===============================
R CMD BUILD
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* 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_0.99.5.tar.gz
===============================
BiocCheckGitClone('RNAshapeQC')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/2c231000113dd8bbc8fa2b361d2bfb89be042111/RNAshapeQC
BiocVersion: 3.23
Package: RNAshapeQC
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/2c231000113dd8bbc8fa2b361d2bfb89be042111/RNAshapeQC.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/2c231000113dd8bbc8fa2b361d2bfb89be042111/RNAshapeQC
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
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4054/2c231000113dd8bbc8fa2b361d2bfb89be042111/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 0.99.5
* 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 ... [15s/15s] OK
* 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 ... [19s/29s] 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 ... [5s/5s] OK
* DONE
Status: OK
===============================
BiocCheck('RNAshapeQC_0.99.5.tar.gz')
===============================
Installing RNAshapeQC
Package installed successfully
RNAshapeQC session metadata
sourceDir: /tmp/Rtmp96aqsE/file2cff00762ad728/RNAshapeQC
BiocVersion: 3.23
Package: RNAshapeQC
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4054/2c231000113dd8bbc8fa2b361d2bfb89be042111/RNAshapeQC.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/Rtmp96aqsE/file2cff00762ad728/RNAshapeQC
installDir: /tmp/Rtmp96aqsE/file2cff0015e87381
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 (31%).
* 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/plot_shape.R (line 503, column 3)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/data_prep.R (line 76, column 15)
...
R/SCISSOR.R (line 977, column 28)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/SCISSOR.R (line 122, column 19)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/data_QC.R (line 73, column 15)
R/SCISSOR.R (line 122, column 25)
* 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...
* 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; 297 lines (8%) are > 80 characters long.
First few lines:
R/data_gen.R#L5 .build_regionsStr <- function(Gene, regi ...
...
vignettes/RNAshapeQC_intro.Rmd#L432 [^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; 1270 lines (33%) are
not.
First few lines:
R/data_gen.R#L7 regionsFormat <- match.arg(regionsForm ...
...
vignettes/RNAshapeQC_intro.Rmd#L403 ...
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...
ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
BiocCheck v1.47.18 results
1 ERRORS | 0 WARNINGS | i 12 NOTES
i See the RNAshapeQC.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.