Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-12 12:12 -0400 (Tue, 12 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
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 128/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bandle 1.13.0 (landing page) Oliver M. Crook
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: bandle |
Version: 1.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bandle_1.13.0.tar.gz |
StartedAt: 2025-08-12 04:06:43 -0000 (Tue, 12 Aug 2025) |
EndedAt: 2025-08-12 04:21:11 -0000 (Tue, 12 Aug 2025) |
EllapsedTime: 867.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: bandle.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:bandle.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings bandle_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/bandle.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bandle/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘bandle’ version ‘1.13.0’ * 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... NOTE Specified C++14: please drop specification unless essential * checking installed package size ... INFO installed size is 8.0Mb sub-directories of 1Mb or more: libs 7.1Mb * 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 44.578 0.288 45.363 bandle-gpfit 29.926 0.091 30.714 bandle 20.938 0.040 21.038 bandle-EFDR 16.990 0.211 17.240 bandle-predict 15.376 0.039 15.513 bandle-plots-translocations 15.346 0.063 15.448 bandle-process 14.493 0.008 14.536 bandle-plots-translocations-table 12.744 0.032 12.809 bandle-plots-convergence 12.719 0.048 12.798 bandle-plots-prob 11.713 0.116 11.863 plotOutliers 9.778 0.044 9.849 calculateGelman 9.739 0.032 9.795 bandle-prior 5.155 0.407 5.578 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 4 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/bandle.Rcheck/00check.log’ for details.
bandle.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL bandle ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘bandle’ ... ** this is package ‘bandle’ version ‘1.13.0’ ** using staged installation ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++14 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c Bessel2ndKind.cpp -o Bessel2ndKind.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c dmvtCpp.cpp -o dmvtCpp.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c leapfrogGPcpp.cpp -o leapfrogGPcpp.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c pg_sample.cpp -o pg_sample.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o bandle.so Bessel2ndKind.o RcppExports.o dmvtCpp.o leapfrogGPcpp.o pg_sample.o -fopenmp -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 0.173 0.050 0.208
bandle.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 2.35.1 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 1.49.0 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 1.47.0. Use 'pRolocdata()' to list available data sets. > > test_check("bandle") [1] "markers" [1] "markers" [1] "markers" | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60%[1] "markers" [1] "markers" | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60%[1] "xx" [1] "xx" | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60%[1] "xx" [1] "xx" | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60%[1] "markers" [1] "markers" | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60%[1] "markers" [1] "markers" | | | 0% | |============== | 20% | |============================ | 40% | |========================================== | 60%[1] "xx" [1] "xx" | | | 0% | 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bandle.Rcheck/bandle-Ex.timings
name | user | system | elapsed | |
bandle-EFDR | 16.990 | 0.211 | 17.240 | |
bandle-cpp | 0.000 | 0.000 | 0.001 | |
bandle-differentiallocalisation | 44.578 | 0.288 | 45.363 | |
bandle-gp | 0 | 0 | 0 | |
bandle-gpfit | 29.926 | 0.091 | 30.714 | |
bandle-internal | 0.767 | 0.000 | 0.769 | |
bandle-meanOrganelle | 0.042 | 0.000 | 0.042 | |
bandle-plots-convergence | 12.719 | 0.048 | 12.798 | |
bandle-plots-prob | 11.713 | 0.116 | 11.863 | |
bandle-plots-spatial | 0.000 | 0.000 | 0.001 | |
bandle-plots-translocations-table | 12.744 | 0.032 | 12.809 | |
bandle-plots-translocations | 15.346 | 0.063 | 15.448 | |
bandle-predict | 15.376 | 0.039 | 15.513 | |
bandle-prior | 5.155 | 0.407 | 5.578 | |
bandle-process | 14.493 | 0.008 | 14.536 | |
bandle-sim | 0.668 | 0.000 | 0.669 | |
bandle | 20.938 | 0.040 | 21.038 | |
calculateGelman | 9.739 | 0.032 | 9.795 | |
method-mr | 3.141 | 0.004 | 3.153 | |
plotOutliers | 9.778 | 0.044 | 9.849 | |