downloading reverse dependencies ‘DIscBIO’, ‘nevada’, ‘stylo’, ‘OTclust’, ‘ProjectionBasedClustering’, ‘rbiom’ trying URL 'file:///data/Repositories/CRAN/src/contrib/DIscBIO_1.2.3.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/nevada_0.2.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/stylo_0.7.5.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/OTclust_1.0.6.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/ProjectionBasedClustering_1.2.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/rbiom_2.2.1.tar.gz' installing dependencies ‘DatabionicSwarm’, ‘FastKNN’, ‘fillpattern’, ‘flipr’, ‘ggdensity’, ‘HDclust’, ‘NetIndices’, ‘pamr’, ‘prettycode’, ‘rgeomstats’, ‘TSCAN’, ‘tsne’ also installing the dependencies ‘TrajectoryUtils’, ‘ABCanalysis’ begin installing package ‘TrajectoryUtils’ begin installing package ‘ABCanalysis’ begin installing package ‘NetIndices’ begin installing package ‘tsne’ begin installing package ‘flipr’ begin installing package ‘rgeomstats’ begin installing package ‘pamr’ begin installing package ‘HDclust’ begin installing package ‘FastKNN’ begin installing package ‘fillpattern’ begin installing package ‘ggdensity’ begin installing package ‘prettycode’ * installing *source* package ‘FastKNN’ ... ** this is package ‘FastKNN’ version ‘0.0.1’ ** package ‘FastKNN’ 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 (FastKNN) * installing *source* package ‘tsne’ ... ** this is package ‘tsne’ version ‘0.2-0’ ** 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 (tsne) * installing *source* package ‘prettycode’ ... ** this is package ‘prettycode’ version ‘1.1.0’ ** package ‘prettycode’ 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 (prettycode) * installing *source* package ‘NetIndices’ ... ** this is package ‘NetIndices’ version ‘1.4.4.1’ ** package ‘NetIndices’ 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 (NetIndices) * installing *source* package ‘ABCanalysis’ ... ** this is package ‘ABCanalysis’ version ‘1.2.1’ ** package ‘ABCanalysis’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ABCanalysis) begin installing package ‘DatabionicSwarm’ * installing *source* package ‘fillpattern’ ... ** this is package ‘fillpattern’ version ‘1.0.3’ ** package ‘fillpattern’ 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 (fillpattern) * installing *source* package ‘ggdensity’ ... ** this is package ‘ggdensity’ version ‘1.0.1’ ** package ‘ggdensity’ 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 (ggdensity) * installing *source* package ‘pamr’ ... ** this is package ‘pamr’ version ‘1.57’ ** package ‘pamr’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (pamr) * installing *source* package ‘rgeomstats’ ... ** this is package ‘rgeomstats’ version ‘0.0.1’ ** package ‘rgeomstats’ 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 ** 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 (rgeomstats) * installing *source* package ‘flipr’ ... ** this is package ‘flipr’ version ‘0.3.3’ ** package ‘flipr’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpZWTgKU/R.INSTALLdc5ad2682ceb/flipr/src' g++-15 -std=gnu++20 -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++20 -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 dissimilarityMatrixStatistics.cpp -o dissimilarityMatrixStatistics.o g++-15 -std=gnu++20 -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 distUtils.cpp -o distUtils.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o flipr.so RcppExports.o dissimilarityMatrixStatistics.o distUtils.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpZWTgKU/R.INSTALLdc5ad2682ceb/flipr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-flipr/00new/flipr/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 (flipr) * installing *source* package ‘TrajectoryUtils’ ... ** this is package ‘TrajectoryUtils’ version ‘1.19.0’ ** 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 (TrajectoryUtils) begin installing package ‘TSCAN’ * installing *source* package ‘HDclust’ ... ** this is package ‘HDclust’ version ‘1.0.4’ ** package ‘HDclust’ successfully unpacked and MD5 sums checked ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++-15 -std=gnu++20 accepts -g... yes checking how to run the C++ preprocessor... g++-15 -std=gnu++20 -E checking for g++-15 -std=gnu++20 option to support OpenMP... -fopenmp configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmprEEs4l/R.INSTALLdc59f684ff7a6/HDclust/src' g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cluster.cpp -o cluster.o cluster.cpp: In function ‘void centroid(double*, int, int, double*, int*, int)’: cluster.cpp:68:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 68 | if (numcdwd < 0 || numcdwd > SIZE_MAX) { | ^ cluster.cpp: In function ‘void encode(double*, int, int, double*, int*, int)’: cluster.cpp:166:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 166 | if (numcdwd < 0 || numcdwd > SIZE_MAX) { | ^ cluster.cpp: In function ‘double lloyd(double*, int, int, double*, int, double)’: cluster.cpp:222:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 222 | if (numdata<0 || numdata>SIZE_MAX || numcdwd*dim<0 || numcdwd*dim > SIZE_MAX){ | ^ cluster.cpp:222:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 222 | if (numdata<0 || numdata>SIZE_MAX || numcdwd*dim<0 || numcdwd*dim > SIZE_MAX){ | ^ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c estimate.cpp -o estimate.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:29, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include/interrupts.hpp:21, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include/interruptable_progress_monitor.hpp:15, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppProgress/include/progress.hpp:12, from estimate.cpp:29: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: ‘#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’ 35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ estimate.cpp: In function ‘void initialize(double*, int, int, HmmModel*, int)’: estimate.cpp:447:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 447 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp:451:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 451 | if (numst*dim <0|| numst*dim >SIZE_MAX) { | ^ estimate.cpp: In function ‘void initialize2(double*, int, int, HmmModel*, double*)’: estimate.cpp:623:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 623 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘void initial_ccm(double**, int, CondChain*)’: estimate.cpp:775:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 775 | if (nseq*m <0||nseq*m > SIZE_MAX) { | ^ estimate.cpp: In function ‘void initial_ccm1(double**, int, CondChain*, int)’: estimate.cpp:809:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 809 | if (nseq2*m<0||nseq2*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp:809:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 809 | if (nseq2*m<0||nseq2*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘void initial_ccm2(double**, int, CondChain*, int)’: estimate.cpp:858:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 858 | if (nseq*m<0||nseq*m>SIZE_MAX || n*m<0 || n*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp:858:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 858 | if (nseq*m<0||nseq*m>SIZE_MAX || n*m<0 || n*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp:858:75: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 858 | if (nseq*m<0||nseq*m>SIZE_MAX || n*m<0 || n*m>SIZE_MAX || nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘double comploglike(CondChain*, double**, int, double*, double*)’: estimate.cpp:915:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 915 | if (m<0|| m>SIZE_MAX) { | ^ estimate.cpp: In function ‘double classlikehd(CondChain*, double**, int, double***, double*)’: estimate.cpp:953:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 953 | if (m<0||m>SIZE_MAX ) { | ^ estimate.cpp: In function ‘int baumwelch(double**, int, CondChain*, double*, double*, double, double*)’: estimate.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1089 | if (m<0|| m>SIZE_MAX ) { | ^ estimate.cpp: In function ‘void ordervar2(double**, double***, int, int, int*, int**)’: estimate.cpp:1401:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1401 | if (nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘void hmmfit(double**, int, int, int*, int**, int*, CondChain*, double*, double*, double, double*)’: estimate.cpp:1439:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1439 | if (nseq<0 || nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘void hmmfit_minit(double**, int, int, int*, int**, int*, CondChain**, double*, double*, double, double*, int, int, int, int)’: estimate.cpp:1483:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1483 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1483:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1483 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1483:87: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1483 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1496:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1496 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘void hmmfit_minit2(double**, int, int, int*, int**, int*, CondChain**, double*, double*, double, double*, int, int, int, int)’: estimate.cpp:1562:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1562 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1562:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1562 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1562:87: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1562 | if (nseq*ninit<0||nseq*ninit>SIZE_MAX || nseq<0 || nseq>SIZE_MAX || ninit<0 || ninit>SIZE_MAX ) { | ^ estimate.cpp:1575:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 1575 | if (nseq<0||nseq>SIZE_MAX) { | ^ estimate.cpp: In function ‘void findbuddy(int*, int*, int*, int, int**, double*, int**, int, int, int)’: estimate.cpp:1758:25: warning: ‘v3’ may be used uninitialized [-Wmaybe-uninitialized] 1758 | if (skipped[i]==0 && lhsum[i]>v3) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ estimate.cpp:1747:10: note: ‘v3’ was declared here 1747 | double v3; | ^~ estimate.cpp: In function ‘void hmmfit_vb(double**, int, int, int*, int**, int***, int, int, int**, CondChain**, double*, double*, double, double*, int, int, int, int, int*, int, int, int)’: estimate.cpp:1986:17: warning: ‘v0’ may be used uninitialized [-Wmaybe-uninitialized] 1986 | lhsum1[k1]=v0; //no change occurred, record the best BIC | ~~~~~~~~~~^~~ estimate.cpp:1856:27: note: ‘v0’ was declared here 1856 | double *lhsum, *lhsum1, v0,v1; | ^~ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c matrix.cpp -o matrix.o matrix.cpp: In function ‘unsigned char ludcmp_float(float**, int, int*, float*)’: matrix.cpp:946:5: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized] 946 | if (j!=imax) { | ^~ matrix.cpp:906:9: note: ‘imax’ was declared here 906 | int i,imax,j,k; | ^~~~ matrix.cpp: In function ‘unsigned char ludcmp_double(double**, int, int*, double*)’: matrix.cpp:1011:5: warning: ‘imax’ may be used uninitialized [-Wmaybe-uninitialized] 1011 | if (j!=imax) { | ^~ matrix.cpp:971:9: note: ‘imax’ was declared here 971 | int i,imax,j,k; | ^~~~ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c modal.cpp -o modal.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:29, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from modal.cpp:28: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: ‘#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’ 35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ modal.cpp: In function ‘void FindDifSeq(int**, int, int, int***, int*, int*)’: modal.cpp:871:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 871 | if (nseq<0||nseq>SIZE_MAX) { | ^ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c prob.cpp -o prob.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/RcppCommon.h:29, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp.h:27, from prob.cpp:30: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/Rcpp/include/Rcpp/r/check_r_headers.h:35:21: note: ‘#pragma message: Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410’ 35 | #pragma message "Rinternals.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_findModes.cpp -o rcpp_findModes.o rcpp_findModes.cpp: In function ‘Rcpp::S4 rcpp_findModes(Rcpp::NumericMatrix, Rcpp::S4, Rcpp::IntegerVector)’: rcpp_findModes.cpp:60:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 60 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_findModes.cpp:132:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 132 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_findModes.cpp:136:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 136 | if (nseq<0||nseq>SIZE_MAX|| md->nb < 0 || md->nb > SIZE_MAX) { | ^ rcpp_findModes.cpp:136:52: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 136 | if (nseq<0||nseq>SIZE_MAX|| md->nb < 0 || md->nb > SIZE_MAX) { | ^ rcpp_findModes.cpp:158:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 158 | if (md->maxnumst<0||md->maxnumst>SIZE_MAX) { | ^ rcpp_findModes.cpp:178:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 178 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_findModes.cpp:186:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 186 | if (newnseq<0 || newnseq>SIZE_MAX){ | ^ rcpp_findModes.cpp:209:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 209 | if (dim<0 || dim>SIZE_MAX){ | ^ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_testsync.cpp -o rcpp_testsync.o rcpp_testsync.cpp: In function ‘void parseRefClust(const Rcpp::List&, double***, double**, int*, int*, int***, int**)’: rcpp_testsync.cpp:84:45: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 84 | if (rvseqid.size()<0||rvseqid.size()>SIZE_MAX) { | ^ rcpp_testsync.cpp:91:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 91 | if (rmode.nrow()<0||rmode.nrow()>SIZE_MAX) { | ^ rcpp_testsync.cpp:96:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 96 | if (rmode.ncol()<0||rmode.ncol()>SIZE_MAX) { | ^ rcpp_testsync.cpp:105:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 105 | if (*rnseq<0||*rnseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:115:43: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 115 | if (rsigma.size()<0||rsigma.size()>SIZE_MAX) { | ^ rcpp_testsync.cpp: In function ‘Rcpp::List augmentrefcls(int, int, double**, double*, int**, int*, int, int, int, int*, int*, double**, int, int**, int*, int*, int, int*, double***)’: rcpp_testsync.cpp:239:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 239 | if (numcls<0|| numcls>SIZE_MAX || dim<0|| dim>SIZE_MAX ) { | ^ rcpp_testsync.cpp:239:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 239 | if (numcls<0|| numcls>SIZE_MAX || dim<0|| dim>SIZE_MAX ) { | ^ rcpp_testsync.cpp:303:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 303 | if (rnseq2<0||rnseq2>SIZE_MAX) { | ^ rcpp_testsync.cpp:317:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 317 | if (numcls+rncls<0||numcls+rncls>SIZE_MAX) { | ^ rcpp_testsync.cpp:330:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 330 | if (rnseq2<0||rnseq2>SIZE_MAX) { | ^ rcpp_testsync.cpp: In function ‘int AdjustCluster(int*, int, int, double**, double**, int, int)’: rcpp_testsync.cpp:374:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 374 | if (rncls<0||rncls>SIZE_MAX) { | ^ rcpp_testsync.cpp: In function ‘Rcpp::S4 rcpp_clust(Rcpp::NumericMatrix, Rcpp::S4, Rcpp::Nullable >, Rcpp::List, Rcpp::IntegerVector)’: rcpp_testsync.cpp:438:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 438 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:552:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 552 | if (nseq<0||nseq>SIZE_MAX || md->nb<0 || md->nb>SIZE_MAX) { | ^ rcpp_testsync.cpp:552:50: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 552 | if (nseq<0||nseq>SIZE_MAX || md->nb<0 || md->nb>SIZE_MAX) { | ^ rcpp_testsync.cpp:559:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 559 | if (md->nb < 0||md->nb > SIZE_MAX) { | ^ rcpp_testsync.cpp:582:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 582 | if (md->maxnumst<0 || md->maxnumst >SIZE_MAX) { | ^ rcpp_testsync.cpp:585:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 585 | if (md->maxnumst <0||md->maxnumst >SIZE_MAX) { | ^ rcpp_testsync.cpp:626:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 626 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:667:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 667 | if (rncls<0||rncls > SIZE_MAX) { | ^ rcpp_testsync.cpp:708:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 708 | if (nseq<0||nseq>SIZE_MAX) { | ^ rcpp_testsync.cpp:714:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 714 | if (noref<0||noref > SIZE_MAX) { | ^ rcpp_testsync.cpp:732:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 732 | if (noref<0||noref > SIZE_MAX) { | ^ rcpp_testsync.cpp:754:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 754 | if (newnseq<0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:766:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 766 | if (dim<0||dim > SIZE_MAX) { | ^ rcpp_testsync.cpp:786:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 786 | if (newnseq<0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:835:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 835 | if (rncls<0||rncls > SIZE_MAX) { | ^ rcpp_testsync.cpp:877:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 877 | if (norefmode<0||norefmode > SIZE_MAX || newnseq <0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:877:64: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 877 | if (norefmode<0||norefmode > SIZE_MAX || newnseq <0||newnseq > SIZE_MAX) { | ^ rcpp_testsync.cpp:948:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 948 | if (rncls+numcls<0||rncls+numcls>SIZE_MAX) { | ^ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c rcpp_trainmaster.cpp -o rcpp_trainmaster.o rcpp_trainmaster.cpp: In function ‘Rcpp::S4 rcpp_trainHmmVb(Rcpp::NumericMatrix, const Rcpp::RObject&, const Rcpp::List&, const Rcpp::List&, Rcpp::IntegerVector, Rcpp::Function, Rcpp::Function, Rcpp::Function, bool)’: rcpp_trainmaster.cpp:31:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 31 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_trainmaster.cpp:98:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 98 | if (nb<0||nb>SIZE_MAX) { | ^ rcpp_trainmaster.cpp:157:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 157 | if (nperm0<0|| nperm0 > SIZE_MAX) { | ^ rcpp_trainmaster.cpp:200:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 200 | if (nseq<0 || nseq>SIZE_MAX){ | ^ rcpp_trainmaster.cpp:225:14: warning: ‘maxDim’ may be used uninitialized [-Wmaybe-uninitialized] 225 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:61:7: note: ‘maxDim’ was declared here 61 | int maxDim; | ^~~~~~ rcpp_trainmaster.cpp:225:14: warning: ‘minDim’ may be used uninitialized [-Wmaybe-uninitialized] 225 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:62:7: note: ‘minDim’ was declared here 62 | int minDim; | ^~~~~~ rcpp_trainmaster.cpp:225:14: warning: ‘relaxsearch’ may be used uninitialized [-Wmaybe-uninitialized] 225 | hmmfit_vb(u, nseq, dim, &nb, &bdim, &var, nperm, nperm0, vlist0, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 226 | &md, loglikehd, &lhsum, (double)epsilon, wt, ninit0, ninit1,ninit2, randomseed, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 | Numst0, maxDim, minDim, relaxsearch); //output lhsum is BIC not loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:63:7: note: ‘relaxsearch’ was declared here 63 | int relaxsearch; | ^~~~~~~~~~~ rcpp_trainmaster.cpp:220:17: warning: ‘numst’ may be used uninitialized [-Wmaybe-uninitialized] 220 | hmmfit_minit(u, nseq, nb, bdim, var, numst, &md, loglikehd, &lhsum, (double)epsilon, wt, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 | ninit0, ninit1, ninit2, randomseed); //lhsum is loglikelihood | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rcpp_trainmaster.cpp:72:8: note: ‘numst’ was declared here 72 | int *numst; // number of states in blocks | ^~~~~ g++-15 -std=gnu++20 -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/RcppProgress/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utils_rcpp.cpp -o utils_rcpp.o utils_rcpp.cpp: In function ‘void parseVbStructure(const Rcpp::S4&, CondChain*)’: utils_rcpp.cpp:43:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 43 | if (md->nb<0 || md->nb>SIZE_MAX) { | ^ utils_rcpp.cpp:70:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 70 | if (md->nb <0 || md->nb>SIZE_MAX) { | ^ utils_rcpp.cpp: In function ‘void parseHmmChain(const Rcpp::List&, CondChain*)’: utils_rcpp.cpp:97:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 97 | if (md->nb <0 || md->nb>SIZE_MAX) { | ^ g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o HDclust.so RcppExports.o cluster.o estimate.o matrix.o modal.o prob.o rcpp_findModes.o rcpp_testsync.o rcpp_trainmaster.o utils_rcpp.o -llapack -L/home/hornik/tmp/R-d-gcc-15/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmprEEs4l/R.INSTALLdc59f684ff7a6/HDclust/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-HDclust/00new/HDclust/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 (HDclust) * installing *source* package ‘TSCAN’ ... ** this is package ‘TSCAN’ version ‘1.49.0’ ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (TSCAN) * installing *source* package ‘DatabionicSwarm’ ... ** this is package ‘DatabionicSwarm’ version ‘2.0.0’ ** package ‘DatabionicSwarm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-14) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpup15wr/R.INSTALLdc969593f5e0a/DatabionicSwarm/src' g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Delta3DWeightsC.cpp -o Delta3DWeightsC.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c DijkstraSSSP.cpp -o DijkstraSSSP.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PswarmRadiusParallel.cpp -o PswarmRadiusParallel.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c PswarmRadiusSequential.cpp -o PswarmRadiusSequential.o g++-15 -std=gnu++20 -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/RcppParallel/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++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c findPossiblePositionsCsingle.cpp -o findPossiblePositionsCsingle.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rDistanceToroidCsingle.cpp -o rDistanceToroidCsingle.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rcppPar_DistanceToroid.cpp -o rcppPar_DistanceToroid.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c sampleC.cpp -o sampleC.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c trainstepC.cpp -o trainstepC.o g++-15 -std=gnu++20 -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/RcppParallel/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c trainstepC2.cpp -o trainstepC2.o g++-15 -std=gnu++20 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o DatabionicSwarm.so Delta3DWeightsC.o DijkstraSSSP.o PswarmRadiusParallel.o PswarmRadiusSequential.o RcppExports.o findPossiblePositionsCsingle.o rDistanceToroidCsingle.o rcppPar_DistanceToroid.o sampleC.o trainstepC.o trainstepC2.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/Rtmpup15wr/R.INSTALLdc969593f5e0a/DatabionicSwarm/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DatabionicSwarm/00new/DatabionicSwarm/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 (DatabionicSwarm) checking tsne_0.2-0.tar.gz ... checking DIscBIO_1.2.3.tar.gz ... checking nevada_0.2.0.tar.gz ... checking stylo_0.7.5.tar.gz ... checking OTclust_1.0.6.tar.gz ... checking ProjectionBasedClustering_1.2.2.tar.gz ... checking rbiom_2.2.1.tar.gz ... Depends: Timings: user system elapsed tsne 13.464 2.413 16.343 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 1 5 Check results summary: tsne ... OK rdepends_DIscBIO ... OK rdepends_nevada ... NOTE * checking DESCRIPTION meta-information ... NOTE rdepends_OTclust ... OK rdepends_ProjectionBasedClustering ... OK rdepends_rbiom ... OK rdepends_stylo ... OK