData
* checking tests ...
Running testthat.R [0s/0s]
[1s/1s] ERROR
Running the tests in tests/testthat.R failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> testthat::skip_on_bioc()
Error: Reason: On Bioconductor
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: 2 ERRORs, 4 WARNINGs, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/CrcBiomeScreen.Rcheck/00check.log
for details.
===============================
BiocCheck('CrcBiomeScreen_0.99.2.tar.gz')
===============================
Installing CrcBiomeScreen
Package installed successfully
CrcBiomeScreen session metadata
sourceDir: /tmp/RtmpKqP72E/filef3dda65f218c/CrcBiomeScreen
BiocVersion: 3.23
Package: CrcBiomeScreen
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/2d491955a68ed065f6a385f80914ffe596ee70b1/CrcBiomeScreen.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/RtmpKqP72E/filef3dda65f218c/CrcBiomeScreen
installDir: /tmp/RtmpKqP72E/filef3dda5bdc12d
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. 70% 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 (30%) 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.