===============================
R CMD BUILD
===============================
* checking for file ‘DaparToolshedData/DESCRIPTION’ ... OK
* preparing ‘DaparToolshedData’:
* 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 ‘DaparToolshedData_0.99.18.tar.gz’
===============================
BiocCheckGitClone('DaparToolshedData')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData
→ BiocVersion: 3.23
→ Package: DaparToolshedData
→ PackageVersion: 0.99.18
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData.BiocCheck
→ BiocCheckVersion: 1.49.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
! WARNING: Data files exceed the 5MB size limit.
Use 'ExperimentHub' or 'AnnotationHub' for the files:
•
/home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData/inst/extdata/Exp1_R25_pept.txt
•
/home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData/inst/extdata/Exp1_R2_pept.txt
* 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.49.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData.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: 2026-06-09 13:29:52 UTC
* using option ‘--no-vignettes’
* checking for file ‘DaparToolshedData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DaparToolshedData’ version ‘0.99.18’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DaparToolshedData’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 24.0Mb
sub-directories of 1Mb or more:
data 6.1Mb
extdata 17.8Mb
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] OK
* checking whether startup messages can be suppressed ... [9s/9s] 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 ... [28s/28s] OK
* 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 ... [10s/10s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/67s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Exp1_R25_pept 1.987 0.206 9.61
Exp1_R2_pept 1.487 0.101 6.68
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/12s]
[11s/12s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData.Rcheck/00check.log’
for details.
===============================
BiocCheck('DaparToolshedData_0.99.18.tar.gz')
===============================
── Installing DaparToolshedData ────────────────────────────────────────────────
✔ Package installed successfully
── DaparToolshedData session metadata ──────────────────────────────────────────
→ sourceDir: /tmp/RtmpE5hGoe/fileabdf4756add88/DaparToolshedData
→ BiocVersion: 3.23
→ Package: DaparToolshedData
→ PackageVersion: 0.99.18
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3950/4d317c4e674daeedca0331ec3cdefb9226b0e308/DaparToolshedData.BiocCheck
→ BiocCheckVersion: 1.49.12
→ sourceDir: /tmp/RtmpE5hGoe/fileabdf4756add88/DaparToolshedData
→ installDir: /tmp/RtmpE5hGoe/fileabdf43c1fc700
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DaparToolshedData ──────────────────────────────────────
* 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...
→ ExperimentData
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
! WARNING: Use biocViews from one category only (one of Software,
ExperimentData, AnnotationData, Workflow)
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* 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 (80%).
* 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:
• DaparToolshedData.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DaparToolshedData...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/get-data.R (line 16, column 6)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 21 lines (2%) are > 80 characters long.
First few lines:
• R/doc-data.R#L14 #' before mass spectrometry analyses. Th ...
• ...
• R/doc-data.R#L481 #' Spiked proteomic standard dataset for ...
i NOTE: Consider multiples of 4 spaces for line indents; 11 lines (1%) are not.
First few lines:
• R/DaparToolshedData.R#L26 fl <- system.file("extdata", "metadata ...
• ...
• R/zzz.R#L8 createHubAccessors(pkgname, titles) ...
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 'dapartoolsheddata' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 6 NOTES
i See the DaparToolshedData.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.