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 17:40 -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: E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mbkmeans.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings mbkmeans_1.20.0.tar.gz |
StartedAt: 2024-08-12 02:37:04 -0400 (Mon, 12 Aug 2024) |
EndedAt: 2024-08-12 02:43:33 -0400 (Mon, 12 Aug 2024) |
EllapsedTime: 388.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: mbkmeans.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:mbkmeans.install-out.txt --library=E:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings mbkmeans_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.19-bioc/meat/mbkmeans.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 whether package 'mbkmeans' can be installed ... OK * used C++ compiler: 'G__~1.EXE (GCC) 13.2.0' * 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 ... 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 for x64 is not available File 'E:/biocbuild/bbs-3.19-bioc/R/library/mbkmeans/libs/x64/mbkmeans.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * 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 'E:/biocbuild/bbs-3.19-bioc/meat/mbkmeans.Rcheck/00check.log' for details.
mbkmeans.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL mbkmeans ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.19-bioc/R/library' * installing *source* package 'mbkmeans' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 13.2.0' using C++11 g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/Rhdf5lib/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/beachmat/include' -I'E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mini_batch.cpp -o mini_batch.o In file included from E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include/armadillo:26, from E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:58, from E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include/RcppArmadillo.h:29, from mini_batch.cpp:2: E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:353:86: note: '#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed' 353 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed") | ^ E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:358:75: note: '#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead' 358 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead") | ^ E:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include/armadillo_bits/config.hpp:361:61: note: '#pragma message: INFO: see the documentation for details' 361 | #pragma message ("INFO: see the documentation for details") | ^ In file included from mini_batch.cpp:3: E:/biocbuild/bbs-3.19-bioc/R/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)': E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] 862 | bool status; | ^~~~~~ E:/biocbuild/bbs-3.19-bioc/R/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>]': E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include/ClusterRHeader.h:1592:65: required from here E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] 1530 | bool status; | ^~~~~~ E:/biocbuild/bbs-3.19-bioc/R/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>]': E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include/ClusterRHeader.h:1626:65: required from here E:/biocbuild/bbs-3.19-bioc/R/library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable 'status' set but not used [-Wunused-but-set-variable] g++ -shared -s -static-libgcc -o mbkmeans.dll tmp.def RcppExports.o mini_batch.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-mbkmeans/00new/mbkmeans/libs/x64 ** 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 ** 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 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 156.23 21.54 179.86
mbkmeans.Rcheck/mbkmeans-Ex.timings
name | user | system | elapsed | |
blocksize | 0 | 0 | 0 | |
compute_wcss | 0 | 0 | 0 | |
mbkmeans | 0.59 | 0.08 | 0.67 | |
mini_batch | 0 | 0 | 0 | |
predict_mini_batch | 0.02 | 0.00 | 0.02 | |
predict_mini_batch_r | 0.01 | 0.00 | 0.02 | |