Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-08-30 12:08 -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 kjohnson3

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.

raw results


Summary

Package: SAIGEgds
Version: 2.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SAIGEgds
StartedAt: 2025-08-29 17:30:36 -0400 (Fri, 29 Aug 2025)
EndedAt: 2025-08-29 17:30:45 -0400 (Fri, 29 Aug 2025)
EllapsedTime: 9.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SAIGEgds
###
##############################################################################
##############################################################################


* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c SPATest.cpp -o SPATest.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c saige_fitnull.cpp -o saige_fitnull.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c saige_main.cpp -o saige_main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c saige_misc.cpp -o saige_misc.o
saige_misc.cpp:518:2: error: no template named 'concurrent_vector' in namespace 'tbb'
        PARALLEL_VECTOR<t_sp_i_j> &sp)
        ^~~~~~~~~~~~~~~
./saige.h:80:33: note: expanded from macro 'PARALLEL_VECTOR'
#define PARALLEL_VECTOR    tbb::concurrent_vector
                           ~~~~~^
saige_misc.cpp:568:2: error: no member named 'concurrent_vector' in namespace 'tbb'
        PARALLEL_VECTOR<t_sp_i_j> sp;
        ^~~~~~~~~~~~~~~
./saige.h:80:33: note: expanded from macro 'PARALLEL_VECTOR'
#define PARALLEL_VECTOR    tbb::concurrent_vector
                           ~~~~~^
saige_misc.cpp:568:18: error: 't_sp_i_j' does not refer to a value
        PARALLEL_VECTOR<t_sp_i_j> sp;
                        ^
saige_misc.cpp:434:8: note: declared here
struct t_sp_i_j
       ^
saige_misc.cpp:568:28: error: use of undeclared identifier 'sp'
        PARALLEL_VECTOR<t_sp_i_j> sp;
                                  ^
saige_misc.cpp:569:2: error: use of undeclared identifier 'sp'
        sp.reserve(nSamp*4);
        ^
saige_misc.cpp:588:23: error: use of undeclared identifier 'sp'
                                G_Pack, G_Lookup, sp);
                                                  ^
saige_misc.cpp:596:19: error: use of undeclared identifier 'sp'
        const size_t n = sp.size();
                         ^
saige_misc.cpp:600:17: error: use of undeclared identifier 'sp'
                t_sp_i_j &v = sp[i];
                              ^
8 errors generated.
make: *** [saige_misc.o] Error 1
ERROR: compilation failed for package ‘SAIGEgds’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpxOKhW6/Rinst11fdb19a86044/SAIGEgds’
      -----------------------------------
ERROR: package installation failed