downloading reverse dependencies ‘numbat’

trying URL 'file:///data/Repositories/CRAN/src/contrib/numbat_1.5.2.tar.gz'
Content type 'unknown' length 4310456 bytes (4.1 MB)
==================================================

installing dependencies ‘hahmmr’, ‘scistreer’

begin installing package ‘hahmmr’
begin installing package ‘scistreer’
* installing *source* package ‘scistreer’ ...
** this is package ‘scistreer’ version ‘1.2.1’
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpRrXGLs/R.INSTALL3aa9645f915322/scistreer/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c scistreer.cpp -o scistreer.o
scistreer.cpp: In function ‘std::vector<std::vector<int, std::allocator<int> > > allChildrenCPP(arma::Mat<int>)’:
scistreer.cpp:22:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
   22 |     for(int i = 0; i<parent.size(); i++) {
      |                    ~^~~~~~~~~~~~~~
scistreer.cpp: In function ‘arma::Mat<int> reorder_rows(arma::Mat<int>, arma::Col<int>)’:
scistreer.cpp:52:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
   52 |     for (int i = 0; i < y.n_elem; ++i) {
      |                     ~~^~~~~~~~~~
'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++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o scistreer.so RcppExports.o scistreer.o -lpthread -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/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/RtmpRrXGLs/R.INSTALL3aa9645f915322/scistreer/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-scistreer/00new/scistreer/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (scistreer)
* installing *source* package ‘hahmmr’ ...
** this is package ‘hahmmr’ version ‘1.0.0’
** package ‘hahmmr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpvcU5lZ/R.INSTALL3aa966411974f9/hahmmr/src'
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c bbinom.cpp -o bbinom.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c hmm.cpp -o hmm.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c misc.cpp -o misc.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c mle.cpp -o mle.o
g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/roptim/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3  -I"../inst/include" -fpic  -g -O2 -Wall -pedantic -mtune=native   -c poilog.cpp -o poilog.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++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o hahmmr.so RcppExports.o bbinom.o hmm.o misc.o mle.o poilog.o -lpthread -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/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/RtmpvcU5lZ/R.INSTALL3aa966411974f9/hahmmr/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-hahmmr/00new/hahmmr/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (hahmmr)

checking scistreer_1.2.1.tar.gz ...
checking numbat_1.5.2.tar.gz ...

Depends:
Package: scistreer
  Depends: R (>= 4.1.0)
  Imports: ape, dplyr, ggplot2, ggtree, igraph, parallelDist,
    patchwork, phangorn, Rcpp, reshape2, RcppParallel, RhpcBLASctl,
    stringr, tidygraph
  LinkingTo: Rcpp, RcppArmadillo, RcppParallel

Timings:
            user system elapsed
scistreer 83.688  8.424  93.163

Results:
Check status summary:
                  OK
  Source packages  1
  Reverse depends  1

Check results summary:
scistreer ... OK
rdepends_numbat ... OK