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R CMD BUILD
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* 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_0.99.0.tar.gz
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BiocCheckGitClone('atacInferCnv')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/atacInferCnv_20260217181736/atacInferCnv
BiocVersion: 3.23
Package: atacInferCnv
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/atacInferCnv_20260217181736/atacInferCnv.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/atacInferCnv_20260217181736/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 v1.47.18 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/4114/atacInferCnv_20260217181736/atacInferCnv.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 atacInferCnv/DESCRIPTION ... OK
* checking extension type ... Package
* this is package atacInferCnv 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 whether package atacInferCnv can be installed ... OK
* used C++ compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 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 ... NOTE
Namespace in Imports field not imported from: RcppEigen
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [41s/41s] NOTE
aggregateBins: no visible global function definition for
keepSeqlevels
aggregateBins: no visible global function definition for queryHits
aggregateBins: no visible global function definition for subjectHits
prepareAnalysis: no visible binding for global variable nCount_ATAC
prepareAnalysis: no visible binding for global variable
nucleosome_signal
prepareAnalysis: no visible binding for global variable
TSS.enrichment
Undefined global functions or variables:
TSS.enrichment keepSeqlevels nCount_ATAC nucleosome_signal queryHits
subjectHits
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 ... [373s/370s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCnvBlocks 154.201 5.503 158.347
runAtacInferCnv 144.032 4.505 147.158
prepareAtacInferCnvInput 47.112 0.816 47.932
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [196s/194s]
[196s/195s] 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: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/4114/atacInferCnv_20260217181736/atacInferCnv.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
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BiocCheck('atacInferCnv_0.99.0.tar.gz')
===============================
Installing atacInferCnv
Package installed successfully
atacInferCnv session metadata
sourceDir: /tmp/RtmpV31E7H/file289cdf427f504d/atacInferCnv
BiocVersion: 3.23
Package: atacInferCnv
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4114/atacInferCnv_20260217181736/atacInferCnv.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/RtmpV31E7H/file289cdf427f504d/atacInferCnv
installDir: /tmp/RtmpV31E7H/file289cdf77c6ae08
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...
i NOTE: Update R version dependency from 4.3.0 to 4.6.0
* 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...
Warning in read.dcf(con, "Package") :
URL 'http://bioconductor.org/packages/3.23/bioc/VIEWS': Timeout of 60 seconds was reached
* 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 (20%).
* 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...
* 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 100, column 5)
print() in R/prepareAnalysis.R (line 84, column 3)
print() in R/prepareAnalysis.R (line 86, 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): 165 lines
...
runAtacInferCnv() (R/runAtacInferCnv.R): 62 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; 72 lines (8%) are > 80 characters long.
First few lines:
R/aggregateBins.R#L17 filtered_regions <- keepSeqlevels(regi ...
...
vignettes/atacInferCnv.Rmd#L70 [K. Okonechnikov et al "Oncogene aberrat ...
i NOTE: Consider multiples of 4 spaces for line indents; 363 lines (42%) 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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
* 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 v1.47.18 results
0 ERRORS | 0 WARNINGS | i 7 NOTES
i See the atacInferCnv.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.