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R CMD BUILD
===============================
* checking for file ‘atacInferCnv/DESCRIPTION’ ... OK
* preparing ‘atacInferCnv’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘atacInferCnv_0.99.2.tar.gz’
===============================
BiocCheckGitClone('atacInferCnv')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/62862668ea89c04ef628346131e1eef4d56165e7/atacInferCnv
→ BiocVersion: 3.23
→ Package: atacInferCnv
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/62862668ea89c04ef628346131e1eef4d56165e7/atacInferCnv.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/62862668ea89c04ef628346131e1eef4d56165e7/atacInferCnv
→ 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 v1.47.20 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/4114/62862668ea89c04ef628346131e1eef4d56165e7/atacInferCnv.Rcheck’
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-13 15:34:52 UTC
* using option ‘--no-vignettes’
* checking for file ‘atacInferCnv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘atacInferCnv’ 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 ‘atacInferCnv’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] 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 ... [40s/40s] NOTE
Found the following assignments to the global environment:
File ‘atacInferCnv/R/runAtacInferCnv.R’:
assign("infercnv_obj", infercnv_obj, envir = .GlobalEnv)
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'prepareAtacInferCnvInput.Rd':
\examples lines wider than 100 characters:
prepareAtacInferCnvInput(inPath,sAnn,resPath, targColumn = "cnvBlock", ctrlGrp = "Normal",performGA = FALSE)
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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [112s/112s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCnvBlocks 42.527 1.220 43.709
runAtacInferCnv 35.876 0.768 36.623
prepareAtacInferCnvInput 14.383 0.686 15.071
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [85s/85s]
[85s/85s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4114/62862668ea89c04ef628346131e1eef4d56165e7/atacInferCnv.Rcheck/00check.log’
for details.
===============================
BiocCheck('atacInferCnv_0.99.2.tar.gz')
===============================
── Installing atacInferCnv ─────────────────────────────────────────────────────
✔ Package installed successfully
── atacInferCnv session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBaWF9I/filef45677f1533d3/atacInferCnv
→ BiocVersion: 3.23
→ Package: atacInferCnv
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/62862668ea89c04ef628346131e1eef4d56165e7/atacInferCnv.BiocCheck
→ BiocCheckVersion: 1.47.20
→ sourceDir: /tmp/RtmpBaWF9I/filef45677f1533d3/atacInferCnv
→ installDir: /tmp/RtmpBaWF9I/filef4567557ee8b0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on atacInferCnv ───────────────────────────────────────────
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (36%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of atacInferCnv...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/customPlots.R (line 114, column 17)
• ...
• print() in R/prepareAnalysis.R (line 70, column 7)
* 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 4
functions greater than 50 lines.
The longest 5 functions are:
• prepareAtacInferCnvInput() (R/prepareAnalysis.R): 173 lines
• ...
• runAtacInferCnv() (R/runAtacInferCnv.R): 74 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/atacInferCnv.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; 80 lines (8%) are > 80 characters long.
First few lines:
• R/aggregateBins.R#L17 filtered_regions <- keepSeqlevels(regi ...
• ...
• vignettes/atacInferCnv.Rmd#L90 [K. Okonechnikov et al "Oncogene aberrat ...
i NOTE: Consider multiples of 4 spaces for line indents; 376 lines (40%) are
not.
First few lines:
• R/aggregateBins.R#L13 #print("Get regions") ...
• ...
• vignettes/atacInferCnv.Rmd#L47 ctrlGrp = "Nor ...
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 v1.47.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 5 NOTES
i See the atacInferCnv.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.