===============================
R CMD BUILD
===============================
* checking for file ‘MetaboAnnotatoR/DESCRIPTION’ ... OK
* preparing ‘MetaboAnnotatoR’:
* 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
* building ‘MetaboAnnotatoR_0.99.6.tar.gz’
===============================
BiocCheckGitClone('MetaboAnnotatoR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/2b153665c2a4102bba6902cfa191fe6170a02daa/MetaboAnnotatoR
→ BiocVersion: 3.23
→ Package: MetaboAnnotatoR
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/2b153665c2a4102bba6902cfa191fe6170a02daa/MetaboAnnotatoR.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/2b153665c2a4102bba6902cfa191fe6170a02daa/MetaboAnnotatoR
→ 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 v1.47.7 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/4016/2b153665c2a4102bba6902cfa191fe6170a02daa/MetaboAnnotatoR.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 ‘MetaboAnnotatoR/DESCRIPTION’ ... OK
* this is package ‘MetaboAnnotatoR’ version ‘0.99.6’
* 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 ‘MetaboAnnotatoR’ 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [39s/39s] NOTE
findFeature: no visible binding for global variable ‘tar’
plotCandidatesAIF: no visible binding for global variable ‘rt’
plotCandidatesAIF: no visible binding for global variable ‘mz’
plotCandidatesAIF: no visible binding for global variable ‘into’
plotCandidatesRC: no visible binding for global variable ‘mz’
plotCandidatesRC: no visible binding for global variable ‘into’
plotISF: no visible binding for global variable ‘rt’
plotISF: no visible binding for global variable ‘mz’
plotISF: no visible binding for global variable ‘into’
plotPseudoMSMS: no visible binding for global variable ‘rt’
plotPseudoMSMS: no visible binding for global variable ‘mz’
plotPseudoMSMS: no visible binding for global variable ‘into’
readData: no visible binding for global variable ‘targets’
Undefined global functions or variables:
into mz rt tar targets
Consider adding
importFrom("stats", "rt")
importFrom("utils", "tar")
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 files in ‘vignettes’ ... OK
* checking examples ... [110s/169s] ERROR
Running examples in ‘MetaboAnnotatoR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotateRC
> ### Title: Annotation of features using LC-MS AIF datasets processed using
> ### RAMClustR.
> ### Aliases: annotateRC
>
> ### ** Examples
>
> # Set working directory as tempdir:
> setwd(tempdir())
> # Read RAMClustR (RC) and XCMS processed example data:
> f <- system.file("/Data/MESA_RAMClustR.rds", package = "MetaboAnnotatoR")
> RC <- readRDS(fpath)
Error: object 'fpath' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [18s/18s]
[19s/19s] 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 ERROR, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4016/2b153665c2a4102bba6902cfa191fe6170a02daa/MetaboAnnotatoR.Rcheck/00check.log’
for details.
===============================
BiocCheck('MetaboAnnotatoR_0.99.6.tar.gz')
===============================
── Installing MetaboAnnotatoR ──────────────────────────────────────────────────
✔ Package installed successfully
── MetaboAnnotatoR session metadata ────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbWx29c/file1f2379ac0477c/MetaboAnnotatoR
→ BiocVersion: 3.23
→ Package: MetaboAnnotatoR
→ PackageVersion: 0.99.6
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/2b153665c2a4102bba6902cfa191fe6170a02daa/MetaboAnnotatoR.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /tmp/RtmpbWx29c/file1f2379ac0477c/MetaboAnnotatoR
→ installDir: /tmp/RtmpbWx29c/file1f23792eb8f1ec
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MetaboAnnotatoR ────────────────────────────────────────
* 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...
i NOTE: Consider adding these automatically suggested biocViews: Proteomics,
ImmunoOncology, QualityControl, DataImport
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 that Package field matches directory/tarball name...
* 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 (60%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MetaboAnnotatoR...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/getPseudoMSMS.R (line 386, column 5)
• cat() in R/getPseudoMSMS.R (line 391, column 9)
• cat() in R/getPseudoMSMS.R (line 394, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* 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:
• annotateAIF() (R/annotateAIF.R): 179 lines
• ...
• plotPseudoMSMS() (R/getPseudoMSMS.R): 94 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; 19 lines (1%) are > 80 characters long.
First few lines:
• R/annotateAIF.R#L44 #' "https://zenodo.org/records/17408169/ ...
• ...
• vignettes/import_from_msp.Rmd#L7 %\VignetteIndexEntry{Import MS/MS spec ...
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 v1.47.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the MetaboAnnotatoR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.