* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘pda’ ...
** this is package ‘pda’ version ‘1.2.8’
** package ‘pda’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.3.0-8) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgnT0tD/R.INSTALL3b19937708e9da/pda/src'
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o
g++-14 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_coxph.cpp -o rcpp_coxph.o
In file included from rcpp_coxph.cpp:22:
rcpp_coxph.h: In member function ‘arma::vec Intsurv::RcppCoxph::gradient_efron_dist(const arma::vec&, const arma::vec&, bool&, int) const’:
rcpp_coxph.h:368:40: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = unsigned int; T1 = arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<double>, arma::op_rel_eq>, arma::op_find>; out_eT = int; typename arma::arma_not_cx<in_eT>::result = unsigned int]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
368 | jk = arma::conv_to<int>::from(arma::find( uni_timek == uni_time(j), 1));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo:496,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:32,
from rcpp_coxph.cpp:18:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
| ^~~~~~~~~~~~~~~
rcpp_coxph.h:377:44: warning: ‘static out_eT arma::conv_to<out_eT>::from(const arma::Base<eT2, expr>&, const typename arma::arma_not_cx<in_eT>::result*) [with in_eT = unsigned int; T1 = arma::mtOp<unsigned int, arma::mtOp<unsigned int, arma::Col<double>, arma::op_rel_eq>, arma::op_find>; out_eT = int; typename arma::arma_not_cx<in_eT>::result = unsigned int]’ is deprecated: replace conv_to<...>::from(X) with as_scalar(X) [-Wdeprecated-declarations]
377 | j0 = arma::conv_to<int>::from(arma::find(uni_time0==uni_time(j), 1));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/current/armadillo_bits/fn_conv_to.hpp:72:1: note: declared here
72 | conv_to<out_eT>::from(const Base<in_eT, T1>& in, const typename arma_not_cx<in_eT>::result* junk)
| ^~~~~~~~~~~~~~~
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o pda.so RcppExports.o rcpp_coxph.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgnT0tD/R.INSTALL3b19937708e9da/pda/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpgnT0tD/R.INSTALL3b19937708e9da/pda/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpgnT0tD/R.INSTALL3b19937708e9da/pda/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-pda/00new/pda/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘pda’
finding HTML links ... done
ADAP.derive html
ADAP.estimate html
ADAP.initialize html
ADAP_data html
DLM.estimate html
DLM.initialize html
DPQL.derive html
DPQL.estimate html
DPQL.initialize html
LOS html
ODAC.derive html
ODAC.deriveUWZ html
ODAC.estimate html
ODAC.initialize html
ODAC.synthesize html
ODACAT.derive html
ODACAT.estimate html
ODACAT.initialize html
ODACAT.synthesize html
ODACATH.derive html
ODACATH.estimate html
ODACATH.initialize html
ODACATH.synthesize html
ODACAT_nominal html
ODACAT_ordinal html
ODAH.derive html
ODAH.estimate html
ODAH.initialize html
ODAL.derive html
ODAL.estimate html
ODAL.initialize html
ODAL.synthesize html
ODAP.derive html
ODAP.estimate html
ODAP.initialize html
ODAPB.derive html
ODAPB.estimate html
ODAPB.initialize html
covid html
cs html
dGEM.derive html
dGEM.estimate html
dGEM.initialize html
dGEM.synthesize html
getCloudConfig html
lung2 html
myglmmPQL html
pda html
pdaGet html
pdaList html
pdaPut html
pdaSync html
** 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 (pda)