===============================
R CMD BUILD
===============================
* checking for file BenchHub/DESCRIPTION ... OK
* preparing BenchHub:
* 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 BenchHub_0.99.12.tar.gz
===============================
BiocCheckGitClone('BenchHub')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/5f166f7056a702baa296e66354fd6d5333976d3b/BenchHub
BiocVersion: 3.23
Package: BenchHub
PackageVersion: 0.99.12
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/5f166f7056a702baa296e66354fd6d5333976d3b/BenchHub.BiocCheck
BiocCheckVersion: 1.47.26
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/5f166f7056a702baa296e66354fd6d5333976d3b/BenchHub
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 for remote package usage...
* 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 v1.47.26 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/3766/5f166f7056a702baa296e66354fd6d5333976d3b/BenchHub.Rcheck
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-21 21:02:21 UTC
* using option --no-vignettes
* checking for file BenchHub/DESCRIPTION ... OK
* this is package BenchHub version 0.99.12
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 BenchHub 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] NOTE
figshareDl: no visible binding for global variable id
figshareDl: no visible binding for global variable name
figshareDl: no visible binding for global variable size
listCuratedTrioDatasets: no visible binding for global variable name
listCuratedTrioDatasets: no visible binding for global variable
datasetID
listCuratedTrioDatasets: no visible binding for global variable
sourceID
listCuratedTrioDatasets: no visible binding for global variable
dataType
listCuratedTrioStudies: no visible binding for global variable
studyName
listCuratedTrioStudies: no visible binding for global variable
studyID
listCuratedTrioStudies: no visible binding for global variable
description
private_extract_gist_id: no visible global function definition for
tail
private_submission_create_gist: no visible global function definition
for createGist
zenodoDl: no visible binding for global variable ZenodoManager
Undefined global functions or variables:
ZenodoManager createGist dataType datasetID description id name size
sourceID studyID studyName tail
Consider adding
importFrom("utils", "tail")
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 ... [10s/13s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [16s/32s]
[16s/32s] 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/4s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3766/5f166f7056a702baa296e66354fd6d5333976d3b/BenchHub.Rcheck/00check.log
for details.
===============================
BiocCheck('BenchHub_0.99.12.tar.gz')
===============================
Installing BenchHub
Package installed successfully
BenchHub session metadata
sourceDir: /tmp/Rtmp3rVOwn/file137541e691e2/BenchHub
BiocVersion: 3.23
Package: BenchHub
PackageVersion: 0.99.12
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/5f166f7056a702baa296e66354fd6d5333976d3b/BenchHub.BiocCheck
BiocCheckVersion: 1.47.26
sourceDir: /tmp/Rtmp3rVOwn/file137541e691e2/BenchHub
installDir: /tmp/Rtmp3rVOwn/file13754654964ed
isTarBall: TRUE
platform: unix
Running BiocCheck on BenchHub
* 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 4.5.0 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...
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 NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
v01_intro_trio.Rmd
...
v05_benchmarkstudy.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of BenchHub...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
downloaders.R (line 275, column 24)
Trio.R (line 621, column 32)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/BenchmarkStudy.R (line 130, column 7)
...
cat() in R/Trio.R (line 676, column 7)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/BenchmarkStudy.R (line 167, column 15)
* Checking parsed R code in R directory, examples, vignettes...
! WARNING: Avoid 'Sys.setenv' (found 1 times)
Sys.setenv() in R/SubmissionDataset.R (line 2315, column 3)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times)
suppressWarnings() in R/BenchmarkInsights.R (line 130, column 35)
...
suppressMessages() in R/utils.R (line 322, column 3)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 51
functions greater than 50 lines.
The longest 5 functions are:
populateTrio() (R/Trio.R): 421 lines
...
interactivePrepareStudyUpdateSubmission() (R/SubmissionStudy.R): 221
lines
* Checking man page documentation...
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
BenchmarkStudy.Rd
...
writeSubmission.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; 398 lines (4%) are > 80 characters long.
First few lines:
R/BenchmarkInsights.R#L27 #' A dataframe containing initial ...
...
vignettes/v05_benchmarkstudy.Rmd#L264 - Method developers: load an
existing ...
i NOTE: Consider multiples of 4 spaces for line indents; 3714 lines (37%) are
not.
First few lines:
R/BenchmarkInsights.R#L18 classname = "BenchmarkInsights", ...
...
vignettes/v05_benchmarkstudy.Rmd#L252 )) ...
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 v1.47.26 results
1 ERRORS | 1 WARNINGS | i 13 NOTES
i See the BenchHub.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.