===============================
R CMD BUILD
===============================
* checking for file RNAshapeQC/DESCRIPTION ... OK
* preparing RNAshapeQC:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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 RNAshapeQC_0.99.0.tar.gz
===============================
BiocCheckGitClone('RNAshapeQC')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/RNAshapeQC_20260127135017/RNAshapeQC
BiocVersion: 3.23
Package: RNAshapeQC
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/RNAshapeQC_20260127135017/RNAshapeQC.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/RNAshapeQC_20260127135017/RNAshapeQC
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
inst/.DS_Store
ERROR: System files found that should not be Git tracked.
data/.DS_Store
...
vignettes/.DS_Store
* 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...
* Checking that provided CITATION file is correctly formatted...
! WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint or
publication associated with this Bioconductor package.
BiocCheck v1.47.16 results
1 ERRORS | 2 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4054/RNAshapeQC_20260127135017/RNAshapeQC.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 RNAshapeQC/DESCRIPTION ... OK
* checking extension type ... Package
* this is package RNAshapeQC 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 RNAshapeQC 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 ... 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [13s/13s] NOTE
process_pileup: warning in normalize_data(inputData =
data.log$outputData, pileup = pileupData, Ranges = Ranges, makePlot =
plotNormalization, ...): partial argument match of 'pileup' to
'pileupData'
ADstat.hy: no visible global function definition for pnorm
decay.rate.hy: no visible binding for global variable data
decay.rate.hy: no visible global function definition for lm
decay.rate.hy: no visible global function definition for coef
estimate_offset: no visible binding for global variable bisquare.sse
estimate_offset: no visible global function definition for lowess
estimate_offset: no visible global function definition for rainbow
estimate_offset: no visible global function definition for lines
estimate_offset: no visible global function definition for abline
estimate_offset: no visible global function definition for legend
getShiftParam: no visible global function definition for abline
getShiftParam: no visible global function definition for text
plot_offset: no visible global function definition for rainbow
plot_offset: no visible global function definition for lines
plot_offset: no visible global function definition for abline
plot_offset: no visible global function definition for legend
scale.factor : <anonymous>: no visible binding for global variable
psi.bisquare
Undefined global functions or variables:
abline bisquare.sse coef data legend lines lm lowess pnorm
psi.bisquare rainbow text
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "abline", "legend", "lines", "text")
importFrom("stats", "coef", "lm", "lowess", "pnorm")
importFrom("utils", "data")
to your NAMESPACE file.
* 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 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 ... [13s/22s] 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: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/4054/RNAshapeQC_20260127135017/RNAshapeQC.Rcheck/00check.log
for details.
===============================
BiocCheck('RNAshapeQC_0.99.0.tar.gz')
===============================
Installing RNAshapeQC
Package installed successfully
RNAshapeQC session metadata
sourceDir: /tmp/RtmpzieC04/file2d45c323178a67/RNAshapeQC
BiocVersion: 3.23
Package: RNAshapeQC
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/RNAshapeQC_20260127135017/RNAshapeQC.BiocCheck
BiocCheckVersion: 1.47.16
sourceDir: /tmp/RtmpzieC04/file2d45c323178a67/RNAshapeQC
installDir: /tmp/RtmpzieC04/file2d45c35e82b37d
isTarBall: TRUE
platform: unix
Running BiocCheck on RNAshapeQC
* 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 4.4 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...
* 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 (27%).
* 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 RNAshapeQC...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/SCISSOR.R (line 287, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
data_prep.R (line 11, column 12)
...
SCISSOR.R (line 840, column 16)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/plot_shape.R (line 392, column 3)
...
print() in R/SCISSOR.R (line 478, column 12)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/data_prep.R (line 76, column 15)
...
R/SCISSOR.R (line 961, column 16)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/data_QC.R (line 73, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 9 times:
F in R/misc.R (line 149, column 40)
...
F in R/SCISSOR.R (line 443, column 32)
* 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 13
functions greater than 50 lines.
The longest 5 functions are:
plot_DIIwt() (R/plot_shape.R): 193 lines
...
estimate_offset() (R/SCISSOR.R): 87 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
dot-build_pileupExon.Rd
...
get_SOI.Rd
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 279 lines (8%) are > 80 characters long.
First few lines:
R/data_gen.R#L5 .build_regionsStr <- function(Gene, regi ...
...
vignettes/RNAshapeQC_intro.Rmd#L393 [^1]: Choi, H.Y., Jo, H., Zhao, X. et al
...
i NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
First few lines:
R/SCISSOR.R#L129 # Positions will be used for introns ...
R/SCISSOR.R#L135 # coverage.col = bp positions that w ...
R/SCISSOR.R#L136 # epl, epr = left and right exon pos ...
i NOTE: Consider multiples of 4 spaces for line indents; 1198 lines (33%) are
not.
First few lines:
R/data_gen.R#L7 regionsFormat <- match.arg(regionsForm ...
...
vignettes/RNAshapeQC_intro.Rmd#L364 ...
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...
ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.16 results
1 ERRORS | 1 WARNINGS | i 12 NOTES
i See the RNAshapeQC.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.