Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:44 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 188/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BiocParallel 1.39.0 (landing page) Martin Morgan
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: BiocParallel |
Version: 1.39.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocParallel_1.39.0.tar.gz |
StartedAt: 2024-08-20 19:40:15 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 19:44:07 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 231.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BiocParallel.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocParallel.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocParallel_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocParallel.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BiocParallel/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘BiocParallel’ version ‘1.39.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘Rmpi’ * 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BatchtoolsParam-class 0.789 0.268 10.434 bpoptions 0.009 0.000 5.032 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘test.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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocParallel.Rcheck/00check.log’ for details.
BiocParallel.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BiocParallel ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘BiocParallel’ ... ** 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 clang++ -arch arm64 -std=gnu++17 accepts -g... yes checking for clang++ -arch arm64 -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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cpp11.cpp -o cpp11.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ipcmutex.cpp -o ipcmutex.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BiocParallel.so cpp11.o ipcmutex.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 0.001 0 Error in DEACTIVATED("'snow' and/or 'Rmpi' package did not load") : 'snow' and/or 'Rmpi' package did not load Timing stopped at: 0 0 0 Error in DEACTIVATED("'snow' and/or 'Rmpi' package did not load") : 'snow' and/or 'Rmpi' package did not load Testing bpaggregate Testing bpexportglobals Testing bpiterate Testing bplapply Testing bploop Testing bpmapply loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment Testing bpoptions Testing bpvalidate Testing bpvec Testing bpvectorize Testing errorhandling loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment loaded BiocParallel and set parent environment Testing internal_rng_stream Testing ipcmutex Testing logging Testing refclass Testing rng Testing utilities Testing worker-number RUNIT TEST PROTOCOL -- Tue Aug 20 19:44:03 2024 *********************************************** Number of test functions: 109 Number of deactivated test functions: 3 Number of errors: 0 Number of failures: 0 1 Test Suite : BiocParallel RUnit Tests - 109 test functions, 0 errors, 0 failures Number of test functions: 109 Number of deactivated test functions: 3 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 22.546 9.093 190.904
BiocParallel.Rcheck/BiocParallel-Ex.timings
name | user | system | elapsed | |
BatchtoolsParam-class | 0.789 | 0.268 | 10.434 | |
BiocParallelParam-class | 0.001 | 0.000 | 0.001 | |
DeveloperInterface | 0 | 0 | 0 | |
DoparParam-class | 0 | 0 | 0 | |
MulticoreParam-class | 0.399 | 0.148 | 2.359 | |
SerialParam-class | 0.008 | 0.004 | 0.011 | |
SnowParam-class | 0.464 | 0.033 | 3.714 | |
bpaggregate | 0.000 | 0.000 | 0.001 | |
bpiterate | 0.163 | 0.067 | 0.190 | |
bplapply | 0.015 | 0.025 | 0.023 | |
bploop | 0 | 0 | 0 | |
bpmapply | 0.085 | 0.031 | 0.108 | |
bpok | 0.182 | 0.017 | 1.159 | |
bpoptions | 0.009 | 0.000 | 5.032 | |
bpschedule | 0.182 | 0.020 | 0.193 | |
bptry | 0.016 | 0.047 | 0.035 | |
bpvalidate | 1.172 | 0.058 | 1.231 | |
bpvec | 0.159 | 0.037 | 0.175 | |
bpvectorize | 0.012 | 0.034 | 0.024 | |
ipcmutex | 0.146 | 0.074 | 0.603 | |
register | 0.297 | 0.122 | 0.394 | |
worker-number | 0.569 | 0.049 | 0.612 | |