===============================
R CMD BUILD
===============================
* checking for file ‘BenchHub/DESCRIPTION’ ... OK
* preparing ‘BenchHub’:
* 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
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘BenchHub/data/lubomski_microbiome_data.RData’
‘BenchHub/inst/extdata/testdata/figshare_26054188/MOBNEW.rds’
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘Trio.R’ ‘downloaders.R’ ‘metrics.R’ ‘utils.R’
* building ‘BenchHub_0.99.2.tar.gz’
===============================
BiocCheckGitClone('BenchHub')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/2cf6c9d34b5a8eb6c407769cc3588c4a22274e9d/BenchHub
→ BiocVersion: 3.21
→ Package: BenchHub
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/2cf6c9d34b5a8eb6c407769cc3588c4a22274e9d/BenchHub.BiocCheck
→ BiocCheckVersion: 1.43.15
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/2cf6c9d34b5a8eb6c407769cc3588c4a22274e9d/BenchHub
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
• inst/.DS_Store
• inst/extdata/.DS_Store
* Checking individual file sizes...
* 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 v1.43.15 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3766/2cf6c9d34b5a8eb6c407769cc3588c4a22274e9d/BenchHub.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BenchHub/DESCRIPTION’ ... OK
* this is package ‘BenchHub’ version ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 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 ... [4s/4s] 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 ... [12s/12s] 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’
Undefined global functions or variables:
id name size
* 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’ [14s/17s]
[15s/18s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3766/2cf6c9d34b5a8eb6c407769cc3588c4a22274e9d/BenchHub.Rcheck/00check.log’
for details.
===============================
BiocCheck('BenchHub_0.99.2.tar.gz')
===============================
── Installing BenchHub ─────────────────────────────────────────────────────────
✔ Package installed successfully
── BenchHub session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpnr6x5M/file32223e1c60ae6d/BenchHub
→ BiocVersion: 3.21
→ Package: BenchHub
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3766/2cf6c9d34b5a8eb6c407769cc3588c4a22274e9d/BenchHub.BiocCheck
→ BiocCheckVersion: 1.43.15
→ sourceDir: /tmp/Rtmpnr6x5M/file32223e1c60ae6d/BenchHub
→ installDir: /tmp/Rtmpnr6x5M/file32223e6e840a1c
→ 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 4.5.0
* 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 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 .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 BenchHub...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• Trio.R (line 440, column 32)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/Trio.R (line 472, column 7)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
• suppressWarnings() in R/benchmarkInsights.R (line 111, column 35)
• ...
• suppressMessages() in R/Trio.R (line 591, column 18)
* 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:
• evaluate() (R/Trio.R): 162 lines
• ...
• geoDl() (R/downloaders.R): 61 lines
* Checking man page documentation...
* 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; 138 lines (5%) are > 80 characters long.
First few lines:
• R/benchmarkInsights.R#L27 #' A dataframe containing initial ...
• ...
• vignettes/v03_intro_bmi.Rmd#L223 | Metric Relationship | ` ...
i NOTE: Consider multiples of 4 spaces for line indents; 725 lines (28%) are
not.
First few lines:
• R/benchmarkInsights.R#L18 classname = "benchmarkInsights", ...
• ...
• vignettes/v03_intro_bmi.Rmd#L96 ) ...
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 v1.43.15 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the BenchHub.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.