downloading reverse dependencies ‘BayesChange’, ‘catSurv’, ‘CLVTools’, ‘coga’, ‘econetwork’, ‘fingerPro’, ‘flan’, ‘frailtyMMpen’, ‘jSDM’, ‘libstable4u’, ‘markets’, ‘mashr’, ‘minimaxALT’, ‘mixture’, ‘mmpca’, ‘mvabund’, ‘PEPBVS’, ‘QF’, ‘rcontroll’, ‘RcppDPR’, ‘RcppZiggurat’, ‘Rsubbotools’, ‘shrinkTVP’, ‘smam’, ‘stpphawkes’, ‘vol2birdR’, ‘dynr’ trying URL 'file:///data/Repositories/CRAN/src/contrib/BayesChange_2.2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/catSurv_1.6.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/CLVTools_0.12.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/coga_1.2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/econetwork_0.7.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/fingerPro_2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/flan_1.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/frailtyMMpen_1.2.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/jSDM_0.2.7.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/libstable4u_1.0.5.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/markets_1.1.7.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mashr_0.2.79.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/minimaxALT_1.0.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mixture_2.2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mmpca_2.0.4.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/mvabund_4.2.8.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/PEPBVS_2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/QF_0.0.9.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/rcontroll_0.1.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/RcppDPR_0.1.10.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/RcppZiggurat_0.1.8.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/Rsubbotools_0.0.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/shrinkTVP_3.1.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/smam_0.7.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/stpphawkes_0.2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/vol2birdR_1.2.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/dynr_0.1.16-114.tar.gz' installing dependencies ‘BAS’, ‘BayesVarSel’, ‘boral’, ‘catIrt’, ‘catR’, ‘ebnm’, ‘ecostats’, ‘flashier’, ‘Hmsc’, ‘RcppGSL’, ‘RcppParallel’, ‘rdiversity’, ‘REBayes’, ‘salso’ also installing the dependencies ‘fishMod’, ‘deconvolveR’, ‘mvabund’, ‘ecoCopula’ begin installing package ‘fishMod’ begin installing package ‘deconvolveR’ begin installing package ‘salso’ begin installing package ‘catIrt’ begin installing package ‘catR’ begin installing package ‘rdiversity’ begin installing package ‘Hmsc’ begin installing package ‘REBayes’ begin installing package ‘BAS’ begin installing package ‘BayesVarSel’ begin installing package ‘RcppGSL’ begin installing package ‘RcppParallel’ * installing *source* package ‘deconvolveR’ ... ** this is package ‘deconvolveR’ version ‘1.2-1’ ** package ‘deconvolveR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (deconvolveR) begin installing package ‘ebnm’ * installing *source* package ‘fishMod’ ... ** this is package ‘fishMod’ version ‘0.29.2’ ** package ‘fishMod’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpGfim3X/R.INSTALL238dba6470b893/fishMod/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Tweedie.cc -o Tweedie.o Tweedie.cc: In function ‘SEXPREC* dTweedie(SEXP, SEXP, SEXP, SEXP, SEXP)’: Tweedie.cc:25:21: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 25 | for( size_t i=0; i&, double*, int, int, double, double, const std::vector&, double, double)’: TweedieDeriv.cc:104:31: warning: unused variable ‘logW’ [-Wunused-variable] 104 | double Beta0, z1, z2, logW; //names are pretty obvious from supporting documentation | ^~~~ TweedieDeriv.cc: In function ‘void findWDeriv(double, double, double, double, double, double, double, std::vector&, std::vector&, std::vector&)’: TweedieDeriv.cc:162:10: warning: unused variable ‘res’ [-Wunused-variable] 162 | double res; | ^~~ g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o fishMod.so Tweedie.o TweedieDeriv.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpGfim3X/R.INSTALL238dba6470b893/fishMod/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-fishMod/00new/fishMod/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (fishMod) begin installing package ‘boral’ * installing *source* package ‘catIrt’ ... ** this is package ‘catIrt’ version ‘0.5.1’ ** package ‘catIrt’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpqed5Ib/R.INSTALL238dbb21bc15d1/catIrt/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c brm.c -o brm.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c catIrt_init.c -o catIrt_init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c grm.c -o grm.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c sim.c -o sim.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o catIrt.so brm.o catIrt_init.o grm.o sim.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpqed5Ib/R.INSTALL238dbb21bc15d1/catIrt/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-catIrt/00new/catIrt/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (catIrt) * installing *source* package ‘rdiversity’ ... ** this is package ‘rdiversity’ version ‘2.2.0’ ** package ‘rdiversity’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (rdiversity) * installing *source* package ‘catR’ ... ** this is package ‘catR’ version ‘3.17’ ** package ‘catR’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (catR) * installing *source* package ‘REBayes’ ... ** this is package ‘REBayes’ version ‘2.60’ ** package ‘REBayes’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** demo ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (REBayes) * installing *source* package ‘RcppGSL’ ... ** this is package ‘RcppGSL’ version ‘0.3.14’ ** using staged installation checking for gsl-config... /usr/bin/gsl-config configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9JnOHs/R.INSTALL238dcd49384cec/RcppGSL/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/include -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/include -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastLm.cpp -o fastLm.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/include -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c setErrorHandler.cpp -o setErrorHandler.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RcppGSL.so RcppExports.o fastLm.o setErrorHandler.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9JnOHs/R.INSTALL238dcd49384cec/RcppGSL/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RcppGSL/00new/RcppGSL/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 (RcppGSL) begin installing package ‘mvabund’ * installing *source* package ‘BAS’ ... ** this is package ‘BAS’ version ‘2.0.2’ ** package ‘BAS’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-13) 15.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpKquJQc/R.INSTALL238dc823cf9d9c/BAS/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c E_ZS.c -o E_ZS.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c MH-funs.c -o MH-funs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ZS_approx_full_np.c -o ZS_approx_full_np.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ZS_approx_null_np.c -o ZS_approx_null_np.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c amcmc-funs.c -o amcmc-funs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bayesglm.c -o bayesglm.o bayesglm.c: In function ‘glm_fit’: bayesglm.c:62:17: warning: variable ‘betapriorfamily’ set but not used [-Wunused-but-set-variable] 62 | betapriorptr *betapriorfamily; | ^~~~~~~~~~~~~~~ bayesglm.c:178:17: warning: ‘disp’ may be used uninitialized [-Wmaybe-uninitialized] 178 | se[j] = sqrt(se[j]*disp); | ^~~~~~~~~~~~~~~~ bayesglm.c:54:10: note: ‘disp’ was declared here 54 | double disp; | ^~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bayesreg.c -o bayesreg.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c betapriorfamily.c -o betapriorfamily.o betapriorfamily.c: In function ‘intrinsic_glm_shrinkage’: betapriorfamily.c:239:38: warning: unused variable ‘u’ [-Wunused-variable] 239 | double a, b, s, r, v, theta, n, p, u, shrinkage; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cch.c -o cch.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c dch1up.f -o dch1up.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c family.c -o family.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_deterministic.c -o glm_deterministic.o glm_deterministic.c: In function ‘glm_deterministic’: glm_deterministic.c:67:35: warning: unused variable ‘logmargy’ [-Wunused-variable] 67 | double *probs,shrinkage_m,logmargy; | ^~~~~~~~ glm_deterministic.c:67:23: warning: unused variable ‘shrinkage_m’ [-Wunused-variable] 67 | double *probs,shrinkage_m,logmargy; | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_fit.c -o glm_fit.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_mcmc.c -o glm_mcmc.o glm_mcmc.c: In function ‘glm_mcmc’: glm_mcmc.c:17:39: warning: variable ‘shrinkage_m’ set but not used [-Wunused-but-set-variable] 17 | double *probs, MH=0.0, prior_m=1.0, shrinkage_m, logmargy, postold, postnew; | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_mcmc_grow.c -o glm_mcmc_grow.o glm_mcmc_grow.c: In function ‘glm_mcmc_grow’: glm_mcmc_grow.c:117:45: warning: variable ‘shrinkage_m’ set but not used [-Wunused-but-set-variable] 117 | double *probs, MH=0.0, prior_m=1.0, shrinkage_m, logmarg_m, postold, postnew; | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_mcmcbas.c -o glm_mcmcbas.o glm_mcmcbas.c: In function ‘glm_mcmcbas’: glm_mcmcbas.c:54:44: warning: variable ‘shrinkage_m’ set but not used [-Wunused-but-set-variable] 54 | double *probs, MH=0.0, prior_m=1.0,shrinkage_m, logmargy, postold, postnew; | ^~~~~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_sampleworep.c -o glm_sampleworep.o glm_sampleworep.c: In function ‘glm_sampleworep’: glm_sampleworep.c:121:33: warning: variable ‘shrinkage_m’ set but not used [-Wunused-but-set-variable] 121 | double *probs,logmargy, shrinkage_m; | ^~~~~~~~~~~ glm_sampleworep.c:121:23: warning: variable ‘logmargy’ set but not used [-Wunused-but-set-variable] 121 | double *probs,logmargy, shrinkage_m; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c glm_sampleworep_grow.c -o glm_sampleworep_grow.o glm_sampleworep_grow.c: In function ‘glm_sampleworep_grow’: glm_sampleworep_grow.c:101:33: warning: variable ‘shrinkage_m’ set but not used [-Wunused-but-set-variable] 101 | double *probs,logmargy, shrinkage_m; | ^~~~~~~~~~~ glm_sampleworep_grow.c:101:23: warning: variable ‘logmargy’ set but not used [-Wunused-but-set-variable] 101 | double *probs,logmargy, shrinkage_m; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hg_approx_null_np.c -o hg_approx_null_np.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hyp1F1.c -o hyp1F1.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hyp2f1.c -o hyp2f1.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hypergeometric1F1.c -o hypergeometric1F1.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hypergeometric2F1.c -o hypergeometric2F1.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_amcmc.c -o lm_amcmc.o lm_amcmc.c: In function ‘amcmc’: lm_amcmc.c:348:35: warning: ‘new_loc’ may be used uninitialized [-Wmaybe-uninitialized] 348 | INTEGER(Rcounts)[old_loc] += 1; | ~~~~~~~~~~~~~~~~^~~~~~~~~ lm_amcmc.c:251:13: note: ‘new_loc’ was declared here 251 | int new_loc; | ^~~~~~~ lm_amcmc.c:445:34: warning: ‘postold’ may be used uninitialized [-Wmaybe-uninitialized] 445 | if (!IS) MH = exp(postnew - postold + log(pigammaold) - log(pigammanew)); | ~~~~~~~~^~~~~~~~~ lm_amcmc.c:135:47: note: ‘postold’ was declared here 135 | R2_m, RSquareFull, logmarg_m, postold, postnew; | ^~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_amcmc_growable.c -o lm_amcmc_growable.o lm_amcmc_growable.c: In function ‘amcmc_grow’: lm_amcmc_growable.c:331:35: warning: ‘new_loc’ may be used uninitialized [-Wmaybe-uninitialized] 331 | INTEGER(Rcounts)[old_loc] += 1; | ~~~~~~~~~~~~~~~~^~~~~~~~~ lm_amcmc_growable.c:234:13: note: ‘new_loc’ was declared here 234 | int new_loc; | ^~~~~~~ lm_amcmc_growable.c:474:34: warning: ‘postold’ may be used uninitialized [-Wmaybe-uninitialized] 474 | if (!IS) MH = exp(postnew - postold + log(pigammaold) - log(pigammanew)); | ~~~~~~~~^~~~~~~~~ lm_amcmc_growable.c:120:47: note: ‘postold’ was declared here 120 | R2_m, RSquareFull, logmarg_m, postold, postnew; | ^~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_deterministic.c -o lm_deterministic.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_mcmc.c -o lm_mcmc.o lm_mcmc.c: In function ‘mcmc’: lm_mcmc.c:137:13: warning: unused variable ‘k’ [-Wunused-variable] 137 | int k = LENGTH(modelprobs); | ^ lm_mcmc.c:312:35: warning: ‘new_loc’ may be used uninitialized [-Wmaybe-uninitialized] 312 | INTEGER(Rcounts)[old_loc] += 1; | ~~~~~~~~~~~~~~~~^~~~~~~~~ lm_mcmc.c:216:13: note: ‘new_loc’ was declared here 216 | int new_loc; | ^~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_mcmc_grow.c -o lm_mcmc_grow.o lm_mcmc_grow.c: In function ‘mcmc_grow’: lm_mcmc_grow.c:306:35: warning: ‘new_loc’ may be used uninitialized [-Wmaybe-uninitialized] 306 | INTEGER(Rcounts)[old_loc] += 1; | ~~~~~~~~~~~~~~~~^~~~~~~~~ lm_mcmc_grow.c:211:13: note: ‘new_loc’ was declared here 211 | int new_loc; | ^~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_mcmcbas.c -o lm_mcmcbas.o lm_mcmcbas.c: In function ‘mcmcbas’: lm_mcmcbas.c:297:22: warning: ‘new_loc’ may be used uninitialized [-Wmaybe-uninitialized] 297 | INTEGER(counts)[old_loc] += 1; | ~~~~~~~~~~~~~~~^~~~~~~~~ lm_mcmcbas.c:194:9: note: ‘new_loc’ was declared here 194 | int new_loc; | ^~~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_sampleworep-grow.c -o lm_sampleworep-grow.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c lm_sampleworep.c -o lm_sampleworep.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mem.c -o mem.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c model_probabilities.c -o model_probabilities.o model_probabilities.c: In function ‘compute_margprobs_Bayes_BAS_MCMC’: model_probabilities.c:129:17: warning: unused variable ‘probNotInS’ [-Wunused-variable] 129 | double *beta, probNotInS = 1.0; | ^~~~~~~~~~ In file included from bas.h:23, from model_probabilities.c:6: /home/hornik/tmp/R-d-gcc-15/include/Rmath.h:221:25: warning: unused variable ‘Rf_beta’ [-Wunused-variable] 221 | #define beta Rf_beta | ^~~~~~~ model_probabilities.c:129:11: note: in expansion of macro ‘beta’ 129 | double *beta, probNotInS = 1.0; | ^~~~ model_probabilities.c:127:22: warning: unused variable ‘n’ [-Wunused-variable] 127 | int m, j, *model, *n; | ^ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mtherr.c -o mtherr.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c resizeVectors.c -o resizeVectors.o resizeVectors.c: In function ‘resizeVector’: resizeVectors.c:78:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 78 | for (i = 0; i < len_new; i++) | ^~~ resizeVectors.c:86:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 86 | break; | ^~~~~ resizeVectors.c:88:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 88 | for (i = 0; i < len_new; i++) | ^~~ resizeVectors.c:94:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 94 | break; | ^~~~~ resizeVectors.c:102:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 102 | for (i = 0; i < len_new; i++) | ^~~ resizeVectors.c:106:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 106 | break; | ^~~~~ resizeVectors.c:108:3: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 108 | for (i = 0; i < len_new; i++) | ^~~ resizeVectors.c:114:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 114 | break; | ^~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c tree_structures.c -o tree_structures.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o BAS.so E_ZS.o MH-funs.o ZS_approx_full_np.o ZS_approx_null_np.o amcmc-funs.o bayesglm.o bayesreg.o betapriorfamily.o cch.o dch1up.o family.o glm_deterministic.o glm_fit.o glm_mcmc.o glm_mcmc_grow.o glm_mcmcbas.o glm_sampleworep.o glm_sampleworep_grow.o hg_approx_null_np.o hyp1F1.o hyp2f1.o hypergeometric1F1.o hypergeometric2F1.o init.o lm_amcmc.o lm_amcmc_growable.o lm_deterministic.o lm_mcmc.o lm_mcmc_grow.o lm_mcmcbas.o lm_sampleworep-grow.o lm_sampleworep.o mem.o model_probabilities.o mtherr.o resizeVectors.o tree_structures.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpKquJQc/R.INSTALL238dc823cf9d9c/BAS/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BAS/00new/BAS/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (BAS) * installing *source* package ‘boral’ ... ** this is package ‘boral’ version ‘2.0.3’ ** package ‘boral’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (boral) * installing *source* package ‘ebnm’ ... ** this is package ‘ebnm’ version ‘1.1-42’ ** package ‘ebnm’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ebnm) begin installing package ‘flashier’ * installing *source* package ‘BayesVarSel’ ... ** this is package ‘BayesVarSel’ version ‘2.4.5’ ** package ‘BayesVarSel’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpMxW4eg/R.INSTALL238dce1db76b6/BayesVarSel/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BayesVarSel_init.c -o BayesVarSel_init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Gibbsauxiliaryfuncs.c -o Gibbsauxiliaryfuncs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c allBF.c -o allBF.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c auxiliaryfuncs.c -o auxiliaryfuncs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c main.c -o main.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mainGibbs.c -o mainGibbs.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mainGibbsF.c -o mainGibbsF.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mainSingle.c -o mainSingle.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c priorprob.c -o priorprob.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o BayesVarSel.so BayesVarSel_init.o Gibbsauxiliaryfuncs.o allBF.o auxiliaryfuncs.o main.o mainGibbs.o mainGibbsF.o mainSingle.o priorprob.o -L/usr/local/lib -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpMxW4eg/R.INSTALL238dce1db76b6/BayesVarSel/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BayesVarSel/00new/BayesVarSel/libs ** R ** data *** moving datasets to lazyload DB ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (BayesVarSel) * installing *source* package ‘Hmsc’ ... ** this is package ‘Hmsc’ version ‘3.3-7’ ** package ‘Hmsc’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Hmsc) * installing *source* package ‘flashier’ ... ** this is package ‘flashier’ version ‘1.0.7’ ** package ‘flashier’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flashier) * installing *source* package ‘RcppParallel’ ... ** this is package ‘RcppParallel’ version ‘5.1.11-2’ ** package ‘RcppParallel’ successfully unpacked and MD5 sums checked ** using staged installation ** preparing to configure package 'RcppParallel' ... 'config' variable 'CXX11' is defunct *** configured file: 'R/tbb-autodetected.R.in' => 'R/tbb-autodetected.R' *** configured file: 'src/Makevars.in' => 'src/Makevars' *** configured file: 'src/install.libs.R.in' => 'src/install.libs.R' ** finished configure for package 'RcppParallel' ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT3bg8P/R.INSTALL238dd4ab02a46/RcppParallel/src' (tbb) Building TBB using bundled sources ... make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpT3bg8P/R.INSTALL238dd4ab02a46/RcppParallel/src/tbb/src' OS: linux arch=intel64 compiler=gcc runtime=cc15.2.0_libc2.42_kernel6.18.12+deb14 tbb_build_prefix=linux_intel64_gcc_cc15.2.0_libc2.42_kernel6.18.12+deb14 work_dir=/home/hornik/tmp/scratch/RtmpT3bg8P/R.INSTALL238dd4ab02a46/RcppParallel/src/build/linux_intel64_gcc_cc15.2.0_libc2.42_kernel6.18.12+deb14_release make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpT3bg8P/R.INSTALL238dd4ab02a46/RcppParallel/src/tbb/src' (tbb) TBB compilation finished successfully. g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++0x -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c init.cpp -o init.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++0x -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c options.cpp -o options.o In file included from ../inst/include/tbb/internal/_concurrent_unordered_impl.h:37, from ../inst/include/tbb/concurrent_unordered_set.h:23, from ../inst/include/RcppParallel/TBB.h:11, from ../inst/include/RcppParallel.h:24, from options.cpp:2: ../inst/include/tbb/internal/../atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: ../inst/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ ../inst/include/tbb/internal/../atomic.h:551:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 551 | return (atomic&)t; | ^~~~~~~~~~~~~ ../inst/include/tbb/internal/../atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: ../inst/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ../inst/include/tbb/internal/../atomic.h:551:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 551 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -std=c++0x -DRCPP_PARALLEL_USE_TBB=1 -DTBB_SUPPRESS_DEPRECATED_MESSAGES=1 -fpic -g -O2 -Wall -pedantic -mtune=native -c tbb.cpp -o tbb.o In file included from ../inst/include/tbb/internal/_concurrent_unordered_impl.h:37, from ../inst/include/tbb/concurrent_unordered_set.h:23, from ../inst/include/RcppParallel/TBB.h:11, from tbb.cpp:5: ../inst/include/tbb/internal/../atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]’: ../inst/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ ../inst/include/tbb/internal/../atomic.h:551:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(long unsigned int)’ [-Wcast-user-defined] 551 | return (atomic&)t; | ^~~~~~~~~~~~~ ../inst/include/tbb/internal/../atomic.h: In instantiation of ‘tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’: ../inst/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ../inst/include/tbb/internal/../atomic.h:551:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic&’ does not use ‘constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined] 551 | return (atomic&)t; | ^~~~~~~~~~~~~ g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RcppParallel.so init.o options.o tbb.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT3bg8P/R.INSTALL238dd4ab02a46/RcppParallel/src' installing via 'install.libs.R' to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RcppParallel/00new/RcppParallel ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (RcppParallel) * installing *source* package ‘mvabund’ ... ** this is package ‘mvabund’ version ‘4.2.8’ ** package ‘mvabund’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyoGiNR/R.INSTALL2395e816457cb8/mvabund/src' g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rinterface.cpp -o Rinterface.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c anova.cpp -o anova.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calctest.cpp -o calctest.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glm.cpp -o glm.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glmtest.cpp -o glmtest.o glmtest.cpp: In member function ‘int GlmTest::resampNonCase(glm*, gsl_matrix*, unsigned int)’: glmtest.cpp:849:23: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 849 | gsl_sort_index(permid, tmp, 1, nRows); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from resampTest.h:26, from glmtest.cpp:5: /usr/include/gsl/gsl_sort_double.h:41:6: note: by argument 2 of type ‘const double*’ to ‘void gsl_sort_index(size_t*, const double*, size_t, size_t)’ declared here 41 | void gsl_sort_index (size_t * p, const double * data, const size_t stride, const size_t n); | ^~~~~~~~~~~~~~ glmtest.cpp:876:23: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 876 | gsl_sort_index(permid, tmp, 1, nRows); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/gsl/gsl_sort_double.h:41:6: note: by argument 2 of type ‘const double*’ to ‘void gsl_sort_index(size_t*, const double*, size_t, size_t)’ declared here 41 | void gsl_sort_index (size_t * p, const double * data, const size_t stride, const size_t n); | ^~~~~~~~~~~~~~ g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c io.cpp -o io.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rnd.cpp -o rnd.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simutility.cpp -o simutility.o g++-15 -std=gnu++20 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I. -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/tmp/CRAN_recheck/Library/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c summary.cpp -o summary.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o mvabund.so RcppExports.o Rinterface.o anova.o calctest.o glm.o glmtest.o io.o rnd.o simutility.o summary.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyoGiNR/R.INSTALL2395e816457cb8/mvabund/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mvabund/00new/mvabund/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (mvabund) begin installing package ‘ecoCopula’ * installing *source* package ‘ecoCopula’ ... ** this is package ‘ecoCopula’ version ‘1.0.6’ ** package ‘ecoCopula’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ecoCopula) begin installing package ‘ecostats’ * installing *source* package ‘ecostats’ ... ** this is package ‘ecostats’ version ‘1.2.2’ ** package ‘ecostats’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ecostats) * installing *source* package ‘salso’ ... ** this is package ‘salso’ version ‘0.3.57’ ** package ‘salso’ successfully unpacked and MD5 sums checked ** using staged installation Timestamp: 2026-03-05 14:54:06 UTC SystemRequirements: Cargo (Rust's package manager), rustc (>= 1.80.1) Minimum Supported Rust Version (MSRV): 1.80.1 Trying to run: cargo --version 'cargo --version' reports: cargo 1.91.1 (ea2d97820 2025-10-10) (built from a source tarball) Found cargo version: 1.91.1 Trying to run: rustc --version 'rustc --version' reports: rustc 1.91.1 (ed61e7d7e 2025-11-07) (built from a source tarball) Found rustc version: 1.91.1 MSRV is met. Found a suitable installation of cargo and rustc. Compiling autocfg v1.5.0 Compiling crossbeam-utils v0.8.21 Compiling libc v0.2.175 Compiling num-traits v0.2.19 Compiling getrandom v0.3.3 Compiling cfg-if v1.0.3 Compiling zerocopy v0.8.26 Compiling proc-macro2 v1.0.101 Compiling rand_core v0.9.3 Compiling crossbeam-epoch v0.9.18 Compiling unicode-ident v1.0.18 Compiling crossbeam-deque v0.8.6 Compiling num-integer v0.1.46 Compiling ppv-lite86 v0.2.21 Compiling matrixmultiply v0.3.10 Compiling quote v1.0.40 Compiling rand_chacha v0.9.0 Compiling rawpointer v0.2.1 Compiling rayon-core v1.13.0 Compiling rand v0.9.2 Compiling syn v2.0.106 Compiling num-complex v0.4.6 Compiling crossbeam-queue v0.3.12 Compiling crossbeam-channel v0.5.15 Compiling crossbeam v0.8.4 Compiling ndarray v0.16.1 Compiling roxido_macro v0.6.0 (/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src/rust/roxido_macro) Compiling dahl-partition v0.5.3 (https://github.com/dbdahl/rust-dahl-partition.git?rev=f3a39e1#f3a39e12) Compiling num-bigint v0.4.6 Compiling rand_pcg v0.9.0 Compiling approx v0.5.1 Compiling approx v0.4.0 Compiling num_cpus v1.17.0 Compiling either v1.15.0 Compiling rbindings v0.6.0 (/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src/rust/rbindings) Compiling rust v0.1.0 (/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src/rust) Compiling roxido v0.6.0 (/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src/rust/roxido) Compiling dahl-bellnumber v0.1.1 Compiling rayon v1.11.0 Compiling dahl-salso v0.6.6 (https://github.com/dbdahl/rust-dahl-salso.git?rev=f019a94#f019a946) Finished `release` profile [optimized + debuginfo] target(s) in 39.61s Compiling rust v0.1.0 (/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src/rust) Finished `release` profile [optimized + debuginfo] target(s) in 17.06s Built Rust static library. Deleting temporary CARGO_HOME directory. ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-13) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c shim.c -o shim.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o salso.so shim.o -L. -lrust -L/home/hornik/tmp/R-d-gcc-15/lib -lR rm librust.a make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpOMQDcL/R.INSTALL238db6756ebd97/salso/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-salso/00new/salso/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** 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 (salso) checking RcppGSL_0.3.14.tar.gz ... checking BayesChange_2.2.0.tar.gz ... checking catSurv_1.6.0.tar.gz ... checking CLVTools_0.12.1.tar.gz ... checking coga_1.2.2.tar.gz ... checking econetwork_0.7.0.tar.gz ... checking fingerPro_2.0.tar.gz ... checking flan_1.0.tar.gz ... checking frailtyMMpen_1.2.1.tar.gz ... checking jSDM_0.2.7.tar.gz ... checking libstable4u_1.0.5.tar.gz ... checking markets_1.1.7.tar.gz ... checking mashr_0.2.79.tar.gz ... checking minimaxALT_1.0.3.tar.gz ... checking mixture_2.2.0.tar.gz ... checking mmpca_2.0.4.tar.gz ... checking mvabund_4.2.8.tar.gz ... checking PEPBVS_2.2.tar.gz ... checking QF_0.0.9.tar.gz ... checking rcontroll_0.1.2.tar.gz ... checking RcppDPR_0.1.10.tar.gz ... checking RcppZiggurat_0.1.8.tar.gz ... checking Rsubbotools_0.0.1.tar.gz ... checking shrinkTVP_3.1.1.tar.gz ... checking smam_0.7.2.tar.gz ... checking stpphawkes_0.2.2.tar.gz ... checking vol2birdR_1.2.1.tar.gz ... checking dynr_0.1.16-114.tar.gz ... Depends: Package: RcppGSL Imports: Rcpp (>= 1.1.1), stats LinkingTo: Rcpp Timings: user system elapsed RcppGSL 41.69 6.019 104.645 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 1 26 Check results summary: RcppGSL ... OK rdepends_BayesChange ... OK rdepends_catSurv ... OK rdepends_CLVTools ... OK rdepends_coga ... OK rdepends_dynr ... OK rdepends_econetwork ... OK rdepends_fingerPro ... OK rdepends_flan ... OK rdepends_frailtyMMpen ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_jSDM ... OK rdepends_libstable4u ... OK rdepends_markets ... OK rdepends_mashr ... OK rdepends_minimaxALT ... OK rdepends_mixture ... OK rdepends_mmpca ... OK rdepends_mvabund ... OK rdepends_PEPBVS ... OK rdepends_QF ... OK rdepends_rcontroll ... OK rdepends_RcppDPR ... OK rdepends_RcppZiggurat ... OK rdepends_Rsubbotools ... OK rdepends_shrinkTVP ... OK rdepends_smam ... OK rdepends_stpphawkes ... OK rdepends_vol2birdR ... OK Check results changes: Package: mvabund Check: CRAN incoming feasibility Old result: NOTE