===============================
R CMD BUILD
===============================
* 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_0.99.0.tar.gz
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BiocCheckGitClone('MultiModalGraphics')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/MultiModalGraphics_20250203194248/MultiModalGraphics
BiocVersion: 3.21
Package: MultiModalGraphics
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/MultiModalGraphics_20250203194248/MultiModalGraphics.BiocCheck
BiocCheckVersion: 1.43.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/MultiModalGraphics_20250203194248/MultiModalGraphics
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
MultiModalGraphics.Rproj
* 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
1 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/3399/MultiModalGraphics_20250203194248/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 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MultiModalGraphics/DESCRIPTION ... OK
* this is package MultiModalGraphics version 0.99.0
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] 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 ... [23s/23s] 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 ... [17s/17s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [9s/9s]
[9s/9s] 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/MultiModalGraphics_20250203194248/MultiModalGraphics.Rcheck/00check.log
for details.
===============================
BiocCheck('MultiModalGraphics_0.99.0.tar.gz')
===============================
Installing MultiModalGraphics
Package installed successfully
MultiModalGraphics session metadata
sourceDir: /tmp/RtmpSvGMT2/file24a6905b4922f1/MultiModalGraphics
BiocVersion: 3.21
Package: MultiModalGraphics
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3399/MultiModalGraphics_20250203194248/MultiModalGraphics.BiocCheck
BiocCheckVersion: 1.43.4
sourceDir: /tmp/RtmpSvGMT2/file24a6905b4922f1/MultiModalGraphics
installDir: /tmp/RtmpSvGMT2/file24a6901acb7b0d
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...
Error in .getYAMLfront(lines) :
More than 2 YAML front matter delimiters, i.e., '---' found
Calls: BiocCheck ... checkVignetteDir -> checkVigTemplate -> .getYAMLfront
Execution halted