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This page was generated on 2023-03-22 11:06:15 -0400 (Wed, 22 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4508
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4293
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4290
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

INSTALL results for SAIGEgds on palomino3


To the developers/maintainers of the SAIGEgds package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1770/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 1.99.0  (landing page)
Xiuwen Zheng
Snapshot Date: 2023-03-21 14:00:22 -0400 (Tue, 21 Mar 2023)
git_url: https://git.bioconductor.org/packages/SAIGEgds
git_branch: master
git_last_commit: 3db9622
git_last_commit_date: 2023-03-07 23:53:23 -0400 (Tue, 07 Mar 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SAIGEgds
Version: 1.99.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
StartedAt: 2023-03-21 15:43:36 -0400 (Tue, 21 Mar 2023)
EndedAt: 2023-03-21 15:44:42 -0400 (Tue, 21 Mar 2023)
EllapsedTime: 65.5 seconds
RetCode: 1
Status:   ERROR  

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SAIGEgds
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'SAIGEgds' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c SPATest.cpp -o SPATest.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_fitnull.cpp -o saige_fitnull.o
In file included from saige_fitnull.cpp:29:
saige_fitnull.cpp: In function 'SEXPREC* saige_store_2b_geno(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp: In function 'SEXPREC* saige_store_sp_geno(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp: In function 'void get_crossprod_b_grm(const arma::dcolvec&, arma::dvec&)':
saige.h:88:27: warning: unused variable 'th_idx' [-Wunused-variable]
   88 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:88:27: note: in definition of macro 'PARALLEL_RANGE'
   88 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_fitnull.cpp: In function 'void get_diag_sigma(const arma::dvec&, const arma::dvec&, arma::dvec&)':
saige.h:88:27: warning: unused variable 'th_idx' [-Wunused-variable]
   88 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:88:27: note: in definition of macro 'PARALLEL_RANGE'
   88 |                 const int th_idx = 0;  \
      |                           ^~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_main.cpp -o saige_main.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c saige_misc.cpp -o saige_misc.o
In file included from saige_misc.cpp:25:
saige_misc.cpp: In function 'void grm_sp_init_lookup(SEXP, SEXP, bool)':
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_misc.cpp: At global scope:
saige_misc.cpp:518:14: error: 'tbb::concurrent_vector' has not been declared
  518 |         tbb::concurrent_vector<t_sp_i_j> &sp)
      |              ^~~~~~~~~~~~~~~~~
saige_misc.cpp:518:31: error: expected ',' or '...' before '<' token
  518 |         tbb::concurrent_vector<t_sp_i_j> &sp)
      |                               ^
saige_misc.cpp: In function 'void grm_sp_calc_block(double, int, int, int, int, size_t, const Rcpp::RawMatrix&, const Rcpp::NumericMatrix&, int)':
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.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_misc.cpp: In function 'SEXPREC* saige_grm_sp_calc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
saige_misc.cpp:568:14: error: 'concurrent_vector' is not a member of 'tbb'
  568 |         tbb::concurrent_vector<t_sp_i_j> sp;
      |              ^~~~~~~~~~~~~~~~~
saige_misc.cpp:568:40: error: expected primary-expression before '>' token
  568 |         tbb::concurrent_vector<t_sp_i_j> sp;
      |                                        ^
saige_misc.cpp:568:42: error: 'sp' was not declared in this scope
  568 |         tbb::concurrent_vector<t_sp_i_j> sp;
      |                                          ^~
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;
      |             ~~~~~~~~~~~~~~~~^~~~~~~~~
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige_misc.cpp: In function 'SEXPREC* saige_grm_ds_calc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
saige.h:84:27: warning: unused variable 'th_idx' [-Wunused-variable]
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
saige.h:84:27: note: in definition of macro 'PARALLEL_FOR'
   84 |                 const int th_idx = 0;  \
      |                           ^~~~~~
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: *** [F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:272: saige_misc.o] Error 1
ERROR: compilation failed for package 'SAIGEgds'
* removing 'F:/biocbuild/bbs-3.17-bioc/R/library/SAIGEgds'