===============================
R CMD BUILD
===============================
* checking for file ‘ExpoRiskR/DESCRIPTION’ ... OK
* preparing ‘ExpoRiskR’:
* 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 ‘ExpoRiskR_0.99.2.tar.gz’
===============================
BiocCheckGitClone('ExpoRiskR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4057/334198402cfe89694a8d18986db0c896feb1949a/ExpoRiskR
→ BiocVersion: 3.23
→ Package: ExpoRiskR
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4057/334198402cfe89694a8d18986db0c896feb1949a/ExpoRiskR.BiocCheck
→ BiocCheckVersion: 1.47.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4057/334198402cfe89694a8d18986db0c896feb1949a/ExpoRiskR
→ 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/4057/334198402cfe89694a8d18986db0c896feb1949a/ExpoRiskR.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 ‘ExpoRiskR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ExpoRiskR’ 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 serialization versions ... OK
* checking whether package ‘ExpoRiskR’ 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 ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [22s/22s] NOTE
align_omics: no visible global function definition for ‘head’
plot_exposure_ranking: no visible binding for global variable
‘exposure’
plot_exposure_ranking: no visible binding for global variable
‘perturbation_score’
plot_feature_importance: no visible binding for global variable
‘feature’
plot_feature_importance: no visible binding for global variable
‘importance’
plot_individual_risk_profile: no visible binding for global variable
‘feature’
plot_individual_risk_profile: no visible binding for global variable
‘contribution’
plot_network_stability: no visible binding for global variable
‘overlap’
plot_risk_roc: no visible binding for global variable ‘fpr’
plot_risk_roc: no visible binding for global variable ‘tpr’
plot_risk_roc: no visible binding for global variable ‘model’
Undefined global functions or variables:
contribution exposure feature fpr head importance model overlap
perturbation_score tpr
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* 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 ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [9s/9s]
[10s/10s] 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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4057/334198402cfe89694a8d18986db0c896feb1949a/ExpoRiskR.Rcheck/00check.log’
for details.
===============================
BiocCheck('ExpoRiskR_0.99.2.tar.gz')
===============================
── Installing ExpoRiskR ────────────────────────────────────────────────────────
✔ Package installed successfully
── ExpoRiskR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiQB1WW/file377c24374b2e43/ExpoRiskR
→ BiocVersion: 3.23
→ Package: ExpoRiskR
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4057/334198402cfe89694a8d18986db0c896feb1949a/ExpoRiskR.BiocCheck
→ BiocCheckVersion: 1.47.12
→ sourceDir: /tmp/RtmpiQB1WW/file377c24374b2e43/ExpoRiskR
→ installDir: /tmp/RtmpiQB1WW/file377c245dc55af0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ExpoRiskR ──────────────────────────────────────────────
* 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...
* 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 (40%).
* 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: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/exporiskr-intro.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ExpoRiskR...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/align_omics_se.R (line 110, column 12)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressWarnings() in R/utils.R (line 27, column 3)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 10
functions greater than 50 lines.
The longest 5 functions are:
• build_exposure_network() (R/build_exposure_network.R): 156 lines
• ...
• generate_dummy_exporisk() (R/generate_dummy_exporisk.R): 81 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 shorter lines; 114 lines (7%) are > 80 characters long.
First few lines:
• R/align_omics_se.R#L12 #' Convenience wrapper to (i) align micr ...
• ...
• vignettes/exporiskr-intro.Rmd#L149 ExpoRiskR provides a Bioconductor-native
...
i NOTE: Consider multiples of 4 spaces for line indents; 750 lines (44%) are
not.
First few lines:
• R/align_omics_se.R#L50 id_col = "sam ...
• ...
• vignettes/exporiskr-intro.Rmd#L138 top_edges = 80 ...
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 7 NOTES
i See the ExpoRiskR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.