===============================
R CMD BUILD
===============================
* checking for file ‘terapadog/DESCRIPTION’ ... OK
* preparing ‘terapadog’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘terapadog_0.99.4.tar.gz’
===============================
BiocCheckGitClone('terapadog')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/86839a56a0f3ad05b20a39cbbb2c7a2418870178/terapadog
→ BiocVersion: 3.21
→ Package: terapadog
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/86839a56a0f3ad05b20a39cbbb2c7a2418870178/terapadog.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/86839a56a0f3ad05b20a39cbbb2c7a2418870178/terapadog
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.4 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/3615/86839a56a0f3ad05b20a39cbbb2c7a2418870178/terapadog.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘terapadog/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘terapadog’ version ‘0.99.4’
* 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 serialization versions ... OK
* checking whether package ‘terapadog’ 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [28s/28s] 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 files in ‘vignettes’ ... OK
* checking examples ... [60s/64s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_FCs 42.032 1.034 43.068
id_converter 2.073 0.189 5.796
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test-assign_Regmode.R’ [9s/9s]
Running ‘test-get_FCs.R’ [9s/9s]
Running ‘test-id_converter.R’ [9s/9s]
Running ‘test-plotDTA.R’ [10s/10s]
Running ‘test-prepareTerapadogData.R’ [10s/10s]
Running ‘test-preprocessing_helpers.R’ [9s/9s]
[56s/56s] 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: OK
===============================
BiocCheck('terapadog_0.99.4.tar.gz')
===============================
── Installing terapadog ────────────────────────────────────────────────────────
✔ Package installed successfully
── terapadog session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpxCKlsD/file2722fe7fcb0318/terapadog
→ BiocVersion: 3.21
→ Package: terapadog
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/86839a56a0f3ad05b20a39cbbb2c7a2418870178/terapadog.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /tmp/RtmpxCKlsD/file2722fe7fcb0318/terapadog
→ installDir: /tmp/RtmpxCKlsD/file2722fe5265a2cf
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on terapadog ──────────────────────────────────────────────
* 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 (33%).
* Checking for pinned package versions in DESCRIPTION...
* 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 terapadog...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/preprocessing_helpers.R (line 129, column 26)
• R/terapadog.R (line 264, column 5)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• get_FCs.R (line 190, column 55)
• terapadog.R (line 182, column 53)
• terapadog.R (line 270, column 15)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/id_converter.R (line 36, column 10)
• ...
• R/id_converter.R (line 69, column 11)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressMessages() in R/get_FCs.R (line 113, column 13)
• suppressMessages() in R/terapadog.R (line 249, column 15)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• terapadog() (R/terapadog.R): 279 lines
• ...
• id_converter() (R/id_converter.R): 78 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• terapadog.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; 139 lines (8%) are > 80 characters long.
First few lines:
• R/assign_Regmode.R#L5 #' regulatory mode to each gene based on ...
• ...
• vignettes/terapadog_vignette.Rmd#L506 Griss J, Viteri G, Sidiropoulos K,
Nguye ...
i NOTE: Consider multiples of 4 spaces for line indents; 453 lines (27%) are
not.
First few lines:
• R/assign_Regmode.R#L30 # Function checks padj (the padj value ...
• ...
• vignettes/terapadog_vignette.Rmd#L420 stop("The package 'apeglm' is required
...
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 v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the terapadog.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.