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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_0.99.6.tar.gz
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BiocCheckGitClone('CrcBiomeScreen')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e4537c62beccbde6d3d40265241596afdb59ffa4/CrcBiomeScreen
BiocVersion: 3.23
Package: CrcBiomeScreen
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e4537c62beccbde6d3d40265241596afdb59ffa4/CrcBiomeScreen.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e4537c62beccbde6d3d40265241596afdb59ffa4/CrcBiomeScreen
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 v1.47.7 results
0 ERRORS | 0 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/e4537c62beccbde6d3d40265241596afdb59ffa4/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 0.99.6
* 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 ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [33s/33s] NOTE
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
Undefined global functions or variables:
Dim1 Dim2 IsOutlier Kingdom SampleID Species i n_cv tmp
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'SplitTaxas.Rd':
\examples lines wider than 100 characters:
"D_0__Bacteria;D_1__Firmicutes;D_2__Clostridia;D_3__Lachnospirales;D_4__Lachnospiraceae;D_5__Roseburia",
"D_0__Bacteria;D_1__Firmicutes;D_2__Bacilli;D_3__Lactobacillales;D_4__Lactobacillaceae;D_5__Lactobacillus"
These lines will be truncated in the PDF manual.
* 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 ... 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 ... [9s/9s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [19s/19s] ERROR
Running examples in CrcBiomeScreen-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ModelingXGBoost
> ### Title: The packaging function for XGBoost modeling
> ### Aliases: ModelingXGBoost
>
> ### ** Examples
>
> # Minimal runnable example for ModelingXGBoost
>
> rel_abund <- data.frame(S1 = 10, S2 = 20)
> rownames(rel_abund) <- "TaxaA"
>
> sample_info <- data.frame(
+ number_reads = c(10000, 12000),
+ condition = c("control", "CRC"),
+ row.names = c("S1", "S2")
+ )
>
> obj <- CreateCrcBiomeScreenObject(
+ RelativeAbundance = rel_abund,
+ TaxaData = data.frame(Taxa = "TaxaA"),
+ SampleData = sample_info
+ )
>
> obj@ModelData <- list(
+ Training = data.frame(x = c(1, 2)),
+ TrainLabel = factor(c("control", "CRC"))
+ )
>
> # out <- ModelingXGBoost(
> # CrcBiomeScreenObject = obj,
> # k.rf = 2,
> # TaskName = "toy_XGB",
> # TrueLabel = c("control", "CRC"),
> # num_cores = 1
> # )
>
> out
Error: object 'out' not found
Execution halted
* checking for unstated dependencies in tests ... WARNING
'library' or 'require' call not declared from: curatedMetagenomicData
* checking tests ...
Running testthat.R [11s/11s]
[11s/11s] 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 ... [4s/4s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3994/e4537c62beccbde6d3d40265241596afdb59ffa4/CrcBiomeScreen.Rcheck/00check.log
for details.
===============================
BiocCheck('CrcBiomeScreen_0.99.6.tar.gz')
===============================
Installing CrcBiomeScreen
Package installed successfully
CrcBiomeScreen session metadata
sourceDir: /tmp/RtmpOps0a0/filefda5e7e7b8813/CrcBiomeScreen
BiocVersion: 3.23
Package: CrcBiomeScreen
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3994/e4537c62beccbde6d3d40265241596afdb59ffa4/CrcBiomeScreen.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /tmp/RtmpOps0a0/filefda5e7e7b8813/CrcBiomeScreen
installDir: /tmp/RtmpOps0a0/filefda5e24fa32
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 (9%).
* 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 83, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/checkClassBalance.Rd
i Found @ in man/EvaluateModel.Rd
i Found @ in man/FilterDataSet.Rd
i Found @ in man/KeepTaxonomicLevel.Rd
i Found @ in man/ModelingRF_noweights.Rd
i Found @ in man/ModelingRF.Rd
i Found @ in man/ModelingXGBoost_noweights.Rd
i Found @ in man/ModelingXGBoost.Rd
i Found @ in man/NormalizeData.Rd
i Found @ in man/PredictCrcBiomeScreen.Rd
i Found @ in man/qcByCmdscale.Rd
i Found @ in man/SplitDataSet.Rd
i NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
The longest 5 functions are:
SplitTaxas() (R/SplitTaxas.R): 94 lines
...
ModelingXGBoost_noweights() (R/ModelingXGBoost_noweights.R): 73 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
RunScreening.Rd
TrainModels.Rd
ValidateModelOnData.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
Found in files:
NormalizeData.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-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; 252 lines (8%) are > 80 characters long.
First few lines:
R/CreateCrcBiomeScreenObject.R#L9 #' @param AbsoluteAbundance A numeric ma
...
...
vignettes/CrcBiomeScreen.Rmd#L585 **Note**: This vignette demonstrates the
...
i NOTE: Consider multiples of 4 spaces for line indents; 752 lines (23%) are
not.
First few lines:
R/checkClassBalance.R#L52 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 v1.47.7 results
1 ERRORS | 0 WARNINGS | i 11 NOTES
i See the CrcBiomeScreen.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.