Oliver M. Crook
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/bandle |
| git_branch: RELEASE_3_21 |
| git_last_commit: 763fda5 |
| git_last_commit_date: 2025-04-15 12:49:18 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:37 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 129/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bandle 1.12.0 (landing page) Oliver M. Crook
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.12.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings bandle_1.12.0.tar.gz |
| StartedAt: 2025-10-15 20:55:53 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 21:09:50 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 836.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: bandle.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings bandle_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/bandle.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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
* checking for file ‘bandle/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘bandle’ version ‘1.12.0’
* 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) 13.3.0’
* checking C++ specification ... NOTE
Specified C++14: please drop specification unless essential
* 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 ... OK
* 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 ... OK
* 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 ... NOTE
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 24.542 0.322 24.868
bandle-gpfit 16.567 0.207 16.774
bandle 10.172 0.026 10.200
bandle-EFDR 9.558 0.236 9.794
bandle-plots-translocations 8.260 0.051 8.311
bandle-predict 8.050 0.061 8.117
bandle-process 7.543 0.013 7.556
bandle-plots-convergence 6.738 0.029 6.770
bandle-plots-translocations-table 6.724 0.027 6.751
bandle-prior 6.063 0.056 6.119
bandle-plots-prob 5.912 0.010 5.922
plotOutliers 5.098 0.016 5.114
calculateGelman 5.043 0.017 5.061
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/bandle.Rcheck/00check.log’
for details.
bandle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL bandle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘bandle’ ... ** this is package ‘bandle’ version ‘1.12.0’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++14 g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c Bessel2ndKind.cpp -o Bessel2ndKind.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c dmvtCpp.cpp -o dmvtCpp.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -Werror=format-security -c pg_sample.cpp -o pg_sample.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-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 4.5.1 (2025-06-13) -- "Great Square Root"
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.
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
0.158 0.032 0.177
bandle.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "Great Square Root"
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.
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 2.34.1
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 1.48.0
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 1.46.0.
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
126.224 2.896 129.115
bandle.Rcheck/bandle-Ex.timings
| name | user | system | elapsed | |
| bandle-EFDR | 9.558 | 0.236 | 9.794 | |
| bandle-cpp | 0.001 | 0.000 | 0.001 | |
| bandle-differentiallocalisation | 24.542 | 0.322 | 24.868 | |
| bandle-gp | 0 | 0 | 0 | |
| bandle-gpfit | 16.567 | 0.207 | 16.774 | |
| bandle-internal | 0.470 | 0.011 | 0.481 | |
| bandle-meanOrganelle | 0.031 | 0.000 | 0.030 | |
| bandle-plots-convergence | 6.738 | 0.029 | 6.770 | |
| bandle-plots-prob | 5.912 | 0.010 | 5.922 | |
| bandle-plots-spatial | 0 | 0 | 0 | |
| bandle-plots-translocations-table | 6.724 | 0.027 | 6.751 | |
| bandle-plots-translocations | 8.260 | 0.051 | 8.311 | |
| bandle-predict | 8.050 | 0.061 | 8.117 | |
| bandle-prior | 6.063 | 0.056 | 6.119 | |
| bandle-process | 7.543 | 0.013 | 7.556 | |
| bandle-sim | 0.463 | 0.011 | 0.475 | |
| bandle | 10.172 | 0.026 | 10.200 | |
| calculateGelman | 5.043 | 0.017 | 5.061 | |
| method-mr | 1.741 | 0.014 | 1.756 | |
| plotOutliers | 5.098 | 0.016 | 5.114 | |