downloading reverse dependencies ...
downloading FlexScan_0.2.2.tar.gz ... ok
downloading PhageCocktail_1.0.3.tar.gz ... ok
downloading smacpod_2.6.tar.gz ... ok

installing dependencies ‘smerc’, ‘SpatialEpi’

begin installing package ‘SpatialEpi’
begin installing package ‘smerc’
* installing *source* package ‘SpatialEpi’ ...
** package ‘SpatialEpi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpyg3D1W/R.INSTALL214fc53cebd597/SpatialEpi/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/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
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/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 bayes_cluster.cpp -o bayes_cluster.o
bayes_cluster.cpp: In function ‘Rcpp::List return_local_moves(Rcpp::NumericVector, Rcpp::List, Rcpp::NumericMatrix)’:
bayes_cluster.cpp:399:23: warning: ‘end’ may be used uninitialized [-Wmaybe-uninitialized]
  399 |     for(int z=start; z<end; z++){
      |                      ~^~~~
bayes_cluster.cpp:359:69: note: ‘end’ was declared here
  359 |   int k = theta.size(), n_zones = cluster_list.size(), zone, start, end, zone_sub,
      |                                                                     ^~~
bayes_cluster.cpp:399:23: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized]
  399 |     for(int z=start; z<end; z++){
      |                      ~^~~~
bayes_cluster.cpp:359:62: note: ‘start’ was declared here
  359 |   int k = theta.size(), n_zones = cluster_list.size(), zone, start, end, zone_sub,
      |                                                              ^~~~~
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/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 cluster_detection.cpp -o cluster_detection.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o SpatialEpi.so RcppExports.o bayes_cluster.o cluster_detection.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpyg3D1W/R.INSTALL214fc53cebd597/SpatialEpi/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-SpatialEpi/00new/SpatialEpi/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 (SpatialEpi)
* installing *source* package ‘smerc’ ...
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-3) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptaOCIM/R.INSTALL214fc7446f3926/smerc/src'
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/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++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c distance_functions.cpp -o distance_functions.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c noc_cpp.cpp -o noc_cpp.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c optimized_statistics.cpp -o optimized_statistics.o
g++-14  -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG  -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/Rcpp/include' -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c scsg2_cpp.cpp -o scsg2_cpp.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o smerc.so RcppExports.o distance_functions.o noc_cpp.o optimized_statistics.o scsg2_cpp.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptaOCIM/R.INSTALL214fc7446f3926/smerc/src'
installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-smerc/00new/smerc/libs
** R
** data
** 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 (smerc)

checking smerc_1.8.4.tar.gz ...
checking FlexScan_0.2.2.tar.gz ...
checking PhageCocktail_1.0.3.tar.gz ...
checking smacpod_2.6.tar.gz ...

Depends:
Package: smerc
  Depends: R (>= 3.6)
  Imports: pbapply, Rcpp
  LinkingTo: Rcpp, RcppProgress

Timings:
         user system elapsed
smerc 151.148  7.039 161.537

Results:
Check status summary:
                  NOTE OK
  Source packages    0  1
  Reverse depends    2  1

Check results summary:
smerc ... OK
rdepends_FlexScan ... OK
rdepends_PhageCocktail ... NOTE
* checking Rd files ... [0s/0s] NOTE
rdepends_smacpod ... NOTE
* checking Rd cross-references ... NOTE
* checking HTML version of manual ... [1s/1s] NOTE