| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-08 11:34 -0500 (Thu, 08 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" | 4815 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 262/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BUSpaRse 1.25.0 (landing page) Lambda Moses
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the BUSpaRse package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUSpaRse.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: BUSpaRse |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BUSpaRse |
| StartedAt: 2026-01-07 16:33:41 -0500 (Wed, 07 Jan 2026) |
| EndedAt: 2026-01-07 16:33:53 -0500 (Wed, 07 Jan 2026) |
| EllapsedTime: 12.0 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 BUSpaRse
###
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* checking for file ‘BUSpaRse/DESCRIPTION’ ... OK
* preparing ‘BUSpaRse’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
-----------------------------------
* installing *source* package ‘BUSpaRse’ ...
** this is package ‘BUSpaRse’ version ‘1.25.0’
** 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/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/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/RcppProgress/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fill_cell_gene.cpp -o fill_cell_gene.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from fill_cell_gene.cpp:7:
/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 /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/concepts.hpp:26,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/size_type.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/size.hpp:21,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/functions.hpp:20,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:41,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/iterator_range.hpp:13,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/range/as_literal.hpp:18,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/algorithm/string/join.hpp:17,
from fill_cell_gene.cpp:17:
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
194 | failed ************ (Pred::************
| ^~~~~~~~~~~~~~~~~~~
| -
195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | );
| ~
| -
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| -
200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
201 | );
| ~
| -
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp.h:58,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:35:
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/DataFrame.h: In instantiation of ‘int Rcpp::DataFrame_Impl<StoragePolicy>::nrow() const [with StoragePolicy = Rcpp::PreserveStorage]’:
fill_cell_gene.cpp:101:31: required from here
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/DataFrame.h:64:26: error: ‘R_nrow’ was not declared in this scope; did you mean ‘nrow’?
64 | return R_nrow( Parent::get__() );
| ~~~~~~^~~~~~~~~~~~~~~~~~~
| nrow
make: *** [/home/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:209: fill_cell_gene.o] Error 1
ERROR: compilation failed for package ‘BUSpaRse’
* removing ‘/tmp/RtmpRwB5f1/Rinst28f34e62137177/BUSpaRse’
-----------------------------------
ERROR: package installation failed