===============================
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_0.99.6.tar.gz
===============================
BiocCheckGitClone('BenchHub')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/0ca99353008487b3960e94e8c98903177db938e4/BenchHub
BiocVersion: 3.23
Package: BenchHub
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/0ca99353008487b3960e94e8c98903177db938e4/BenchHub.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/0ca99353008487b3960e94e8c98903177db938e4/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 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 v1.47.1 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/3766/0ca99353008487b3960e94e8c98903177db938e4/BenchHub.Rcheck
* using R Under development (unstable) (2025-10-20 r88955)
* 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 BenchHub/DESCRIPTION ... OK
* this is package BenchHub version 0.99.6
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 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 ... NOTE
Found the following hidden files and directories:
.lintr
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 BenchHub can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] 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 ... [10s/10s] 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
zenodoDl: no visible binding for global variable ZenodoManager
Undefined global functions or variables:
ZenodoManager dataType datasetID description id name size sourceID
studyID studyName
* 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 ... [7s/11s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [12s/15s]
[12s/16s] 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: 3 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3766/0ca99353008487b3960e94e8c98903177db938e4/BenchHub.Rcheck/00check.log
for details.
===============================
BiocCheck('BenchHub_0.99.6.tar.gz')
===============================
Installing BenchHub
Package installed successfully
BenchHub session metadata
sourceDir: /tmp/Rtmp8e76gt/file1955c73480a2f/BenchHub
BiocVersion: 3.23
Package: BenchHub
PackageVersion: 0.99.6
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/0ca99353008487b3960e94e8c98903177db938e4/BenchHub.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/Rtmp8e76gt/file1955c73480a2f/BenchHub
installDir: /tmp/Rtmp8e76gt/file1955cb12a27e
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 4.1.0 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...
Error in .getYAMLfront(lines) :
More than 2 YAML front matter delimiters, i.e., '---' found
Calls: BiocCheck ... checkVignetteDir -> checkVigTemplate -> .getYAMLfront
Execution halted