Oliver M. Crook
| Snapshot Date: 2026-05-05 13:40 -0400 (Tue, 05 May 2026) |
| git_url: https://git.bioconductor.org/packages/bandle |
| git_branch: RELEASE_3_23 |
| git_last_commit: 4595e52 |
| git_last_commit_date: 2026-04-28 08:58:10 -0400 (Tue, 28 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-06 11:35 -0400 (Wed, 06 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4989 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 Patched (2026-04-24 r89963) -- "Because it was There" | 4722 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 136/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bandle 1.16.0 (landing page) Oliver M. Crook
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| See other builds for bandle in R Universe. | ||||||||||||||
|
To the developers/maintainers of the bandle package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bandle.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: bandle |
| Version: 1.16.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bandle_1.16.0.tar.gz |
| StartedAt: 2026-05-05 21:30:19 -0400 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 21:42:36 -0400 (Tue, 05 May 2026) |
| EllapsedTime: 737.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: bandle.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings bandle_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/bandle.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: 2026-05-06 01:30:20 UTC
* checking for file ‘bandle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bandle’ version ‘1.16.0’
* 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 ‘bandle’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... NOTE
Obsolete C++14 standard request will be ignored
* checking installed package size ... OK
* checking package directory ... 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 ... WARNING
Found the following file with non-ASCII characters:
R/bandle-function.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Biobase’ which was already attached by Depends.
Please remove these calls from your code.
':::' call which should be '::': ‘dplyr:::summarise’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'bandle_get_outliers.Rd'
‘params’
Documented arguments not in \usage in Rd file 'bandle_get_outliers.Rd':
‘x’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... NOTE
Auto-generated content requiring editing in Rd file 'bandle-package.Rd':
\details: ‘...o use the package, including the most important functions ~~’
\references: ‘~~ Literature or other references for background information ~~’
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... WARNING
Non-portable flags in variable 'PKG_CXXFLAGS':
-O3
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bandle-differentiallocalisation 22.701 0.315 23.017
bandle-gpfit 17.478 0.239 17.729
bandle 9.868 0.047 9.916
bandle-EFDR 8.992 0.355 9.347
bandle-plots-translocations 8.186 0.025 8.211
bandle-predict 7.723 0.018 7.763
bandle-process 7.413 0.017 7.431
bandle-plots-translocations-table 6.579 0.049 6.628
bandle-plots-convergence 6.484 0.123 6.607
bandle-prior 5.890 0.247 6.138
bandle-plots-prob 5.694 0.080 5.775
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘v01-getting-started.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/loadpkgdat-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/plotsims-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/plotgps-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/unnamed-chunk-4-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/plotoutliers-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/unnamed-chunk-11-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/allocspost-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/unnamed-chunk-16-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/unnamed-chunk-17-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/heatmap_control-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/heatmap_treatment-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/extractdiffloc-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/alluvial-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/chord-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/diffloc_boot-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v01-getting-started_files/figure-html/diffloc_binom-1.png" but not available.
--- finished re-building ‘v01-getting-started.Rmd’
--- re-building ‘v02-workflow.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/vign_test/bandle/vignettes/v02-workflow_files/figure-html/exampledata-1.png" but not available.
Quitting from v02-workflow.Rmd:238-241 [runhyppar]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! Parameters nu, a, rho must be positive
---
Backtrace:
▆
1. ├─BiocGenerics::lapply(thplopit, function(x) fitGPmaternPC(x, hyppar = pc_prior))
2. ├─MSnbase (local) lapply(thplopit, function(x) fitGPmaternPC(x, hyppar = pc_prior))
3. │ ├─BiocGenerics::lapply(msnsets(X), FUN, ...)
4. │ └─base::lapply(msnsets(X), FUN, ...)
5. │ └─global FUN(X[[i]], ...)
6. │ └─bandle::fitGPmaternPC(x, hyppar = pc_prior)
7. │ └─base::apply(...)
8. │ └─bandle (local) FUN(newX[, i], ...)
9. │ └─lbfgs::lbfgs(...)
10. └─bandle (local) `<fn>`(`<dbl>`, ...)
11. └─bandle:::likelihoodGPcpp(Xk, tau, h, nk, D, materncov, nu)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'v02-workflow.Rmd' failed with diagnostics:
Parameters nu, a, rho must be positive
--- failed re-building ‘v02-workflow.Rmd’
SUMMARY: processing the following file failed:
‘v02-workflow.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.23-bioc/meat/bandle.Rcheck/00check.log’
for details.
bandle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL bandle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘bandle’ ... ** this is package ‘bandle’ version ‘1.16.0’ ** using staged installation ** libs specified C++14 using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’ g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -O3 -DARMA_NO_DEBUG -fpic -g -O2 -Wall -Werror=format-security -c Bessel2ndKind.cpp -o Bessel2ndKind.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -O3 -DARMA_NO_DEBUG -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -O3 -DARMA_NO_DEBUG -fpic -g -O2 -Wall -Werror=format-security -c dmvtCpp.cpp -o dmvtCpp.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -O3 -DARMA_NO_DEBUG -fpic -g -O2 -Wall -Werror=format-security -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_NO_DEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -O3 -DARMA_NO_DEBUG -fpic -g -O2 -Wall -Werror=format-security -c pg_sample.cpp -o pg_sample.o g++ -std=gnu++20 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o bandle.so Bessel2ndKind.o RcppExports.o dmvtCpp.o leapfrogGPcpp.o pg_sample.o -fopenmp -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-bandle/00new/bandle/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function from function ‘posteriorEstimates’ in package ‘bandle’ Creating a generic function from function ‘bandleJoint’ in package ‘bandle’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (bandle)
bandle.Rcheck/tests/spelling.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.
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.
> #if(requireNamespace('spelling', quietly = TRUE))
> # spelling::spell_check_test(vignettes = TRUE, error = FALSE,
> # skip_on_cran = TRUE)
>
> proc.time()
user system elapsed
0.149 0.032 0.169
bandle.Rcheck/tests/testthat.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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.
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.
> # The setting of R_TESTS exists to work around an R bug. See
> # https://github.com/hadley/testthat/issues/144
> # We should remove it when the issue is resolved.
> Sys.setenv("R_TESTS" = "")
>
> library("testthat")
> library("bandle")
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: MSnbase
Loading required package: mzR
Loading required package: Rcpp
Loading required package: ProtGenerics
Attaching package: 'ProtGenerics'
The following object is masked from 'package:stats':
smooth
This is MSnbase version 2.38.0
Visit https://lgatto.github.io/MSnbase/ to get started.
Consider switching to the 'R for Mass Spectrometry'
packages - see https://RforMassSpectrometry.org for details.
Attaching package: 'MSnbase'
The following object is masked from 'package:base':
trimws
Loading required package: pRoloc
Loading required package: MLInterfaces
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: XML
Attaching package: 'annotate'
The following object is masked from 'package:mzR':
nChrom
Loading required package: cluster
Loading required package: BiocParallel
This is pRoloc version 1.52.0
Visit https://lgatto.github.io/pRoloc/ to get started.
Attaching package: 'bandle'
The following object is masked from 'package:pRoloc':
spatial2D
> library("pRolocdata")
This is pRolocdata version 1.50.0.
Use 'pRolocdata()' to list available data sets.
>
> test_check("bandle")
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[ FAIL 0 | WARN 0 | SKIP 0 | PASS 37 ]
>
> proc.time()
user system elapsed
128.897 1.962 131.737
bandle.Rcheck/bandle-Ex.timings
| name | user | system | elapsed | |
| bandle-EFDR | 8.992 | 0.355 | 9.347 | |
| bandle-cpp | 0 | 0 | 0 | |
| bandle-differentiallocalisation | 22.701 | 0.315 | 23.017 | |
| bandle-gp | 0 | 0 | 0 | |
| bandle-gpfit | 17.478 | 0.239 | 17.729 | |
| bandle-internal | 0.494 | 0.003 | 0.497 | |
| bandle-meanOrganelle | 0.029 | 0.002 | 0.032 | |
| bandle-plots-convergence | 6.484 | 0.123 | 6.607 | |
| bandle-plots-prob | 5.694 | 0.080 | 5.775 | |
| bandle-plots-spatial | 0.000 | 0.000 | 0.001 | |
| bandle-plots-translocations-table | 6.579 | 0.049 | 6.628 | |
| bandle-plots-translocations | 8.186 | 0.025 | 8.211 | |
| bandle-predict | 7.723 | 0.018 | 7.763 | |
| bandle-prior | 5.890 | 0.247 | 6.138 | |
| bandle-process | 7.413 | 0.017 | 7.431 | |
| bandle-sim | 0.479 | 0.004 | 0.483 | |
| bandle | 9.868 | 0.047 | 9.916 | |
| calculateGelman | 4.749 | 0.013 | 4.762 | |
| method-mr | 1.754 | 0.037 | 1.791 | |
| plotOutliers | 4.822 | 0.049 | 4.872 | |