Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-10-25 11:41:40 -0400 (Wed, 25 Oct 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4727 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4465 |
lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4476 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
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 1167/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
mbkmeans 1.18.0 (landing page) Davide Risso
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: mbkmeans |
Version: 1.18.0 |
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings mbkmeans_1.18.0.tar.gz |
StartedAt: 2023-10-25 12:58:47 -0000 (Wed, 25 Oct 2023) |
EndedAt: 2023-10-25 13:13:37 -0000 (Wed, 25 Oct 2023) |
EllapsedTime: 890.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mbkmeans.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:mbkmeans.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings mbkmeans_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/mbkmeans.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * checking for file ‘mbkmeans/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mbkmeans’ version ‘1.18.0’ * 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: ‘g++ (GCC) 10.3.1’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: libs 6.4Mb * 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 R 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 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 in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/mbkmeans.Rcheck/00check.log’ for details.
mbkmeans.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL mbkmeans ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘mbkmeans’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/site-library/ClusterR/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.3.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.3.1/site-library/ClusterR/include' -I/usr/local/include -fPIC -g -O2 -Wall -c mini_batch.cpp -o mini_batch.o In file included from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/armadillo:26, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/RcppArmadillo.h:29, from mini_batch.cpp:2: /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’ 321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’ 326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ /home/biocbuild/R/R-4.3.1/site-library/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’ 329 | #pragma message ("INFO: see the documentation for details") | ^ In file included from mini_batch.cpp:3: /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h: In member function ‘arma::mat clustR::ClustHeader::KMEANS_arma(arma::mat&, int, int, bool, std::string, Rcpp::Nullable<Rcpp::Matrix<14> >, int)’: /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 862 | bool status; | ^~~~~~ /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h: In instantiation of ‘T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_full<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]’: /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h:1601:70: required from here /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 1530 | bool status; | ^~~~~~ /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h: In instantiation of ‘T clustR::ClustHeader::GMM_arma_covariance_type(T, arma::mat&, int, std::string, std::string, int, int, bool, double, int) [with T = arma::gmm_priv::gmm_diag<double>; arma::mat = arma::Mat<double>; std::string = std::__cxx11::basic_string<char>]’: /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h:1635:70: required from here /home/biocbuild/R/R-4.3.1/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o mbkmeans.so RcppExports.o mini_batch.o -L/home/biocbuild/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/site-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 4.3.1 (2023-06-16) -- "Beagle Scouts" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) 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 580.822 8.304 590.140
mbkmeans.Rcheck/mbkmeans-Ex.timings
name | user | system | elapsed | |
blocksize | 0.000 | 0.000 | 0.001 | |
compute_wcss | 0.000 | 0.000 | 0.001 | |
mbkmeans | 0.620 | 0.076 | 0.697 | |
mini_batch | 0.001 | 0.000 | 0.001 | |
predict_mini_batch | 0.005 | 0.000 | 0.005 | |
predict_mini_batch_r | 0.020 | 0.004 | 0.024 | |