Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-08-13 17:41 -0400 (Tue, 13 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4758 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4493 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4522 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4471 |
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 1180/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mbkmeans 1.20.0 (landing page) Davide Risso
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the mbkmeans package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mbkmeans.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: mbkmeans |
Version: 1.20.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mbkmeans_1.20.0.tar.gz |
StartedAt: 2024-08-12 06:56:44 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 07:07:58 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 674.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mbkmeans.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mbkmeans_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/mbkmeans.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-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 Monterey 12.7.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘mbkmeans/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mbkmeans’ version ‘1.20.0’ * 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 ‘mbkmeans’ can be installed ... OK * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * 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 ... NOTE License stub is invalid DCF. * 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 Namespace in Imports field not imported from: ‘S4Vectors’ All declared Imports should be used. * 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 C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/mbkmeans.Rcheck/00check.log’ for details.
mbkmeans.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mbkmeans ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘mbkmeans’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ClusterR/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ClusterR/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c mini_batch.cpp -o mini_batch.o In file included from mini_batch.cpp:2: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58: In file included from /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include/armadillo:26: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:353:11: warning: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed [-W#pragma-messages] #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:358:13: warning: INFO: suggest to use ARMA_WARN_LEVEL option instead [-W#pragma-messages] #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include/armadillo_bits/config.hpp:361:11: warning: INFO: see the documentation for details [-W#pragma-messages] #pragma message ("INFO: see the documentation for details") ^ In file included from mini_batch.cpp:3: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] bool status; ^ /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] bool status; ^ 5 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o mbkmeans.so RcppExports.o mini_batch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-mbkmeans/00new/mbkmeans/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 (mbkmeans)
mbkmeans.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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. > library(testthat) > library(mbkmeans) > > test_check("mbkmeans") [ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 29 ] > > proc.time() user system elapsed 203.435 44.292 288.939
mbkmeans.Rcheck/mbkmeans-Ex.timings
name | user | system | elapsed | |
blocksize | 0.000 | 0.001 | 0.001 | |
compute_wcss | 0.001 | 0.001 | 0.002 | |
mbkmeans | 0.984 | 0.132 | 1.340 | |
mini_batch | 0.001 | 0.001 | 0.001 | |
predict_mini_batch | 0.006 | 0.003 | 0.009 | |
predict_mini_batch_r | 0.013 | 0.005 | 0.022 | |