Xiuwen Zheng
| Snapshot Date: 2026-03-06 13:40 -0500 (Fri, 06 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: devel |
| git_last_commit: 29ab70a |
| git_last_commit_date: 2026-02-20 00:19:22 -0500 (Fri, 20 Feb 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-07 11:33 -0500 (Sat, 07 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4453 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-02-28 r89501) -- "Unsuffered Consequences" | 3376 |
| 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 1879/2357 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.11.2 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for SAIGEgds in R Universe. | ||||||||||||||
|
To the developers/maintainers of the SAIGEgds package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SAIGEgds.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: SAIGEgds |
| Version: 2.11.2 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SAIGEgds |
| StartedAt: 2026-03-06 21:12:11 -0500 (Fri, 06 Mar 2026) |
| EndedAt: 2026-03-06 21:12:24 -0500 (Fri, 06 Mar 2026) |
| EllapsedTime: 13.0 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 SAIGEgds
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* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* preparing ‘SAIGEgds’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
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* installing *source* package ‘SAIGEgds’ ...
** this is package ‘SAIGEgds’ version ‘2.11.2’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c SPATest.cpp -o SPATest.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -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/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c saige_fitnull.cpp -o saige_fitnull.o
saige_fitnull.cpp: In function ‘double calcCV(const arma::dvec&, int)’:
saige_fitnull.cpp:826:25: error: reference to ‘span’ is ambiguous
826 | return(calcCV(x(span(st, x.size()-1))));
| ^~~~
In file included from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo:155,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/RcppArmadillo.h:32,
from saige_fitnull.cpp:28:
/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo_bits/span.hpp:38:8: note: candidates are: ‘struct arma::span’
38 | struct span : public span_base<>
| ^~~~
In file included from /usr/include/c++/13/format:44,
from /usr/include/c++/13/bits/chrono_io.h:39,
from /usr/include/c++/13/chrono:3370,
from /home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include/current/armadillo:53:
/usr/include/c++/13/span:56:11: note: ‘template<class _Type, long unsigned int _Extent> class std::span’
56 | class span;
| ^~~~
make: *** [/home/biocbuild/bbs-3.23-bioc/R/etc/Makeconf:197: saige_fitnull.o] Error 1
ERROR: compilation failed for package ‘SAIGEgds’
* removing ‘/tmp/RtmptFe7sv/Rinst1abb102053be77/SAIGEgds’
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ERROR: package installation failed