* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘mashr’ ...
** package ‘mashr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpiqB88a/R.INSTALLb4c0042b3ad8a/mashr/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I/usr/include -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I/usr/include -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c extreme_deconvolution.cpp -o extreme_deconvolution.o
extreme_deconvolution.cpp: In function ‘_Z12proj_EM_stepP9datapointiP8gaussianiPbS3_S3_Pdbdbbb._omp_fn.0’:
extreme_deconvolution.cpp:728:47: warning: ‘Rtrans’ may be used uninitialized [-Wmaybe-uninitialized]
728 | gsl_blas_dsymm(CblasLeft, CblasUpper, 1.0, thisgaussian->VV, Rtrans, 0.0, VRT);// Only the upper right part of VV is calculated --> use only that part
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
extreme_deconvolution.cpp:47:14: note: ‘Rtrans’ was declared here
47 | gsl_matrix * Rtrans = NULL;
| ^~~~~~
extreme_deconvolution.cpp:729:47: warning: ‘VRT’ may be used uninitialized [-Wmaybe-uninitialized]
729 | gsl_blas_dgemm(CblasNoTrans, CblasNoTrans, 1.0, thisdata->RR, VRT, 1.0, Tij);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
extreme_deconvolution.cpp:45:14: note: ‘VRT’ was declared here
45 | gsl_matrix * VRT = NULL;
| ^~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppGSL/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -I/usr/include -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c mash.cpp -o mash.o
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o mashr.so RcppExports.o extreme_deconvolution.o mash.o -fopenmp -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -Wl,-O1 -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpiqB88a/R.INSTALLb4c0042b3ad8a/mashr/src'
make[1]: Entering directory '/tmp/RtmpiqB88a/R.INSTALLb4c0042b3ad8a/mashr/src'
make[1]: Leaving directory '/tmp/RtmpiqB88a/R.INSTALLb4c0042b3ad8a/mashr/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-mashr/00new/mashr/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘mashr’
finding HTML links ... done
bovy_wrapper html
calc_lik_matrix html
calc_lik_matrix_common_cov html
calc_lik_vector html
calc_relative_lik_matrix html
compute_alt_loglik_from_matrix_and_pi html
compute_loglik_from_matrix_and_pi html
compute_null_loglik_from_matrix html
compute_posterior_matrices html
compute_posterior_matrices_common_cov_R
html
compute_posterior_matrices_general_R html
compute_posterior_weights html
compute_vloglik_from_matrix_and_pi html
contrast_matrix html
cov_all_zeros html
cov_canonical html
cov_ed html
cov_equal_effects html
cov_first_singleton html
cov_flash html
cov_from_factors html
cov_pca html
cov_simple_het html
cov_udi html
cov_udi_single html
estimate_null_correlation_simple html
expand_cov html
extreme_deconvolution html
get_estimated_pi html
get_log10bf html
get_n_significant_conditions html
get_pairwise_sharing html
get_pairwise_sharing_from_samples html
get_samples html
get_significant_results html
make_names html
mash html
mash_1by1 html
mash_compute_loglik html
mash_compute_posterior_matrices html
mash_compute_vloglik html
mash_estimate_corr_em html
mash_plot_meta html
mash_set_data html
mash_set_data_contrast html
mash_update_data html
optimize_pi html
posterior_cov html
posterior_mean html
posterior_mean_matrix html
scale_cov html
sim_contrast1 html
sim_contrast2 html
simple_sims html
simple_sims2 html
teem_wrapper html
udi_model_matrix html
** 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 (mashr)