SAIGEgds.install

[Yikun]

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SAIGEgds
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppParallel/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c SPATest.cpp -o SPATest.o
SPATest.cpp:42:15: error: ‘COREARRAY_TARGET_CLONES’ does not name a type
   42 | inline static COREARRAY_TARGET_CLONES
      |               ^~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:56:15: error: ‘COREARRAY_TARGET_CLONES’ does not name a type
   56 | inline static COREARRAY_TARGET_CLONES
      |               ^~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:71:15: error: ‘COREARRAY_TARGET_CLONES’ does not name a type
   71 | inline static COREARRAY_TARGET_CLONES
      |               ^~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:93:9: error: expected initializer before ‘getroot_K1’
   93 |         getroot_K1(const double g_pos, const double g_neg,
      |         ^~~~~~~~~~
SPATest.cpp:140:9: error: expected initializer before ‘getroot_K1_fast’
  140 |         getroot_K1_fast(const double g_pos, const double g_neg, double &root,
      |         ^~~~~~~~~~~~~~~
SPATest.cpp:189:9: error: expected initializer before ‘get_saddle_prob’
  189 |         get_saddle_prob(double t, size_t n_g, const double mu[], const double g[],
      |         ^~~~~~~~~~~~~~~
SPATest.cpp:212:9: error: expected initializer before ‘get_saddle_prob_fast’
  212 |         get_saddle_prob_fast(double t, size_t n_nonzero, const double mu[],
      |         ^~~~~~~~~~~~~~~~~~~~
SPATest.cpp:238:9: error: expected initializer before ‘Saddle_Prob’
  238 |         Saddle_Prob(double q, double m1, double var1, size_t n_g, const double mu[],
      |         ^~~~~~~~~~~
SPATest.cpp:300:9: error: expected initializer before ‘Saddle_Prob_Fast’
  300 |         Saddle_Prob_Fast(double q, double m1, double var1, size_t n_g,
      |         ^~~~~~~~~~~~~~~~
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: SPATest.o] Error 1
ERROR: compilation failed for package ‘SAIGEgds’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/SAIGEgds’

[martin-g]

Reported upstream: https://github.com/AbbVie-ComputationalGenomics/SAIGEgds/issues/8

[martin-g]

Pull Request: https://github.com/AbbVie-ComputationalGenomics/SAIGEgds/pull/9

[martin-g]

The PR has been merged!

I'll leave this issue open for now. We can close it if the next run is successful.

[martin-g]

The report from 23.03.2023 is OK!