===============================
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_0.99.6.tar.gz
===============================
BiocCheckGitClone('atacInferCnv')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/e9986d81ef0a666732225ef1c6de0f39c4aea5c6/atacInferCnv
BiocVersion: 3.23
Package: atacInferCnv
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/e9986d81ef0a666732225ef1c6de0f39c4aea5c6/atacInferCnv.BiocCheck
BiocCheckVersion: 1.47.25
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/e9986d81ef0a666732225ef1c6de0f39c4aea5c6/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 v1.47.25 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/e9986d81ef0a666732225ef1c6de0f39c4aea5c6/atacInferCnv.Rcheck
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-14 07:18:25 UTC
* using option --no-vignettes
* checking for file atacInferCnv/DESCRIPTION ... OK
* checking extension type ... Package
* this is package atacInferCnv 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 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [15s/15s] 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 ... [48s/48s] NOTE
plotCnvBlocks: no visible binding for global variable x
plotCnvBlocks: no visible binding for global variable value
Undefined global functions or variables:
value x
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 ... 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 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 ... [132s/132s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCnvBlocks 51.098 1.747 52.811
runAtacInferCnv 41.167 0.964 42.139
prepareAtacInferCnvInput 16.689 0.799 17.490
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [109s/110s]
[109s/110s] 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: 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4114/e9986d81ef0a666732225ef1c6de0f39c4aea5c6/atacInferCnv.Rcheck/00check.log
for details.
===============================
BiocCheck('atacInferCnv_0.99.6.tar.gz')
===============================
Registered S3 method overwritten by 'bit64':
method from
print.bitstring tools
Installing atacInferCnv
Package installed successfully
atacInferCnv session metadata
sourceDir: /tmp/RtmpcoyMU1/file88271317d43a9/atacInferCnv
BiocVersion: 3.23
Package: atacInferCnv
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/e9986d81ef0a666732225ef1c6de0f39c4aea5c6/atacInferCnv.BiocCheck
BiocCheckVersion: 1.47.25
sourceDir: /tmp/RtmpcoyMU1/file88271317d43a9/atacInferCnv
installDir: /tmp/RtmpcoyMU1/file882716dae93bc
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (42%).
* 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/prepareAnalysis.R (line 100, column 5)
print() in R/prepareAnalysis.R (line 103, column 7)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/prepareAnalysis.R (line 39, column 5)
* 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 5
functions greater than 50 lines.
The longest 5 functions are:
prepareAtacInferCnvInput() (R/prepareAnalysis.R): 175 lines
...
prepareAnalysis() (R/prepareAnalysis.R): 52 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; 18 lines (2%) are > 80 characters long.
First few lines:
R/RcppExports.R#L4 aggregate_bins_cpp_sparse <- function(ta ...
...
vignettes/atacInferCnv.Rmd#L96 [K. Okonechnikov et al "Oncogene aberrat
...
i NOTE: Consider multiples of 4 spaces for line indents; 404 lines (38%) are
not.
First few lines:
R/aggregateBins.R#L13 #print("Get regions") ...
...
vignettes/atacInferCnv.Rmd#L51 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 v1.47.25 results
0 ERRORS | 0 WARNINGS | i 5 NOTES
i See the atacInferCnv.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.