downloading reverse dependencies ... downloading phylosem_1.1.4.tar.gz ... ok downloading dsem_1.6.0.tar.gz ... ok installing dependencies ‘fishtree’, ‘MARSS’, ‘phylopath’, ‘phylosignal’, ‘phyr’, ‘Rphylopars’, ‘RTMB’ begin installing package ‘phylopath’ begin installing package ‘Rphylopars’ begin installing package ‘fishtree’ begin installing package ‘phyr’ begin installing package ‘phylosignal’ begin installing package ‘RTMB’ begin installing package ‘MARSS’ * installing *source* package ‘fishtree’ ... ** this is package ‘fishtree’ version ‘0.3.4’ ** package ‘fishtree’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fishtree) * installing *source* package ‘phylopath’ ... ** this is package ‘phylopath’ version ‘1.3.1’ ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (phylopath) * installing *source* package ‘MARSS’ ... ** this is package ‘MARSS’ version ‘3.11.9’ ** package ‘MARSS’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MARSS) * installing *source* package ‘phylosignal’ ... ** this is package ‘phylosignal’ version ‘1.3.1’ ** package ‘phylosignal’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpxeFbSV/R.INSTALL255bc03fa0b329/phylosignal/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c signaltest.cpp -o signaltest.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from signaltest.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o phylosignal.so RcppExports.o signaltest.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpxeFbSV/R.INSTALL255bc03fa0b329/phylosignal/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-phylosignal/00new/phylosignal/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (phylosignal) * installing *source* package ‘Rphylopars’ ... ** this is package ‘Rphylopars’ version ‘0.3.10’ ** package ‘Rphylopars’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpFEow72/R.INSTALL255bbe4b586a4/Rphylopars/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c phylopars_rcpp.cpp -o phylopars_rcpp.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from phylopars_rcpp.cpp:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Rphylopars.so RcppExports.o phylopars_rcpp.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpFEow72/R.INSTALL255bbe4b586a4/Rphylopars/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rphylopars/00new/Rphylopars/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (Rphylopars) * installing *source* package ‘phyr’ ... ** this is package ‘phyr’ version ‘1.1.0’ ** package ‘phyr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpNVpo2u/R.INSTALL255bba15045910/phyr/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from RcppExports.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c binaryPGLMM.cpp -o binaryPGLMM.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cor_phylo.cpp -o cor_phylo.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from cor_phylo.cpp:3: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pcd.cpp -o pcd.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from pcd.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pglmm_binary.cpp -o pglmm_binary.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from pglmm_binary.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c pglmm_gaussian.cpp -o pglmm_gaussian.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from pglmm_gaussian.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c psv.cpp -o psv.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:29, from psv.cpp:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/version/arma.h:71:153: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.’ 71 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT. See GitHub issue #475 for more.") | ^ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o phyr.so RcppExports.o binaryPGLMM.o cor_phylo.o pcd.o pglmm_binary.o pglmm_gaussian.o psv.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpNVpo2u/R.INSTALL255bba15045910/phyr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-phyr/00new/phyr/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (phyr) * installing *source* package ‘RTMB’ ... ** this is package ‘RTMB’ version ‘1.7’ ** package ‘RTMB’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpV7mYdm/R.INSTALL255bc21f2b19cc/RTMB/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RTMB.cpp -o RTMB.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RTMB_tape.cpp -o RTMB_tape.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TMB.cpp -o TMB.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distributions.cpp -o distributions.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c interpol.cpp -o interpol.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lapack.cpp -o lapack.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c math.cpp -o math.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c math_complex.cpp -o math_complex.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.cpp -o misc.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -DTMB_EIGEN_DISABLE_WARNINGS -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TMB/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppEigen/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c poshess.cpp -o poshess.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o RTMB.so RTMB.o RTMB_tape.o RcppExports.o TMB.o distributions.o interpol.o lapack.o math.o math_complex.o misc.o poshess.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpV7mYdm/R.INSTALL255bc21f2b19cc/RTMB/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-RTMB/00new/RTMB/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for ‘fft’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘colSums’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘rowSums’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘diag’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘dexp’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dweibull’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dbeta’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘df’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dt’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dnbinom’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dgamma’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pgamma’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pexp’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pweibull’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘pbeta’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qgamma’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qexp’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qweibull’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qbeta’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘besselK’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘besselI’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘besselJ’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘besselY’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘eigen’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘svd’ from ‘base’ in package ‘RTMB’ (from the saved implicit definition) Creating a generic function for ‘svd’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘cov2cor’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dlnorm’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘matrix’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘apply’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘sapply’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘ifelse’ from package ‘base’ in package ‘RTMB’ Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘RTMB’ Creating a generic function for ‘dmultinom’ from package ‘stats’ in package ‘RTMB’ ** help *** installing help indices ** 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 (RTMB) checking phylopath_1.3.1.tar.gz ... checking dsem_1.6.0.tar.gz ... checking phylosem_1.1.4.tar.gz ... Depends: Package: phylopath Depends: R (>= 2.10) Imports: ape (>= 4.1), future.apply, ggm (>= 2.3), ggplot2 (>= 3.0.0), ggraph (>= 1.0.0), igraph (>= 1.0.1), phylolm (>= 2.5), purrr (>= 0.2.3), tibble Timings: user system elapsed phylopath 60.65 5.154 67.334 Results: Check status summary: OK Source packages 1 Reverse depends 2 Check results summary: phylopath ... OK rdepends_dsem ... OK rdepends_phylosem ... OK