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R CMD BUILD
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* checking for file tidyprint/DESCRIPTION ... OK
* preparing tidyprint:
* 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 tidyprint_0.99.9.tar.gz
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BiocCheckGitClone('tidyprint')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/db7905639f5a3255eba4d090ac4bbb9c26ec5f04/tidyprint
BiocVersion: 3.23
Package: tidyprint
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/db7905639f5a3255eba4d090ac4bbb9c26ec5f04/tidyprint.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/db7905639f5a3255eba4d090ac4bbb9c26ec5f04/tidyprint
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 v1.47.7 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/3934/db7905639f5a3255eba4d090ac4bbb9c26ec5f04/tidyprint.Rcheck
* using R Under development (unstable) (2025-12-22 r89219)
* 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 tidyprint/DESCRIPTION ... OK
* this is package tidyprint version 0.99.9
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section Package
structure in the Writing R Extensions manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package tidyprint 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [24s/24s] NOTE
.as_tibble_optimised: no visible global function definition for
tibble
.as_tibble_optimised: no visible binding for global variable .
.as_tibble_optimised: no visible global function definition for
subset_tibble_output
eliminate_GRanges_metadata_columns_also_present_in_Rowdata: no visible
global function definition for one_of
get_special_datasets: no visible binding for global variable .
get_special_datasets: no visible global function definition for
tibble
get_special_datasets: no visible global function definition for is
get_special_datasets: no visible binding for global variable
group_name
get_special_datasets: no visible global function definition for :=
Undefined global functions or variables:
. := group_name is one_of subset_tibble_output tibble
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [10s/10s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [8s/8s]
[9s/9s] 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 ... [3s/3s] OK
* DONE
Status: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3934/db7905639f5a3255eba4d090ac4bbb9c26ec5f04/tidyprint.Rcheck/00check.log
for details.
===============================
BiocCheck('tidyprint_0.99.9.tar.gz')
===============================
Installing tidyprint
Package installed successfully
tidyprint session metadata
sourceDir: /tmp/Rtmp8IrZ8C/file938b82e3477cc/tidyprint
BiocVersion: 3.23
Package: tidyprint
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/db7905639f5a3255eba4d090ac4bbb9c26ec5f04/tidyprint.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /tmp/Rtmp8IrZ8C/file938b82e3477cc/tidyprint
installDir: /tmp/Rtmp8IrZ8C/file938b84d1a0f0
isTarBall: TRUE
platform: unix
Running BiocCheck on tidyprint
* 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 4.4.0 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...
* 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 (13%).
* 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...
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/Rtmp8IrZ8C/file938b82e3477cc/tidyprint/vignettes/Introduction.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of tidyprint...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/print_methods.R (line 55, column 24)
...
R/tidyse_utils.R (line 416, column 42)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
suppressWarnings() in R/print_methods.R (line 128, column 16)
suppressMessages() in R/tibble_methods.R (line 104, column 9)
suppressWarnings() in R/tidyse_utils.R (line 268, column 5)
* 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:
print.SummarizedExperiment() (R/print_methods.R): 107 lines
...
.as_tibble_optimised() (R/tibble_methods.R): 57 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 22% of man
pages use at least one of these tags.
Found in files:
as_tibble.SummarizedExperiment.Rd
print.SummarizedExperiment.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
as_tibble.SummarizedExperiment.Rd
print.SummarizedExperiment.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; 96 lines (6%) are > 80 characters long.
First few lines:
R/print_methods.R#L3 #' Provides a compact tibble-like displa ...
...
vignettes/Introduction.Rmd#L210 The above code demonstrates calling `tid ...
i NOTE: Consider multiples of 4 spaces for line indents; 436 lines (27%) are
not.
First few lines:
R/pillar_utlis.R#L5 if (length(x) == 0L) { ...
...
R/tidyse_utils.R#L422 } ...
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 v1.47.7 results
0 ERRORS | 0 WARNINGS | i 9 NOTES
i See the tidyprint.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.