* installing *source* package ‘mashr’ ...
** package ‘mashr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-13 (GCC) 13.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mashr/src'
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include -fopenmp -I/usr/include -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c RcppExports.cpp -o RcppExports.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include -fopenmp -I/usr/include -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c extreme_deconvolution.cpp -o extreme_deconvolution.o
g++-13 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/RcppArmadillo/include' -I'/data/gannet/ripley/R/test-dev/RcppGSL/include' -I/usr/local/include -fopenmp -I/usr/include -DARMA_64BIT_WORD=1 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -c mash.cpp -o mash.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 -shared -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o mashr.so RcppExports.o extreme_deconvolution.o mash.o -fopenmp -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -lgsl -lgslcblas -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mashr/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/mashr/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/mashr/src'
installing to /data/gannet/ripley/R/packages/tests-devel/mashr.Rcheck/00LOCK-mashr/00new/mashr/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 (mashr)