downloading reverse dependencies ... downloading Rogue_2.1.7.tar.gz ... ok downloading rwty_1.0.3.tar.gz ... ok downloading TBRDist_1.0.2.tar.gz ... ok downloading TreeSearch_1.7.0.tar.gz ... ok downloading TreeTools_1.16.1.tar.gz ... ok installing dependencies ‘hypervolume’, ‘kdensity’, ‘protoclust’, ‘Quartet’, ‘Rogue’, ‘Ternary’, ‘TreeDist’, ‘TreeDistData’, ‘TreeSearch’, ‘Umatrix’ Warning: package ‘TreeDistData’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘poilog’, ‘GUILDS’, ‘nakagami’, ‘sads’, ‘ttutils’, ‘univariateML’, ‘EQL’, ‘AdaptGauss’ begin installing package ‘poilog’ begin installing package ‘GUILDS’ begin installing package ‘ttutils’ begin installing package ‘nakagami’ begin installing package ‘AdaptGauss’ begin installing package ‘protoclust’ begin installing package ‘hypervolume’ begin installing package ‘Ternary’ begin installing package ‘TreeDist’ * installing *source* package ‘ttutils’ ... ** this is package ‘ttutils’ version ‘1.0-1.1’ ** package ‘ttutils’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ttutils) begin installing package ‘EQL’ * installing *source* package ‘nakagami’ ... ** this is package ‘nakagami’ version ‘1.1.0’ ** package ‘nakagami’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (nakagami) * installing *source* package ‘protoclust’ ... ** this is package ‘protoclust’ version ‘1.6.4’ ** package ‘protoclust’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpEKdyHC/R.INSTALL6608f40b23af0/protoclust/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c hier.c -o hier.o hier.c: In function ‘hier’: hier.c:194:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 194 | for(j = 0; j < imerge; j++) | ^~~ hier.c:204:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 204 | ii = lt(imerge+1,imerge,n); | ^~ hier.c: In function ‘minimaxpoint’: hier.c:442:10: warning: ‘mm’ may be used uninitialized [-Wmaybe-uninitialized] 442 | return mm; | ^~ hier.c:428:7: note: ‘mm’ was declared here 428 | int mm; | ^~ hier.c: In function ‘findNN’: hier.c:346:29: warning: ‘nn’ may be used uninitialized [-Wmaybe-uninitialized] 346 | mincomplete = completelink(dmax, n, clusters[nn], nn, clusters[i], i); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hier.c:328:7: note: ‘nn’ was declared here 328 | int nn; | ^~ hier.c: In function ‘hier’: hier.c:274:26: warning: ‘imerge’ may be used uninitialized [-Wmaybe-uninitialized] 274 | Cluster *cur = clusters[imerge]; | ^ hier.c:28:20: note: ‘imerge’ was declared here 28 | int i, j, k, ii, imerge, jmerge, reverse; | ^~~~~~ gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c protoclust_init.c -o protoclust_init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o protoclust.so hier.o protoclust_init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpEKdyHC/R.INSTALL6608f40b23af0/protoclust/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-protoclust/00new/protoclust/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 (protoclust) * installing *source* package ‘poilog’ ... ** this is package ‘poilog’ version ‘0.4.2.1’ ** package ‘poilog’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpXkb9yZ/R.INSTALL6609748c2e24d/poilog/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c bipoilog_s_cint.c -o bipoilog_s_cint.o bipoilog_s_cint.c:24:30: warning: missing braces around initializer [-Wmissing-braces] 24 | R_CMethodDef cMethods[] = { | ^ gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o poilog.so bipoilog_s_cint.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpXkb9yZ/R.INSTALL6609748c2e24d/poilog/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-poilog/00new/poilog/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 (poilog) * installing *source* package ‘EQL’ ... ** this is package ‘EQL’ version ‘1.0-1’ ** package ‘EQL’ 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 ** 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 (EQL) * installing *source* package ‘Ternary’ ... ** this is package ‘Ternary’ version ‘2.3.4’ ** package ‘Ternary’ 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 ** 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 (Ternary) begin installing package ‘Quartet’ * installing *source* package ‘GUILDS’ ... ** this is package ‘GUILDS’ version ‘1.4.7’ ** package ‘GUILDS’ 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/Rtmp2kf6m2/R.INSTALL660885efc3a72/GUILDS/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c KDA_R.cpp -o KDA_R.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/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 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o GUILDS.so KDA_R.o RcppExports.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp2kf6m2/R.INSTALL660885efc3a72/GUILDS/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GUILDS/00new/GUILDS/libs ** 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 ** 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 (GUILDS) begin installing package ‘sads’ * installing *source* package ‘AdaptGauss’ ... ** this is package ‘AdaptGauss’ version ‘1.6’ ** package ‘AdaptGauss’ 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/Rtmpx4Hxjm/R.INSTALL6608c4e4cb0f6/AdaptGauss/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/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 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c meanC.cpp -o meanC.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o AdaptGauss.so RcppExports.o meanC.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpx4Hxjm/R.INSTALL6608c4e4cb0f6/AdaptGauss/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-AdaptGauss/00new/AdaptGauss/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 (AdaptGauss) begin installing package ‘Umatrix’ * installing *source* package ‘sads’ ... ** this is package ‘sads’ version ‘0.6.3’ ** package ‘sads’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZSwNTG/R.INSTALL6630a49cb61c1/sads/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c gauss_legendre.c -o gauss_legendre.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c volkov.c -o volkov.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o sads.so gauss_legendre.o init.o volkov.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZSwNTG/R.INSTALL6630a49cb61c1/sads/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-sads/00new/sads/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 (sads) begin installing package ‘univariateML’ * installing *source* package ‘univariateML’ ... ** this is package ‘univariateML’ version ‘1.5.0’ ** package ‘univariateML’ 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 (univariateML) begin installing package ‘kdensity’ * installing *source* package ‘kdensity’ ... ** this is package ‘kdensity’ version ‘1.1.1’ ** package ‘kdensity’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 (kdensity) * installing *source* package ‘Umatrix’ ... ** this is package ‘Umatrix’ version ‘4.0.2’ ** package ‘Umatrix’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpolX3q6/R.INSTALL6636b6045378e/Umatrix/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/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 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c addRowWiseC.cpp -o addRowWiseC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bestmatchC.cpp -o bestmatchC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bestmatchesC.cpp -o bestmatchesC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c esomTrainedWeightVectorsConeC.cpp -o esomTrainedWeightVectorsConeC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c esomTrainedWeightVectorsGaussC.cpp -o esomTrainedWeightVectorsGaussC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c esomTrainedWeightVectorsMexicanHatC.cpp -o esomTrainedWeightVectorsMexicanHatC.o gcc-15 -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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c registerDynamicSymbol.c -o registerDynamicSymbol.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Umatrix.so RcppExports.o addRowWiseC.o bestmatchC.o bestmatchesC.o esomTrainedWeightVectorsConeC.o esomTrainedWeightVectorsGaussC.o esomTrainedWeightVectorsMexicanHatC.o registerDynamicSymbol.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpolX3q6/R.INSTALL6636b6045378e/Umatrix/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Umatrix/00new/Umatrix/libs ** R ** data ** 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 (Umatrix) * installing *source* package ‘TreeDist’ ... ** this is package ‘TreeDist’ version ‘2.10.1’ ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpa8xjV1/R.INSTALL660966d7a40f8/TreeDist/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/TreeTools/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 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c day_1985.cpp -o day_1985.o In file included from tree_distances.h:4, from day_1985.cpp:4: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TreeTools/include/TreeTools/SplitList.h:45:16: warning: ‘TreeTools::bitcounts’ defined but not used [-Wunused-variable] 45 | static int16 bitcounts[65536]; | ^~~~~~~~~ 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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c lap.cpp -o lap.o In file included from tree_distances.h:4, from lap.cpp:29: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TreeTools/include/TreeTools/SplitList.h:45:16: warning: ‘TreeTools::bitcounts’ defined but not used [-Wunused-variable] 45 | static int16 bitcounts[65536]; | ^~~~~~~~~ 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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c mast.cpp -o mast.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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c nni_distance.cpp -o nni_distance.o In file included from nni_distance.cpp:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TreeTools/include/TreeTools/SplitList.h:45:16: warning: ‘TreeTools::bitcounts’ defined but not used [-Wunused-variable] 45 | static int16 bitcounts[65536]; | ^~~~~~~~~ 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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c path_vector.cpp -o path_vector.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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c reduce_tree.cpp -o reduce_tree.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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c spr.cpp -o spr.o In file included from spr.cpp:6: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TreeTools/include/TreeTools/SplitList.h:45:16: warning: ‘TreeTools::bitcounts’ defined but not used [-Wunused-variable] 45 | static int16 bitcounts[65536]; | ^~~~~~~~~ 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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree_distance_functions.cpp -o tree_distance_functions.o In file included from tree_distance_functions.cpp:2: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TreeTools/include/TreeTools/SplitList.h:45:16: warning: ‘TreeTools::bitcounts’ defined but not used [-Wunused-variable] 45 | static int16 bitcounts[65536]; | ^~~~~~~~~ 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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c tree_distances.cpp -o tree_distances.o In file included from tree_distances.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/TreeTools/include/TreeTools/SplitList.h:45:16: warning: ‘TreeTools::bitcounts’ defined but not used [-Wunused-variable] 45 | static int16 bitcounts[65536]; | ^~~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o TreeDist.so RcppExports.o day_1985.o lap.o mast.o nni_distance.o path_vector.o reduce_tree.o spr.o tree_distance_functions.o tree_distances.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpa8xjV1/R.INSTALL660966d7a40f8/TreeDist/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TreeDist/00new/TreeDist/libs ** R ** 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 (TreeDist) begin installing package ‘Rogue’ * installing *source* package ‘hypervolume’ ... ** this is package ‘hypervolume’ version ‘3.1.6’ ** package ‘hypervolume’ 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/Rtmp0D2Ksd/R.INSTALL660913009ca61/hypervolume/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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/progress/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 -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/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c convert.cpp -o convert.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'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/progress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fastPdist2.cpp -o fastPdist2.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o hypervolume.so RcppExports.o convert.o fastPdist2.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/Rtmp0D2Ksd/R.INSTALL660913009ca61/hypervolume/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-hypervolume/00new/hypervolume/libs ** R ** data ** demo ** 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 (hypervolume) * installing *source* package ‘Rogue’ ... ** this is package ‘Rogue’ version ‘2.1.7’ ** package ‘Rogue’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdL0jVt/R.INSTALL6654021c5bb07/Rogue/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c graph_geodesic.c -o graph_geodesic.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Array.c -o rnr/Array.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/BitVector.c -o rnr/BitVector.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Dropset.c -o rnr/Dropset.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/HashTable.c -o rnr/HashTable.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/List.c -o rnr/List.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Node.c -o rnr/Node.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/ProfileElem.c -o rnr/ProfileElem.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/RogueNaRok.c -o rnr/RogueNaRok.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/Tree.c -o rnr/Tree.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/common.c -o rnr/common.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/legacy.c -o rnr/legacy.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c rnr/newFunctions.c -o rnr/newFunctions.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c Rogue_init.c -o Rogue_init.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Rogue.so graph_geodesic.o rnr/Array.o rnr/BitVector.o rnr/Dropset.o rnr/HashTable.o rnr/List.o rnr/Node.o rnr/ProfileElem.o rnr/RogueNaRok.o rnr/Tree.o rnr/common.o rnr/legacy.o rnr/newFunctions.o Rogue_init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdL0jVt/R.INSTALL6654021c5bb07/Rogue/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Rogue/00new/Rogue/libs ** R ** 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 (Rogue) begin installing package ‘TreeSearch’ * installing *source* package ‘Quartet’ ... ** this is package ‘Quartet’ version ‘1.2.7’ ** package ‘Quartet’ 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/RtmpT3i7cZ/R.INSTALL662aa252de66a/Quartet/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AbstractDistanceCalculator.cpp -o AbstractDistanceCalculator.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c AllQuartets.cpp -o AllQuartets.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c EdgeParser.cpp -o EdgeParser.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDT.cpp -o HDT.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingCCToC.cpp -o HDTCountingCCToC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingCTransform.cpp -o HDTCountingCTransform.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingG.cpp -o HDTCountingG.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingIGToC.cpp -o HDTCountingIGToC.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTCountingLeaf.cpp -o HDTCountingLeaf.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTFactory.cpp -o HDTFactory.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HDTListUtils.cpp -o HDTListUtils.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c NewickParser.cpp -o NewickParser.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c QuartetDistanceCalculator.cpp -o QuartetDistanceCalculator.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/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 -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RootedTree.cpp -o RootedTree.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RootedTreeFactory.cpp -o RootedTreeFactory.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c TripletDistanceCalculator.cpp -o TripletDistanceCalculator.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c int_stuff.cpp -o int_stuff.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rQuartetDist.cpp -o rQuartetDist.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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rTripletDist.cpp -o rTripletDist.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o Quartet.so AbstractDistanceCalculator.o AllQuartets.o EdgeParser.o HDT.o HDTCountingCCToC.o HDTCountingCTransform.o HDTCountingG.o HDTCountingIGToC.o HDTCountingLeaf.o HDTFactory.o HDTListUtils.o NewickParser.o QuartetDistanceCalculator.o RcppExports.o RootedTree.o RootedTreeFactory.o TripletDistanceCalculator.o int_stuff.o rQuartetDist.o rTripletDist.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT3i7cZ/R.INSTALL662aa252de66a/Quartet/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-Quartet/00new/Quartet/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 (Quartet) * installing *source* package ‘TreeSearch’ ... ** this is package ‘TreeSearch’ version ‘1.7.0’ ** package ‘TreeSearch’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-1) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-1) 15.2.0’ using C++17 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpngYT33/R.INSTALL665cf34bafa83/TreeSearch/src' gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RMorphy.c -o RMorphy.o gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c RMorphyUtils.c -o RMorphyUtils.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/TreeTools/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 gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c TreeSearch-init.c -o TreeSearch-init.o gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fitch.c -o fitch.o gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c morphy.c -o morphy.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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c morphy_score.cpp -o morphy_score.o gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c mpl.c -o mpl.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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rearrange.cpp -o rearrange.o gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c statedata.c -o statedata.o gcc-15 -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/TreeTools/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c wagner.c -o wagner.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o TreeSearch.so RMorphy.o RMorphyUtils.o RcppExports.o TreeSearch-init.o fitch.o morphy.o morphy_score.o mpl.o rearrange.o statedata.o wagner.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpngYT33/R.INSTALL665cf34bafa83/TreeSearch/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-TreeSearch/00new/TreeSearch/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 (TreeSearch) checking TreeDist_2.10.1.tar.gz ... checking Rogue_2.1.7.tar.gz ... checking rwty_1.0.3.tar.gz ... checking TBRDist_1.0.2.tar.gz ... checking TreeSearch_1.7.0.tar.gz ... checking TreeTools_1.16.1.tar.gz ... Depends: Package: TreeDist Depends: R (>= 4.0), stats, Imports: ape (>= 5.0), cli (>= 3.0), colorspace, Rdpack (>= 0.7), shiny, shinyjs, TreeTools (>= 1.16), LinkingTo: Rcpp, TreeTools (>= 1.16.1), Timings: user system elapsed TreeDist 140.659 11.043 155.803 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 1 4 Check results summary: TreeDist ... NOTE * checking CRAN incoming feasibility ... [7s/10s] NOTE rdepends_Rogue ... OK rdepends_rwty ... OK rdepends_TBRDist ... NOTE * checking C++ specification ... NOTE rdepends_TreeSearch ... OK rdepends_TreeTools ... OK Check results changes: Package: TBRDist Check: CRAN incoming feasibility Old result: NOTE