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This page was generated on 2024-03-29 11:37:15 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 1835/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 2.2.1  (landing page)
Xiuwen Zheng
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/SAIGEgds
git_branch: RELEASE_3_18
git_last_commit: 511d2b8
git_last_commit_date: 2024-01-27 01:17:00 -0400 (Sat, 27 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for SAIGEgds on palomino4


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: 2.2.1
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
StartedAt: 2024-03-27 15:49:51 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 15:51:31 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 100.6 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SPATest.cpp -o SPATest.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_fitnull.cpp -o saige_fitnull.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_main.cpp -o saige_main.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_misc.cpp -o saige_misc.o
saige_misc.cpp: In function 'SEXPREC* saige_grm_sp_calc_ijx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_misc.cpp:626:29: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare]
  626 |         if (SAIGE_NumThread > n_block) SAIGE_NumThread = n_block;
      |             ~~~~~~~~~~~~~~~~^~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vec_ext_avx2.cpp -o vec_ext_avx2.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vec_ext_def.cpp -o vec_ext_def.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"  -DRCPP_PARALLEL_USE_TBB=1   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vectorization.cpp -o vectorization.o
g++ -shared -s -static-libgcc -o SAIGEgds.dll tmp.def SPATest.o saige_fitnull.o saige_main.o saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.18-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -lgcc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAIGEgds)