| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-01-10 11:34 -0500 (Sat, 10 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4818 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4594 |
| 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 1198/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| mbkmeans 1.27.0 (landing page) Davide Risso
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
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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: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data mbkmeans |
| StartedAt: 2026-01-09 18:26:03 -0500 (Fri, 09 Jan 2026) |
| EndedAt: 2026-01-09 18:26:17 -0500 (Fri, 09 Jan 2026) |
| EllapsedTime: 14.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data mbkmeans
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* checking for file ‘mbkmeans/DESCRIPTION’ ... OK
* preparing ‘mbkmeans’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
-----------------------------------
Warning: SystemRequirements specified C++11: support will be removed soon
* installing *source* package ‘mbkmeans’ ...
** this is package ‘mbkmeans’ version ‘1.27.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/ClusterR/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rhdf5lib/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/ClusterR/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c mini_batch.cpp -o mini_batch.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from mini_batch.cpp:2:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
In file included from mini_batch.cpp:3:
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/site-library/ClusterR/include/ClusterRHeader.h:862:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
862 | bool status;
| ^~~~~~
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/site-library/ClusterR/include/ClusterRHeader.h:1592:65: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
1530 | bool status;
| ^~~~~~
/home/biocbuild/bbs-3.23-bioc/R/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/bbs-3.23-bioc/R/site-library/ClusterR/include/ClusterRHeader.h:1626:65: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/ClusterR/include/ClusterRHeader.h:1530:14: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/proxy/proxy.h:24,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/RcppCommon.h:133,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:26,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32:
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/proxy/AttributeProxy.h: In instantiation of ‘bool Rcpp::AttributeProxyPolicy<CLASS>::hasAttribute(const std::string&) const [with CLASS = Rcpp::RObject_Impl<Rcpp::PreserveStorage>; std::string = std::__cxx11::basic_string<char>]’:
/home/biocbuild/bbs-3.23-bioc/R/site-library/beachmat/include/beachmat/input/../utils/utils.h:41:32: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/proxy/AttributeProxy.h:91:27: error: ‘R_hasAttrib’ was not declared in this scope; did you mean ‘R_mapAttrib’?
91 | return R_hasAttrib(static_cast<const CLASS&>(*this).get__(),
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | Rf_install(attr.c_str()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:209: mini_batch.o] Error 1
ERROR: compilation failed for package ‘mbkmeans’
* removing ‘/tmp/RtmpWXXQ6W/Rinst1759581f5bf44c/mbkmeans’
-----------------------------------
ERROR: package installation failed