boennecd / dynamichazard Goto Github PK

$ uname -a
Linux apsrp07947 3.10.0-1160.2.1.el7.x86_64 #1 SMP Mon Sep 21 21:00:09 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux


$ g++ --version
g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.




> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.0 tools_3.6.0    remotes_2.4.0 

> install.packages("dynamichazard")
Installing package into ‘<MYDIR>/app/R_Library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/dynamichazard_0.6.8.tar.gz'
Content type 'application/x-gzip' length 4447834 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

* installing *source* package ‘dynamichazard’ ...
** package ‘dynamichazard’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/PF_score_n_Hess.cpp -o PF/PF_score_n_Hess.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/PFs.cpp -o PF/PFs.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/covarmat.cpp -o PF/covarmat.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/resamplers.cpp -o PF/resamplers.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/densities.cpp -o PF/densities.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/cond_approx.cpp -o PF/cond_approx.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DUSE_FC_LEN_T -I"<MYDIR>/app/R_Library/Rcpp/include" -I"<MYDIR>/app/R_Library/RcppArmadillo/include" -I/usr/local/include -fopenmp -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  -c PF/dists.cpp -o PF/dists.o
PF/dists.cpp:219:0: warning: ignoring #pragma omp declare [-Wunknown-pragmas]
 #pragma omp declare reduction(armaVP: arma::vec: omp_out += omp_in)
 ^
PF/dists.cpp:220:0: warning: ignoring #pragma omp declare [-Wunknown-pragmas]
 #pragma omp declare reduction(armaMP: arma::mat: omp_out += omp_in)
 ^
PF/dists.cpp: In member function ‘arma::vec observational_cdist<T>::gradient(const vec&) const’:
PF/dists.cpp:292:13: error: expected ‘+’, ‘*’, ‘-’, ‘&’, ‘^’, ‘|’, ‘&&’, ‘||’, ‘min’ or ‘max’ before ‘armaVP’
   reduction(armaVP:result) firstprivate(first_it)
             ^
PF/dists.cpp: In member function ‘arma::mat observational_cdist<T>::neg_Hessian(const vec&) const’:
PF/dists.cpp:330:53: error: expected ‘+’, ‘*’, ‘-’, ‘&’, ‘^’, ‘|’, ‘&&’, ‘||’, ‘min’ or ‘max’ before ‘armaMP’
 #pragma omp parallel for schedule(static) reduction(armaMP:result) \
                                                     ^
make: *** [PF/dists.o] Error 1
ERROR: compilation failed for package ‘dynamichazard’
* removing ‘<MYDIR>/app/R_Library/dynamichazard’
Warning in install.packages :
  installation of package ‘dynamichazard’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmps7OTdz/downloaded_packages’