* 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/Rtmpbu34Mq/R.INSTALL170d80439206b9/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/Rtmpbu34Mq/R.INSTALL170d80439206b9/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<struct_old_variable>&, size_t, size_t, const Base*, const CppAD::vector<long unsigned int>&, short unsigned int&) [with Base = CppAD::AD<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 | );
| ~
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<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];
| ^~~~~~~
/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<struct_old_variable>&, size_t, size_t, const Base*, const CppAD::vector<long unsigned int>&, 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/Rtmpbu34Mq/R.INSTALL170d80439206b9/plantmix/src/TMB'
make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmpbu34Mq/R.INSTALL170d80439206b9/plantmix/src/TMB'
make[2]: Leaving directory '/home/hornik/tmp/scratch/Rtmpbu34Mq/R.INSTALL170d80439206b9/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/Rtmpbu34Mq/R.INSTALL170d80439206b9/plantmix/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpbu34Mq/R.INSTALL170d80439206b9/plantmix/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpbu34Mq/R.INSTALL170d80439206b9/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)