downloading reverse dependencies ... downloading cisp_0.1.0.tar.gz ... ok downloading localsp_0.1.0.tar.gz ... ok downloading GD_10.8.tar.gz ... ok downloading sshicm_0.1.0.tar.gz ... ok installing dependencies ‘BAMMtools’, ‘gdverse’, ‘itmsa’, ‘sdsfun’ begin installing package ‘sdsfun’ begin installing package ‘BAMMtools’ * installing *source* package ‘BAMMtools’ ... ** this is package ‘BAMMtools’ version ‘2.1.12’ ** package ‘BAMMtools’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp0nGOBD/R.INSTALLd9af3259af317/BAMMtools/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BAMMtools_init.c -o BAMMtools_init.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cohort_matrix.c -o cohort_matrix.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c dtrates.c -o dtrates.o dtrates.c: In function ‘dtrates’: dtrates.c:188:17: warning: ‘erates’ may be used uninitialized [-Wmaybe-uninitialized] 188 | SET_VECTOR_ELT(retlist, 1, erates); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dtrates.c:71:21: note: ‘erates’ was declared here 71 | SEXP rates, erates; | ^~~~~~ dtrates.c:145:44: warning: ‘nnode’ may be used uninitialized [-Wmaybe-uninitialized] 145 | if (node == nnode) { | ^ dtrates.c:83:25: note: ‘nnode’ was declared here 83 | int nrow, node, nnode, event, nxtevent, isGoodStart, isGoodEnd, place_holder; | ^~~~~ dtrates.c:157:103: warning: ‘nxtevent’ may be used uninitialized [-Wmaybe-uninitialized] 157 | lam1 = REAL(getListElement(eventData, "lam1"))[nxtevent-1]; | ^ dtrates.c:83:39: note: ‘nxtevent’ was declared here 83 | int nrow, node, nnode, event, nxtevent, isGoodStart, isGoodEnd, place_holder; | ^~~~~~~~ dtrates.c:140:63: warning: ‘mu1’ may be used uninitialized [-Wmaybe-uninitialized] 140 | ret = getMeanRateExponential(relStart,relEnd,mu1,mu2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dtrates.c:84:47: note: ‘mu1’ was declared here 84 | double begin, end, Start, lam1, lam2, mu1, mu2, relStart, relEnd, rightshift, leftshift, erightshift, eleftshift, ret; | ^~~ dtrates.c:140:63: warning: ‘mu2’ may be used uninitialized [-Wmaybe-uninitialized] 140 | ret = getMeanRateExponential(relStart,relEnd,mu1,mu2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ dtrates.c:84:52: note: ‘mu2’ was declared here 84 | double begin, end, Start, lam1, lam2, mu1, mu2, relStart, relEnd, rightshift, leftshift, erightshift, eleftshift, ret; | ^~~ dtrates.c:168:82: warning: ‘eleftshift’ may be used uninitialized [-Wmaybe-uninitialized] 168 | ret = (eleftshift+erightshift)/(getDblMatrixELT(segmat, l, 2) - getDblMatrixELT(segmat, l, 1)); | ~~~~~~~~~~~^~~~~~~~~~~~~ dtrates.c:84:111: note: ‘eleftshift’ was declared here 84 | double begin, end, Start, lam1, lam2, mu1, mu2, relStart, relEnd, rightshift, leftshift, erightshift, eleftshift, ret; | ^~~~~~~~~~ gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c jenksBrks.c -o jenksBrks.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c treetraverse.c -o treetraverse.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o BAMMtools.so BAMMtools_init.o cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp0nGOBD/R.INSTALLd9af3259af317/BAMMtools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BAMMtools/00new/BAMMtools/libs ** R ** data ** 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 ** 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 (BAMMtools) * installing *source* package ‘sdsfun’ ... ** this is package ‘sdsfun’ version ‘0.7.0’ ** package ‘sdsfun’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3U1Xt3/R.INSTALLd9af148a8af09/sdsfun/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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Disc.cpp -o Disc.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c DummyVar.cpp -o DummyVar.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c GeoDetector.cpp -o GeoDetector.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c GlobalMoranI_Test.cpp -o GlobalMoranI_Test.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c HClustGeo.cpp -o HClustGeo.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c JenksBreaks.cpp -o JenksBreaks.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c LinearRegression.cpp -o LinearRegression.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c PrintSPtest.cpp -o PrintSPtest.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 -fopenmp -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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c SDSUtils.cpp -o SDSUtils.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c SPADE_PSD.cpp -o SPADE_PSD.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c SpatialVariance.cpp -o SpatialVariance.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 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c Tbl2Mat.cpp -o Tbl2Mat.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o sdsfun.so Disc.o DummyVar.o GeoDetector.o GlobalMoranI_Test.o HClustGeo.o JenksBreaks.o LinearRegression.o PrintSPtest.o RcppExports.o SDSUtils.o SPADE_PSD.o SpatialVariance.o Tbl2Mat.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3U1Xt3/R.INSTALLd9af148a8af09/sdsfun/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-sdsfun/00new/sdsfun/libs ** 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 ** 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 (sdsfun) begin installing package ‘itmsa’ begin installing package ‘gdverse’ * installing *source* package ‘gdverse’ ... ** this is package ‘gdverse’ version ‘1.3-2’ ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpTDRpSo/R.INSTALLd9bc036168ea8/gdverse/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/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c roughset.cpp -o roughset.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o gdverse.so RcppExports.o roughset.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpTDRpSo/R.INSTALLd9bc036168ea8/gdverse/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-gdverse/00new/gdverse/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 (gdverse) * installing *source* package ‘itmsa’ ... ** this is package ‘itmsa’ version ‘0.1.0’ ** package ‘itmsa’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-16) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp8hMAse/R.INSTALLd9bbf516178c4/itmsa/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/RcppThread/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CppICM.cpp -o CppICM.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/RcppThread/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CppStats.cpp -o CppStats.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/RcppThread/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CppVM.cpp -o CppVM.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/RcppThread/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/RcppThread/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppWrapperExp.cpp -o RcppWrapperExp.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o itmsa.so CppICM.o CppStats.o CppVM.o RcppExports.o RcppWrapperExp.o -latomic -lpthread -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp8hMAse/R.INSTALLd9bbf516178c4/itmsa/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-itmsa/00new/itmsa/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 (itmsa) checking gdverse_1.3-2.tar.gz ... checking cisp_0.1.0.tar.gz ... checking localsp_0.1.0.tar.gz ... checking GD_10.8.tar.gz ... checking sshicm_0.1.0.tar.gz ... Depends: Package: gdverse Depends: R (>= 4.1.0) Imports: dplyr, forcats, ggplot2, magrittr, parallel, patchwork, purrr, reticulate, rpart, scatterpie, sdsfun (>= 0.7.0), sf, stats, tibble, tidyr, utils LinkingTo: Rcpp Timings: user system elapsed gdverse 65.51 6.663 77.17 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 0 4 Check results summary: gdverse ... NOTE * checking CRAN incoming feasibility ... [6s/9s] NOTE rdepends_cisp ... OK rdepends_GD ... OK rdepends_localsp ... OK rdepends_sshicm ... OK