===============================
BiocCheckGitClone('MetaboAnnotatoR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/6444fcf08ba41c0b295f892fee4d42a95c9dc831/MetaboAnnotatoR
→ BiocVersion: 3.23
→ Package: MetaboAnnotatoR
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/6444fcf08ba41c0b295f892fee4d42a95c9dc831/MetaboAnnotatoR.BiocCheck
→ BiocCheckVersion: 1.47.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4016/6444fcf08ba41c0b295f892fee4d42a95c9dc831/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 v1.47.6 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/4016/6444fcf08ba41c0b295f892fee4d42a95c9dc831/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 ‘0.99.5’
* 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] 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 ... [13s/13s] OK
* checking loading without being on the library search path ... [10s/10s] WARNING
Loading required package: xcms
Loading required package: BiocParallel
Error: package or namespace load failed for ‘xcms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘preprocessCore’
Error: package ‘xcms’ could not be loaded
Execution halted
It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Error: there is no package called ‘S4Vectors’
Call sequence:
12: doWithOneRestart(return(expr), restart)
11: withOneRestart(expr, restarts[[1L]])
10: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
9: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
8: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
* checking S3 generic/method consistency ... WARNING
Error: there is no package called ‘S4Vectors’
Call sequence:
12: doWithOneRestart(return(expr), restart)
11: withOneRestart(expr, restarts[[1L]])
10: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
9: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
8: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Error: there is no package called ‘S4Vectors’
Call sequence:
12: doWithOneRestart(return(expr), restart)
11: withOneRestart(expr, restarts[[1L]])
10: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
9: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
8: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Error: there is no package called ‘S4Vectors’
Call sequence:
12: doWithOneRestart(return(expr), restart)
11: withOneRestart(expr, restarts[[1L]])
10: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
9: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
8: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [41s/41s] NOTE
Error: there is no package called ‘pcaMethods’
Call sequence:
10: doWithOneRestart(return(expr), restart)
9: withOneRestart(expr, restarts[[1L]])
8: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
7: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
6: asNamespace(ns)
5: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
4: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
3: asNamespace(ns)
2: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
1: loadNamespace(package, lib.loc)
Execution halted
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 ... WARNING
Error: package ‘xcms’ could not be loaded
Call sequence:
3: stop(gettextf("package %s could not be loaded", sQuote(pkg)),
call. = FALSE, domain = NA)
2: .getRequiredPackages2(pkgInfo, quietly = quietly, lib.loc = c(lib.loc,
.libPaths()))
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
* checking Rd \usage sections ... NOTE
Error: there is no package called ‘IRanges’
Call sequence:
20: doWithOneRestart(return(expr), restart)
19: withOneRestart(expr, restarts[[1L]])
18: withRestarts(stop(cond), retry_loadNamespace = function() NULL)
17: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
16: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
15: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
14: asNamespace(ns)
13: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
.libPaths()), versionCheck = vI[[j]]), i[[2L]], from = package)
12: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
11: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),
versionCheck = vI[[i]]), from = package)
10: loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
9: asNamespace(ns)
8: namespaceImportFrom(ns, loadNamespace(j <- i[[1L]], c(lib.loc,
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘MetaboAnnotatoR-Ex.R’ failed
The error occurred in:
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> pkgname <- "MetaboAnnotatoR"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> base::assign(".ExTimings", "MetaboAnnotatoR-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+ options(OutDec = '.')
+ format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
>
> ### * </HEADER>
> library('MetaboAnnotatoR')
Loading required package: xcms
Loading required package: BiocParallel
Error: package or namespace load failed for ‘xcms’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘IRanges’
Error: package ‘xcms’ could not be loaded
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [1s/1s]
[1s/1s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MetaboAnnotatoR)
Loading required package: xcms
Loading required package: BiocParallel
Error: package or namespace load failed for 'xcms' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called 'IRanges'
Error: package 'xcms' could not be loaded
Execution halted
* 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: 2 ERRORs, 4 WARNINGs, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4016/6444fcf08ba41c0b295f892fee4d42a95c9dc831/MetaboAnnotatoR.Rcheck/00check.log’
for details.
===============================
BiocCheck('MetaboAnnotatoR_0.99.5.tar.gz')
===============================
Error: package or namespace load failed for ‘BiocCheck’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘RBGL’
Execution halted