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INSTALL report for SAIGEgds on malbec1

This page was generated on 2020-04-15 12:16:18 -0400 (Wed, 15 Apr 2020).

Package 1509/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SAIGEgds 1.0.2
Xiuwen Zheng
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SAIGEgds
Branch: RELEASE_3_10
Last Commit: 39ef568
Last Changed Date: 2020-04-08 18:49:04 -0400 (Wed, 08 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SAIGEgds
Version: 1.0.2
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SAIGEgds
StartedAt: 2020-04-14 18:31:14 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:31:59 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 45.0 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL SAIGEgds
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘SAIGEgds’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c SPATest.cpp -o SPATest.o
SPATest.cpp: In function ‘double Saddle_Prob_Fast.sse2.4(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)’:
SPATest.cpp:350:19: warning: ‘NAsigma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    getroot_K1_fast(g_pos, g_neg, root2, ni2, conv2, 0, n_nonzero,
    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     mu, g, qinv, NAmu, NAsigma);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:350:19: warning: ‘NAmu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SPATest.cpp: In function ‘double Saddle_Prob_Fast.sse3.3(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)’:
SPATest.cpp:350:19: warning: ‘NAsigma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    getroot_K1_fast(g_pos, g_neg, root2, ni2, conv2, 0, n_nonzero,
    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     mu, g, qinv, NAmu, NAsigma);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:350:19: warning: ‘NAmu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SPATest.cpp: In function ‘double Saddle_Prob_Fast.avx.2(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)’:
SPATest.cpp:350:19: warning: ‘NAsigma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    getroot_K1_fast(g_pos, g_neg, root2, ni2, conv2, 0, n_nonzero,
    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     mu, g, qinv, NAmu, NAsigma);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:350:19: warning: ‘NAmu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SPATest.cpp: In function ‘double Saddle_Prob_Fast.avx2.1(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)’:
SPATest.cpp:350:19: warning: ‘NAsigma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    getroot_K1_fast(g_pos, g_neg, root2, ni2, conv2, 0, n_nonzero,
    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     mu, g, qinv, NAmu, NAsigma);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:350:19: warning: ‘NAmu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SPATest.cpp: In function ‘double Saddle_Prob_Fast.avx512f.0(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)’:
SPATest.cpp:350:19: warning: ‘NAsigma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    getroot_K1_fast(g_pos, g_neg, root2, ni2, conv2, 0, n_nonzero,
    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     mu, g, qinv, NAmu, NAsigma);
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:350:19: warning: ‘NAmu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
SPATest.cpp: In function ‘double Saddle_Prob_Fast(double, double, double, size_t, const double*, const double*, size_t, const int*, double, bool&, double*)’:
SPATest.cpp:348:19: warning: ‘NAsigma’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    getroot_K1_fast(g_pos, g_neg, root1, ni1, conv1, 0, n_nonzero,
    ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     mu, g, q, NAmu, NAsigma);
     ~~~~~~~~~~~~~~~~~~~~~~~~
SPATest.cpp:348:19: warning: ‘NAmu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c saige_fitnull.cpp -o saige_fitnull.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c saige_main.cpp -o saige_main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2  -Wall -c vectorization.cpp -o vectorization.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o vectorization.o -lm -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.10-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -lgcc -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-SAIGEgds/00new/SAIGEgds/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SAIGEgds)