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This page was generated on 2025-08-30 12:06 -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 | ||||||||||
|
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: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data SAIGEgds |
| StartedAt: 2025-08-29 18:18:48 -0400 (Fri, 29 Aug 2025) |
| EndedAt: 2025-08-29 18:19:19 -0400 (Fri, 29 Aug 2025) |
| EllapsedTime: 30.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SPATest.cpp -o SPATest.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_fitnull.cpp -o saige_fitnull.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_main.cpp -o saige_main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppParallel/include' -I/opt/R/x86_64/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/tmp/RtmpYNsFzb/Rinsta4201d8a71d9/SAIGEgds’
-----------------------------------
ERROR: package installation failed