* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’ * installing *source* package ‘plantmix’ ... ** this is package ‘plantmix’ version ‘1.0.3’ ** package ‘plantmix’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src' g++-16 -std=gnu++20 -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/TMB/include' -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/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init_dummy_file.cpp -o init_dummy_file.o (cd TMB; /home/hornik/tmp/R.check/r-patched-gcc/Work/build/bin/Rscript \ --no-save --no-restore compile.R '') Note: Using Makevars in /home/hornik/.R/Makevars-gcc using C++ compiler: ‘g++-16 (Debian 16.2.0-1) 16.2.0’ make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src/TMB' g++-16 -std=gnu++20 -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/TMB/include" -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_plantmix_TMBExports -DCPPAD_FRAMEWORK -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include' -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/RcppEigen/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c plantmix_TMBExports.cpp -o plantmix_TMBExports.o In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/ad_fun.hpp:602, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/cppad.hpp:86, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/TMB.hpp:125, from plantmix_TMBExports.cpp:4: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/optimize.hpp: In function ‘CppAD::addr_t CppAD::optimize::binary_match(const CppAD::vector&, size_t, size_t, const Base*, const CppAD::vector&, short unsigned int&) [with Base = CppAD::AD]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/optimize.hpp:782:25: warning: ‘new_arg’ may be used uninitialized [-Wmaybe-uninitialized] 782 | code = hash_code( | ~~~~~~~~~^ 783 | op , | ~~~~~~~~~~~~~~~~~~~~~ 784 | new_arg , | ~~~~~~~~~~~~~~~~~~~~~ 785 | npar , | ~~~~~~~~~~~~~~~~~~~~~ 786 | par | ~~~ 787 | ); | ~ In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/recorder.hpp:14, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/ad.hpp:22, from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/cppad.hpp:78: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/hash_code.hpp:125:16: note: by argument 2 of type ‘const CppAD::addr_t*’ {aka ‘const unsigned int*’} to ‘short unsigned int CppAD::hash_code(OpCode, const addr_t*, size_t, const Base*) [with Base = AD]’ declared here 125 | unsigned short hash_code( | ^~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/optimize.hpp:715:23: note: ‘new_arg’ declared here 715 | addr_t new_arg[2]; | ^~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/optimize.hpp: In function ‘CppAD::addr_t CppAD::optimize::binary_match(const CppAD::vector&, size_t, size_t, const Base*, const CppAD::vector&, short unsigned int&) [with Base = double]’: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/optimize.hpp:782:25: warning: ‘new_arg’ may be used uninitialized [-Wmaybe-uninitialized] 782 | code = hash_code( | ~~~~~~~~~^ 783 | op , | ~~~~~~~~~~~~~~~~~~~~~ 784 | new_arg , | ~~~~~~~~~~~~~~~~~~~~~ 785 | npar , | ~~~~~~~~~~~~~~~~~~~~~ 786 | par | ~~~ 787 | ); | ~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/hash_code.hpp:125:16: note: by argument 2 of type ‘const CppAD::addr_t*’ {aka ‘const unsigned int*’} to ‘short unsigned int CppAD::hash_code(OpCode, const addr_t*, size_t, const Base*) [with Base = double]’ declared here 125 | unsigned short hash_code( | ^~~~~~~~~ /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/TMB/include/cppad/local/optimize.hpp:715:23: note: ‘new_arg’ declared here 715 | addr_t new_arg[2]; | ^~~~~~~ g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o plantmix_TMBExports.so plantmix_TMBExports.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src/TMB' make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src/TMB' make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src/TMB' [1] TRUE g++-16 -std=gnu++20 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o plantmix.so init_dummy_file.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src' make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src' make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpScY442/R.INSTALL3625cf476f7c22/plantmix/src' installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-plantmix/00new/plantmix/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘plantmix’ finding HTML links ... done CC html LER html RII html RIInet html RY html RYM html RYP html RYT html aaa-plantmix-package html estimGRM html estimRYMRep html estimRYRep html fitDBVSBVinter html fitGMASMA html getDesignBinaryCropMix html getDesignBinaryVarMix html getMixtureList html getMixturesPerGeno html imageMat html infoCriterion html invvec html invvecMixes html mixSowingWeight html mkAllZSMA html mkZGMA html mkZSMA html mkZinterspe html nbSeedsToSownInPure html normBiasError html paramBoot4TMB html pivotMixData2Long html pivotMixData2Wide html plotDesignCropMix html plotDesignVarMix html plotDiallel html rmatnorm html simulDBVSBVinter html simulGenosDoseStruct html summarizeGMASMAs html vec 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 (plantmix)