* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘marked’ ...
** package ‘marked’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpBrTppv/R.INSTALL1970ec198e914c/marked/src'
g++-13 -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-13 -fpic -g -O2 -Wall -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-13 -fpic -g -O2 -Wall -mtune=native -c cjs1tldmat.f -o cjs1tldmat.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs1tlgam.f -o cjs1tlgam.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs2tldmat.f -o cjs2tldmat.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs2tlgam.f -o cjs2tlgam.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjsdmat.f -o cjsdmat.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjsgamma.f -o cjsgamma.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c hmm_like.f -o hmm_like.o
gcc-13 -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-13 -fpic -g -O2 -Wall -mtune=native -c ms2gamma.f -o ms2gamma.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c msdmat.f -o msdmat.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c msgamma.f -o msgamma.o
gfortran-13 -fpic -g -O2 -Wall -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-13 -fpic -g -O2 -Wall -mtune=native -c ums2dmat.f -o ums2dmat.o
gfortran-13 -fpic -g -O2 -Wall -mtune=native -c umsdmat.f -o umsdmat.o
g++-13 -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
make[1]: Leaving directory '/tmp/RtmpBrTppv/R.INSTALL1970ec198e914c/marked/src'
make[1]: Entering directory '/tmp/RtmpBrTppv/R.INSTALL1970ec198e914c/marked/src'
make[1]: Leaving directory '/tmp/RtmpBrTppv/R.INSTALL1970ec198e914c/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)