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This page was generated on 2025-08-30 12:09 -0400 (Sat, 30 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4615
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4562
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1850/2320HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 2.9.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025)
git_url: https://git.bioconductor.org/packages/SAIGEgds
git_branch: devel
git_last_commit: b67d8b4
git_last_commit_date: 2025-04-15 11:51:09 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  ERROR    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  ERROR    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  ERROR    ERROR  skipped


BUILD results for SAIGEgds on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: SAIGEgds
Version: 2.9.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data SAIGEgds
StartedAt: 2025-08-29 02:37:14 -0000 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 02:38:19 -0000 (Fri, 29 Aug 2025)
EllapsedTime: 65.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/R/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 to build vignettes
      -----------------------------------
* installing *source* package ‘SAIGEgds’ ...
** this is package ‘SAIGEgds’ version ‘2.9.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c SPATest.cpp -o SPATest.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_fitnull.cpp -o saige_fitnull.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c saige_main.cpp -o saige_main.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.5.0/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/R/R-4.5.0/etc/Makeconf:211: saige_misc.o] Error 1
ERROR: compilation failed for package ‘SAIGEgds’
* removing ‘/home/biocbuild/tmp/RtmpQDiPXL/Rinst21b9b769a162a4/SAIGEgds’
      -----------------------------------
ERROR: package installation failed