downloading reverse dependencies ... downloading ecan_0.2.1.tar.gz ... ok downloading fso_2.1-2.tar.gz ... ok downloading maotai_0.2.6.tar.gz ... ok downloading ecoCopula_1.0.2.tar.gz ... ok downloading RVAideMemoire_0.9-83-12.tar.gz ... ok downloading vegdata_0.9.12.tar.gz ... ok installing dependencies ‘dgof’, ‘EMT’, ‘FSA’, ‘fso’, ‘indicspecies’, ‘labdsv’, ‘mvabund’, ‘mvnormtest’, ‘RGCCA’ also installing the dependency ‘FlexParamCurve’ begin installing package ‘FlexParamCurve’ begin installing package ‘mvabund’ begin installing package ‘dgof’ begin installing package ‘EMT’ begin installing package ‘mvnormtest’ begin installing package ‘RGCCA’ begin installing package ‘indicspecies’ begin installing package ‘labdsv’ * installing *source* package ‘mvnormtest’ ... ** this is package ‘mvnormtest’ version ‘0.1-9-3’ ** package ‘mvnormtest’ 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 (mvnormtest) * installing *source* package ‘EMT’ ... ** this is package ‘EMT’ version ‘1.3.1’ ** package ‘EMT’ 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 (EMT) * installing *source* package ‘dgof’ ... ** this is package ‘dgof’ version ‘1.5.1’ ** package ‘dgof’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpT4I4RC/R.INSTALL10ef2e253d5644/dgof/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/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-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c ks.c -o ks.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o dgof.so init.o ks.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpT4I4RC/R.INSTALL10ef2e253d5644/dgof/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-dgof/00new/dgof/libs ** 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 ** 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 (dgof) * installing *source* package ‘indicspecies’ ... ** this is package ‘indicspecies’ version ‘1.8.0’ ** package ‘indicspecies’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** 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 (indicspecies) * installing *source* package ‘FlexParamCurve’ ... ** this is package ‘FlexParamCurve’ version ‘1.5-6’ ** package ‘FlexParamCurve’ 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 ** 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 (FlexParamCurve) begin installing package ‘FSA’ * installing *source* package ‘labdsv’ ... ** this is package ‘labdsv’ version ‘2.1-2’ ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpP2edl0/R.INSTALL10ef2a388e8176/labdsv/src' gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c dsvdis.f90 -o dsvdis.o dsvdis.f90:85:18: 85 | a = a + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:86:18: 86 | b = b + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:88:18: 88 | b = b + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:129:18: 129 | a = a + 2 * weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:130:18: 130 | b = b + 2 * weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:132:18: 132 | b = b + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:175:18: 175 | a = a + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:177:18: 177 | b = b + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:179:18: 179 | c = c + weight(k) | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] dsvdis.f90:389:27: 389 | double precision temp | 1 Warning: Unused variable ‘temp’ declared at (1) [-Wunused-variable] dsvdis.f90:388:29: 388 | double precision totsum | 1 Warning: Unused variable ‘totsum’ declared at (1) [-Wunused-variable] dsvdis.f90:376:34: 376 | subroutine hellin(mat,weight,nrow,ncol,dis,rowsum) | 1 Warning: Unused dummy argument ‘weight’ at (1) [-Wunused-dummy-argument] gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c euclid.f90 -o euclid.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c indval.f90 -o indval.o indval.f90:156:16: 156 | index = unifrnd()*pool+1 | 1 Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c ismetric.f90 -o ismetric.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c metric.f90 -o metric.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c orddist.f90 -o orddist.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c pip.f90 -o pip.o pip.f90:32:18: 32 | r = (y(i) - polyy(j)) / ydiff | 1 Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion] gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c random.c -o random.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c stepdist.f90 -o stepdist.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c thull.f90 -o thull.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o labdsv.so dsvdis.o euclid.o indval.o ismetric.o metric.o orddist.o pip.o random.o stepdist.o thull.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpP2edl0/R.INSTALL10ef2a388e8176/labdsv/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-labdsv/00new/labdsv/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 (labdsv) begin installing package ‘fso’ * installing *source* package ‘RGCCA’ ... ** this is package ‘RGCCA’ version ‘3.0.3’ ** package ‘RGCCA’ 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 (RGCCA) * installing *source* package ‘fso’ ... ** this is package ‘fso’ version ‘2.1-2’ ** package ‘fso’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpC5ewUH/R.INSTALL10f0e82b6b5678/fso/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c fso_init.c -o fso_init.o gfortran-14 -fpic -g -O2 -Wall -pedantic -mtune=native -c thull.f -o thull.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o fso.so fso_init.o thull.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpC5ewUH/R.INSTALL10f0e82b6b5678/fso/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-fso/00new/fso/libs ** 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 ** 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 (fso) * installing *source* package ‘FSA’ ... ** this is package ‘FSA’ version ‘0.10.0’ ** package ‘FSA’ 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 ** 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 (FSA) * installing *source* package ‘mvabund’ ... ** this is package ‘mvabund’ version ‘4.2.1’ ** package ‘mvabund’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ using C++11 make[1]: Entering directory '/home/hornik/tmp/scratch/RtmptOfnco/R.INSTALL10ef22267c19d0/mvabund/src' g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/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++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Rinterface.cpp -o Rinterface.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c anova.cpp -o anova.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c calctest.cpp -o calctest.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glm.cpp -o glm.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glmtest.cpp -o glmtest.o glmtest.cpp: In member function ‘int GlmTest::resampNonCase(glm*, gsl_matrix*, unsigned int)’: glmtest.cpp:849:23: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 849 | gsl_sort_index(permid, tmp, 1, nRows); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from resampTest.h:26, from glmtest.cpp:5: /usr/include/gsl/gsl_sort_double.h:41:6: note: by argument 2 of type ‘const double*’ to ‘void gsl_sort_index(size_t*, const double*, size_t, size_t)’ declared here 41 | void gsl_sort_index (size_t * p, const double * data, const size_t stride, const size_t n); | ^~~~~~~~~~~~~~ glmtest.cpp:876:23: warning: ‘tmp’ may be used uninitialized [-Wmaybe-uninitialized] 876 | gsl_sort_index(permid, tmp, 1, nRows); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/gsl/gsl_sort_double.h:41:6: note: by argument 2 of type ‘const double*’ to ‘void gsl_sort_index(size_t*, const double*, size_t, size_t)’ declared here 41 | void gsl_sort_index (size_t * p, const double * data, const size_t stride, const size_t n); | ^~~~~~~~~~~~~~ g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c io.cpp -o io.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c rnd.cpp -o rnd.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c simutility.cpp -o simutility.o g++-14 -std=gnu++11 -I"/home/hornik/tmp/R/include" -DNDEBUG -I. -I../inst/include -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/RcppGSL/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c summary.cpp -o summary.o g++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o mvabund.so RcppExports.o Rinterface.o anova.o calctest.o glm.o glmtest.o io.o rnd.o simutility.o summary.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmptOfnco/R.INSTALL10ef22267c19d0/mvabund/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-mvabund/00new/mvabund/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 (mvabund) checking labdsv_2.1-2.tar.gz ... checking ecan_0.2.1.tar.gz ... checking fso_2.1-2.tar.gz ... checking maotai_0.2.6.tar.gz ... checking ecoCopula_1.0.2.tar.gz ... checking RVAideMemoire_0.9-83-12.tar.gz ... checking vegdata_0.9.12.tar.gz ... Depends: Package: labdsv Depends: R (>= 3.0), mgcv Imports: cluster, Rtsne, MASS Timings: user system elapsed labdsv 59.303 5.94 65.643 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 2 4 Check results summary: labdsv ... NOTE * checking Rd cross-references ... NOTE rdepends_ecan ... OK rdepends_ecoCopula ... NOTE * checking Rd cross-references ... NOTE rdepends_fso ... NOTE * checking Rd cross-references ... NOTE rdepends_maotai ... OK rdepends_RVAideMemoire ... OK rdepends_vegdata ... OK Check results changes: Package: ecoCopula Check: CRAN incoming feasibility Old result: NOTE Package: fso Check: CRAN incoming feasibility Old result: NOTE Package: vegdata Check: CRAN incoming feasibility Old result: NOTE