===============================
R CMD BUILD
===============================
* checking for file ‘tidyprint/DESCRIPTION’ ... OK
* preparing ‘tidyprint’:
* 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘tidyprint_0.99.0.tar.gz’
===============================
BiocCheckGitClone('tidyprint')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/tidyprint_20250904152427/tidyprint
→ BiocVersion: 3.22
→ Package: tidyprint
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/tidyprint_20250904152427/tidyprint.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/tidyprint_20250904152427/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 v1.45.18 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/3934/tidyprint_20250904152427/tidyprint.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘0.99.0’
* 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 ... 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 ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] 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 ... [21s/21s] 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 ‘:=’
print.SummarizedExperiment : print_tidyprint_1: no visible global
function definition for ‘all_of’
print.SummarizedExperiment : print_tidyprint_1: no visible binding for
global variable ‘.’
Undefined global functions or variables:
. := all_of 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [8s/8s]
[8s/8s] 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/tidyprint_20250904152427/tidyprint.Rcheck/00check.log’
for details.
===============================
BiocCheck('tidyprint_0.99.0.tar.gz')
===============================
── Installing tidyprint ────────────────────────────────────────────────────────
✔ Package installed successfully
── tidyprint session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJ3MEkP/file48cb84309e62b/tidyprint
→ BiocVersion: 3.22
→ Package: tidyprint
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3934/tidyprint_20250904152427/tidyprint.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpJ3MEkP/file48cb84309e62b/tidyprint
→ installDir: /tmp/RtmpJ3MEkP/file48cb827199ae2
→ 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 4.5.0
* 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...
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 (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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• Introduction.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmpJ3MEkP/file48cb84309e62b/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 sapply(); use vapply()
Found in files:
• R/print_methods.R (line 304, column 24)
• R/tidyse_utils.R (line 309, column 9)
• R/tidyse_utils.R (line 310, column 9)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• print_methods.R (line 69, column 22)
• ...
• tidyse_utils.R (line 290, column 43)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/print_methods.R (line 248, column 11)
• ...
• R/tidyse_utils.R (line 417, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 3 times:
• T in R/print_methods.R (line 251, column 30)
• T in R/print_methods.R (line 313, column 60)
• F in R/print_methods.R (line 249, column 30)
* 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 317, column 20)
• suppressMessages() in R/tibble_methods.R (line 66, 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 8
functions greater than 50 lines.
The longest 5 functions are:
• print.SummarizedExperiment() (R/print_methods.R): 306 lines
• ...
• get_count_datasets() (R/tidyse_utils.R): 91 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/demo_tidy_message.Rd
• man/tbl_format_header.SE_print_abstraction.Rd
• man/tidy_message.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• format_covariate_header.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 17% of man
pages use at least one of these tags.
Found in files:
• print.SummarizedExperiment.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• print.SummarizedExperiment.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 79 lines (5%) are > 80 characters long.
First few lines:
• R/print_methods.R#L3 #' Provides alternative console displays ...
• ...
• vignettes/Introduction.Rmd#L182 The above code demonstrates calling `tid ...
i NOTE: Consider multiples of 4 spaces for line indents; 480 lines (32%) 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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | i 14 NOTES
i See the tidyprint.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.