Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-27 12:07 -0400 (Wed, 27 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4612 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 194/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocParallel 1.43.4 (landing page) Jiefei Wang
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | TIMEOUT | ||||||||||
To the developers/maintainers of the BiocParallel package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocParallel.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: BiocParallel |
Version: 1.43.4 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocParallel_1.43.4.tar.gz |
StartedAt: 2025-08-26 04:59:15 -0000 (Tue, 26 Aug 2025) |
EndedAt: 2025-08-26 06:07:43 -0000 (Tue, 26 Aug 2025) |
EllapsedTime: 4108.5 seconds |
RetCode: None |
Status: TIMEOUT |
CheckDir: BiocParallel.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BiocParallel_1.43.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BiocParallel.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 ‘BiocParallel/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocParallel’ version ‘1.43.4’ * 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 ‘BiocParallel’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... NOTE Specified C++11: 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 ':::' calls which should be '::': ‘parallel:::closeNode’ ‘parallel:::recvData’ ‘parallel:::recvOneData’ ‘parallel:::sendData’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.workerLapply_impl’ * 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 ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... 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 bpvalidate 3.885 0.222 5.601 BatchtoolsParam-class 2.404 0.450 11.090 SnowParam-class 1.004 0.043 7.505 bpoptions 0.029 0.002 5.075 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.R’
BiocParallel.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL BiocParallel ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘BiocParallel’ ... ** this is package ‘BiocParallel’ version ‘1.43.4’ ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 accepts -g... yes checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 option to enable C++11 features... none needed checking for library containing shm_open... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ using C++11 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I"./" -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/cpp11/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cpp11.cpp -o cpp11.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I"./" -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/cpp11/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c ipcmutex.cpp -o ipcmutex.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o BiocParallel.so cpp11.o ipcmutex.o -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-BiocParallel/00new/BiocParallel/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** 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 (BiocParallel)
BiocParallel.Rcheck/tests/test.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. > BiocGenerics:::testPackage("BiocParallel") Testing BatchtoolsParam Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ... Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ... Submitting 5 jobs in 4 chunks using cluster functions 'Socket' ... > > > > > > > > Submitting 5 jobs in 4 chunks using cluster functions 'Multicore' ... > > > > > > > > Testing BiocParallelParam Testing DoparParam loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment Testing MulticoreParam Testing SerialParam Testing SnowParam Timing stopped at: 0 0 0 Error in DEACTIVATED("MPI tests not run") : MPI tests not run Timing stopped at: 0.001 0 0.005 Error in DEACTIVATED("'snow' and/or 'Rmpi' package did not load") : 'snow' and/or 'Rmpi' package did not load
BiocParallel.Rcheck/BiocParallel-Ex.timings
name | user | system | elapsed | |
BatchtoolsParam-class | 2.404 | 0.450 | 11.090 | |
BiocParallelParam-class | 0.002 | 0.000 | 0.002 | |
DeveloperInterface | 0 | 0 | 0 | |
DoparParam-class | 0 | 0 | 0 | |
MulticoreParam-class | 0.947 | 0.307 | 3.010 | |
SerialParam-class | 0.035 | 0.004 | 0.039 | |
SnowParam-class | 1.004 | 0.043 | 7.505 | |
bpaggregate | 0.000 | 0.000 | 0.007 | |
bpiterate | 0.377 | 0.130 | 0.814 | |
bplapply | 0.056 | 0.045 | 0.076 | |
bploop | 0.001 | 0.000 | 0.000 | |
bpmapply | 0.206 | 0.096 | 0.386 | |
bpok | 0.439 | 0.003 | 4.547 | |
bpoptions | 0.029 | 0.002 | 5.075 | |
bpschedule | 0.382 | 0.027 | 0.830 | |
bptry | 0.056 | 0.083 | 0.120 | |
bpvalidate | 3.885 | 0.222 | 5.601 | |
bpvec | 0.340 | 0.126 | 0.434 | |
bpvectorize | 0.019 | 0.116 | 0.090 | |
ipcmutex | 0.295 | 0.232 | 0.894 | |
register | 0.568 | 0.276 | 0.792 | |
worker-number | 1.008 | 0.165 | 1.124 | |