* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘marked’ ...
** this is package ‘marked’ version ‘1.2.8’
** package ‘marked’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-14 (Debian 14.3.0-10) 14.3.0’
using Fortran compiler: ‘GNU Fortran (Debian 14.3.0-10) 14.3.0’
using C++ compiler: ‘g++-14 (Debian 14.3.0-10) 14.3.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpVh8sMy/R.INSTALL17e624437c23c9/marked/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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bayesCR.cpp -o bayesCR.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjs.f -o cjs.o
cjs.f:9:25:
9 | DOUBLE PRECISION X,Y
| 1
Warning: Unused variable ‘x’ declared at (1) [-Wunused-variable]
cjs.f:9:27:
9 | DOUBLE PRECISION X,Y
| 1
Warning: Unused variable ‘y’ declared at (1) [-Wunused-variable]
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjs1tldmat.f -o cjs1tldmat.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjs1tlgam.f -o cjs1tlgam.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjs2tldmat.f -o cjs2tldmat.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjs2tlgam.f -o cjs2tlgam.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjsdmat.f -o cjsdmat.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c cjsgamma.f -o cjsgamma.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c hmm_like.f -o hmm_like.o
gcc-14 -std=gnu23 -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/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c ms2gamma.f -o ms2gamma.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c msdmat.f -o msdmat.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c msgamma.f -o msgamma.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c mvmsdmat.f -o mvmsdmat.o
mvmsdmat.f:1:55:
1 | SUBROUTINE MVMSP(P,DELTA,N,M,F,T,NP,NOBS,PCOUNTS,INDICES,
| 1
Warning: Unused dummy argument ‘pcounts’ at (1) [-Wunused-dummy-argument]
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c ums2dmat.f -o ums2dmat.o
gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c umsdmat.f -o umsdmat.o
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o marked.so bayesCR.o cjs.o cjs1tldmat.o cjs1tlgam.o cjs2tldmat.o cjs2tlgam.o cjsdmat.o cjsgamma.o hmm_like.o init.o ms2gamma.o msdmat.o msgamma.o mvmsdmat.o ums2dmat.o umsdmat.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpVh8sMy/R.INSTALL17e624437c23c9/marked/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpVh8sMy/R.INSTALL17e624437c23c9/marked/src'
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpVh8sMy/R.INSTALL17e624437c23c9/marked/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-marked/00new/marked/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘marked’
finding HTML links ... done
HMMLikelihood html
Paradise_shelduck html
Phi.mean html
R_HMMLikelihood html
backward_prob html
cjs.accumulate html
cjs.hessian html
cjs.initial html
cjs.lnl html
cjs_admb html
cjs_delta html
cjs_gamma html
cjs_tmb html
coef.crm html
compute_matrices html
compute_real html
convert.link.to.real html
create.dm html
create.dmdf html
create.fixed.matrix html
create.links html
crm html
crm.wrapper html
deriv_inverse.link html
dipper html
dmat_hsmm2hmm html
fix.parameters html
function.wrapper html
global_decode html
hmmDemo html
hsmm2hmm html
initiate_pi html
inverse.link html
js html
js.accumulate html
js.hessian html
js.lnl html
local_decode html
make.design.data html
merge_design.covariates html
mixed.model.admb html
mscjs html
mscjs_tmb html
msld_tmb html
mstrata html
mvms_design_data html
mvms_dmat html
mvmscjs html
mvmscjs_tmb html
omega html
predict.crm html
print.crm html
print.crmlist html
probitCJS html
proc.form html
process.ch html
process.data html
resight.matrix html
sealions html
set.fixed html
set.initial html
set_mvms html
set_scale html
setup.model html
setup.parameters html
setup_admb html
setup_tmb html
simHMM html
skagit html
smsld_tmb html
splitCH html
tagloss html
valid.parameters 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 (marked)