| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:05 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 1850/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.9.0 (landing page) Xiuwen Zheng
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | ERROR | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
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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: 2.9.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SAIGEgds |
| StartedAt: 2025-08-29 19:13:32 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 19:14:14 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 42.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SAIGEgds
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* checking for file ‘SAIGEgds/DESCRIPTION’ ... OK
* preparing ‘SAIGEgds’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
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* installing *source* package ‘SAIGEgds’ ...
** this is package ‘SAIGEgds’ version ‘2.9.0’
** 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-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-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
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c saige_misc.cpp -o saige_misc.o
In file included from saige_misc.cpp:25:
saige.h:80:33: error: ‘tbb::concurrent_vector’ has not been declared
80 | #define PARALLEL_VECTOR tbb::concurrent_vector
| ^~~~~~~~~~~~~~~~~
saige_misc.cpp:518:9: note: in expansion of macro ‘PARALLEL_VECTOR’
518 | PARALLEL_VECTOR<t_sp_i_j> &sp)
| ^~~~~~~~~~~~~~~
saige_misc.cpp:518:24: error: expected ‘,’ or ‘...’ before ‘<’ token
518 | PARALLEL_VECTOR<t_sp_i_j> &sp)
| ^
saige_misc.cpp: In lambda function:
saige_misc.cpp:540:41: error: ‘sp’ was not declared in this scope
540 | sp.push_back(t_sp_i_j(i_b+i_st, j_b+j_st));
| ^~
saige_misc.cpp: In function ‘SEXPREC* saige_grm_sp_calc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
saige.h:80:33: error: ‘concurrent_vector’ is not a member of ‘tbb’
80 | #define PARALLEL_VECTOR tbb::concurrent_vector
| ^~~~~~~~~~~~~~~~~
saige_misc.cpp:568:9: note: in expansion of macro ‘PARALLEL_VECTOR’
568 | PARALLEL_VECTOR<t_sp_i_j> sp;
| ^~~~~~~~~~~~~~~
saige_misc.cpp:568:33: error: expected primary-expression before ‘>’ token
568 | PARALLEL_VECTOR<t_sp_i_j> sp;
| ^
saige_misc.cpp:568:35: error: ‘sp’ was not declared in this scope
568 | PARALLEL_VECTOR<t_sp_i_j> sp;
| ^~
saige_misc.cpp: At global scope:
saige_misc.cpp:515:13: warning: ‘void grm_sp_calc_block(double, int, int, int, int, size_t, const Rcpp::RawMatrix&, const Rcpp::NumericMatrix&, int)’ defined but not used [-Wunused-function]
515 | static void grm_sp_calc_block(const double rel,
| ^~~~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.22-bioc/R/etc/Makeconf:209: saige_misc.o] Error 1
ERROR: compilation failed for package ‘SAIGEgds’
* removing ‘/tmp/RtmpnG9q6n/Rinsta0b942d8cf819/SAIGEgds’
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ERROR: package installation failed