| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-08 11:35 -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 2268/2332 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| universalmotif 1.29.0 (landing page) Benjamin Jean-Marie Tremblay
| 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 universalmotif package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/universalmotif.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: universalmotif |
| Version: 1.29.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data universalmotif |
| StartedAt: 2026-01-07 20:35:57 -0500 (Wed, 07 Jan 2026) |
| EndedAt: 2026-01-07 20:37:13 -0500 (Wed, 07 Jan 2026) |
| EllapsedTime: 76.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data universalmotif
###
##############################################################################
##############################################################################
* checking for file ‘universalmotif/DESCRIPTION’ ... OK
* preparing ‘universalmotif’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
-----------------------------------
* installing *source* package ‘universalmotif’ ...
** this is package ‘universalmotif’ version ‘1.29.0’
** 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/RcppThread/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/Rcpp/include/RcppCommon.h:30,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp.h:27,
from RcppExports.cpp:5:
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/r/check_r_headers.h:27:21: note: ‘#pragma message: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’
27 | #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: ‘#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’
35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410"
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c add_multifreq.cpp -o add_multifreq.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c calc_complexity.cpp -o calc_complexity.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c compare_motifs.cpp -o compare_motifs.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c get_bkg.cpp -o get_bkg.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c motif_finder.cpp -o motif_finder.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c motif_peaks.cpp -o motif_peaks.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c motif_pvalue.cpp -o motif_pvalue.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c scan_sequences.cpp -o scan_sequences.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c shuffle_sequences.cpp -o shuffle_sequences.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c trim_motifs.cpp -o trim_motifs.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c universalmotif-class.cpp -o universalmotif-class.o
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/RcppThread/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c utils-exported.cpp -o utils-exported.o
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include/Rcpp.h:58,
from utils-exported.cpp:1:
/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]’:
utils-exported.cpp:279:47: 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: utils-exported.o] Error 1
ERROR: compilation failed for package ‘universalmotif’
* removing ‘/tmp/RtmpFjKeie/Rinst1fd9a267f19710/universalmotif’
-----------------------------------
ERROR: package installation failed