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R CMD BUILD
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* checking for file ‘MultiModalGraphics/DESCRIPTION’ ... OK
* preparing ‘MultiModalGraphics’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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 ‘MultiModalGraphics_0.99.4.tar.gz’
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BiocCheckGitClone('MultiModalGraphics')
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→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/3c3bb9f6864655a96a31281e4c1282481c1521f4/MultiModalGraphics
→ BiocVersion: 3.21
→ Package: MultiModalGraphics
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/3c3bb9f6864655a96a31281e4c1282481c1521f4/MultiModalGraphics.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/3c3bb9f6864655a96a31281e4c1282481c1521f4/MultiModalGraphics
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.4 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/3399/3c3bb9f6864655a96a31281e4c1282481c1521f4/MultiModalGraphics.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiModalGraphics/DESCRIPTION’ ... OK
* this is package ‘MultiModalGraphics’ version ‘0.99.4’
* 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 ‘MultiModalGraphics’ 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 ... NOTE
License stub is invalid DCF.
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [26s/26s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'ClearScatterplot_MAE.Rd':
\examples lines wider than 100 characters:
colnames(expression_data) <- paste0(combination_name, "_Sample", 1:num_samples_for_this_combination)
TimePoint = rep(c("T1", "T1", "T2", "T2"), length.out = num_samples_for_this_combination), # Example time points
SampleType = rep(c("Tissue", "Organ"), length.out = num_samples_for_this_combination) # Example sample types
final_metadata <- combined_metadata[, c("SampleID", "TimePoint", "SampleType", "Group", "Condition1", "Condition2", "Condition3")]
mae <- MultiAssayExperiment::MultiAssayExperiment(experiments = expression_data_list, colData = final_metadata)
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 ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [10s/10s]
[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: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3399/3c3bb9f6864655a96a31281e4c1282481c1521f4/MultiModalGraphics.Rcheck/00check.log’
for details.
===============================
BiocCheck('MultiModalGraphics_0.99.4.tar.gz')
===============================
── Installing MultiModalGraphics ───────────────────────────────────────────────
✔ Package installed successfully
── MultiModalGraphics session metadata ─────────────────────────────────────────
→ sourceDir: /tmp/Rtmp1X81lw/file25af2558858427/MultiModalGraphics
→ BiocVersion: 3.21
→ Package: MultiModalGraphics
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/3c3bb9f6864655a96a31281e4c1282481c1521f4/MultiModalGraphics.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /tmp/Rtmp1X81lw/file25af2558858427/MultiModalGraphics
→ installDir: /tmp/Rtmp1X81lw/file25af254a764ca5
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MultiModalGraphics ─────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, DifferentialExpression
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (38%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/ClearScatterplotExample1.Rmd
• ...
• vignettes/MultifeatureGridExample1.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MultiModalGraphics...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/ClearScatterplot_MAE.Rd
i Found @ in vignettes/ClearScatterplotMAEExample.Rmd
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 6
functions greater than 50 lines.
The longest 5 functions are:
• get_clear_scatterplot_df() (R/generate_data.R): 198 lines
• ...
• _anonymous_.153() (R/MultifeatureGrid.R): 69 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• createPlot.Rd
• ...
• updateLayerFun.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 16% of man
pages use at least one of these tags.
Found in files:
• getHeatmapObject-InformativeHeatmap-method.Rd
• InformativeHeatmap.Rd
• updateLayerFun-InformativeHeatmap-method.Rd
* 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; 204 lines (8%) are > 80 characters long.
First few lines:
• R/ClearScatterplot.R#L6 #' A class for creating and managing sca ...
• ...
• vignettes/MultiModalGraphics.Rmd#L185 This comprehensive guide provided
exampl ...
i NOTE: Consider multiples of 4 spaces for line indents; 672 lines (27%) are
not.
First few lines:
• R/ClearScatterplot.R#L21 slots = c( ...
• ...
• vignettes/MultiModalGraphics.Rmd#L94 ) ...
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 v1.43.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the MultiModalGraphics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.