downloading reverse dependencies ... downloading AgroR_1.3.5.tar.gz ... ok downloading FSA_0.9.5.tar.gz ... ok downloading MultBiplotR_23.11.0.tar.gz ... ok downloading multiclassPairs_0.4.3.tar.gz ... ok downloading visxhclust_1.1.0.tar.gz ... ok installing dependencies ‘Boruta’, ‘dae’, ‘dunn.test’, ‘fishmethods’, ‘FSAdata’, ‘leukemiasEset’, ‘marked’, ‘Rcapture’, ‘shinyhelper’, ‘switchBox’ also installing the dependencies ‘R2admb’, ‘tryCatchLog’ begin installing package ‘R2admb’ begin installing package ‘tryCatchLog’ begin installing package ‘dunn.test’ begin installing package ‘fishmethods’ begin installing package ‘FSAdata’ begin installing package ‘Rcapture’ begin installing package ‘Boruta’ begin installing package ‘switchBox’ begin installing package ‘leukemiasEset’ begin installing package ‘shinyhelper’ * installing *source* package ‘shinyhelper’ ... ** package ‘shinyhelper’ 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 (shinyhelper) * installing *source* package ‘tryCatchLog’ ... ** package ‘tryCatchLog’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tryCatchLog) begin installing package ‘dae’ * installing *source* package ‘Boruta’ ... ** package ‘Boruta’ successfully unpacked and MD5 sums checked ** 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 (Boruta) * installing *source* package ‘dunn.test’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (dunn.test) * installing *source* package ‘leukemiasEset’ ... ** using staged installation ** data ** 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 (leukemiasEset) * installing *source* package ‘R2admb’ ... ** package ‘R2admb’ 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 (R2admb) begin installing package ‘marked’ * installing *source* package ‘FSAdata’ ... ** package ‘FSAdata’ 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 (FSAdata) * installing *source* package ‘switchBox’ ... ** using staged installation ** libs using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’ using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmpr6lzqm/R.INSTALL3cf6aa16bb373a/switchBox/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o CalculateSignedScoreCore.cc: In function ‘void CalculateSignedScoreCore(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*)’: CalculateSignedScoreCore.cc:36:26: warning: variable ‘pairsNo’ set but not used [-Wunused-but-set-variable] 36 | int i,j,l,countplace,pairsNo; | ^~~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreCoreTieHandler.cc: In function ‘void CalculateSignedScoreCoreTieHandler(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*)’: CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable ‘score1’ [-Wunused-variable] 49 | double score1, score2, type; | ^~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCore.cc: In function ‘void CalculateSignedScoreRestrictedPairsCore(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*)’: CalculateSignedScoreRestrictedPairsCore.cc:22:25: warning: variable ‘countplace’ set but not used [-Wunused-but-set-variable] 22 | int i,l,countplace,pairsNo; | ^~~~~~~~~~ g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o CalculateSignedScoreRestrictedPairsCoreTieHandler.cc: In function ‘void CalculateSignedScoreRestrictedPairsCoreTieHandler(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)’: CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:25: warning: unused variable ‘countplace’ [-Wunused-variable] 25 | int i,l,countplace,pairsNo; | ^~~~~~~~~~ CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:24: warning: unused variable ‘score1’ [-Wunused-variable] 35 | double score1, score2, type; | ^~~~~~ gcc-13 -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 rinit.c -o rinit.o g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c vect2compC.cc -o vect2compC.o g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o switchBox.so CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmpr6lzqm/R.INSTALL3cf6aa16bb373a/switchBox/src' installing to /home/hornik/tmp/CRAN/Library/00LOCK-switchBox/00new/switchBox/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 (switchBox) * installing *source* package ‘Rcapture’ ... ** package ‘Rcapture’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rcapture) * installing *source* package ‘dae’ ... ** package ‘dae’ successfully unpacked and MD5 sums checked ** 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 (dae) * installing *source* package ‘marked’ ... ** package ‘marked’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (Debian 13.2.0-13) 13.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 13.2.0-13) 13.2.0’ using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpPa6HPK/R.INSTALL3cf8252f3cd8f9/marked/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/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 bayesCR.cpp -o bayesCR.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs.f -o cjs.o cjs.f:9:25: 9 | DOUBLE PRECISION X,Y | 1 Warning: Unused variable ‘x’ declared at (1) [-Wunused-variable] cjs.f:9:27: 9 | DOUBLE PRECISION X,Y | 1 Warning: Unused variable ‘y’ declared at (1) [-Wunused-variable] gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs1tldmat.f -o cjs1tldmat.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs1tlgam.f -o cjs1tlgam.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs2tldmat.f -o cjs2tldmat.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjs2tlgam.f -o cjs2tlgam.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjsdmat.f -o cjsdmat.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c cjsgamma.f -o cjsgamma.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c hmm_like.f -o hmm_like.o gcc-13 -I"/home/hornik/tmp/R/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 -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c ms2gamma.f -o ms2gamma.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c msdmat.f -o msdmat.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c msgamma.f -o msgamma.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c mvmsdmat.f -o mvmsdmat.o mvmsdmat.f:1:55: 1 | SUBROUTINE MVMSP(P,DELTA,N,M,F,T,NP,NOBS,PCOUNTS,INDICES, | 1 Warning: Unused dummy argument ‘pcounts’ at (1) [-Wunused-dummy-argument] gfortran-13 -fpic -g -O2 -Wall -mtune=native -c ums2dmat.f -o ums2dmat.o gfortran-13 -fpic -g -O2 -Wall -mtune=native -c umsdmat.f -o umsdmat.o g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o marked.so bayesCR.o cjs.o cjs1tldmat.o cjs1tlgam.o cjs2tldmat.o cjs2tlgam.o cjsdmat.o cjsgamma.o hmm_like.o init.o ms2gamma.o msdmat.o msgamma.o mvmsdmat.o ums2dmat.o umsdmat.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpPa6HPK/R.INSTALL3cf8252f3cd8f9/marked/src' installing to /home/hornik/tmp/CRAN/Library/00LOCK-marked/00new/marked/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 (marked) * installing *source* package ‘fishmethods’ ... ** package ‘fishmethods’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9q68OI/R.INSTALL3cf69849acd7eb/fishmethods/src' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/TMB/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c init_dummy_file.cpp -o init_dummy_file.o (cd TMB; /home/hornik/tmp/R/bin/Rscript \ --no-save --no-restore compile.R '') Note: Using Makevars in /home/hornik/.R/Makevars-gcc using C++ compiler: ‘g++-13 (Debian 13.2.0-13) 13.2.0’ make[2]: Entering directory '/home/hornik/tmp/scratch/Rtmp9q68OI/R.INSTALL3cf69849acd7eb/fishmethods/src/TMB' g++-13 -std=gnu++17 -I"/home/hornik/tmp/R/include" -DNDEBUG -I"/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/TMB/include" -I"/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/RcppEigen/include" -DTMB_EIGEN_DISABLE_WARNINGS -DTMB_LIB_INIT=R_init_fishmethods_TMBExports -DCPPAD_FRAMEWORK -I'/home/hornik/lib/R/Library/4.5/x86_64-linux-gnu/TMB/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c fishmethods_TMBExports.cpp -o fishmethods_TMBExports.o g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o fishmethods_TMBExports.so fishmethods_TMBExports.o -L/home/hornik/tmp/R/lib -lR make[2]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9q68OI/R.INSTALL3cf69849acd7eb/fishmethods/src/TMB' [1] TRUE g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o fishmethods.so init_dummy_file.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9q68OI/R.INSTALL3cf69849acd7eb/fishmethods/src' installing to /home/hornik/tmp/CRAN/Library/00LOCK-fishmethods/00new/fishmethods/libs ** R ** data *** moving datasets to lazyload DB ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (fishmethods) checking dunn.test_1.3.6.tar.gz ... checking AgroR_1.3.5.tar.gz ... checking FSA_0.9.5.tar.gz ... checking MultBiplotR_23.11.0.tar.gz ... checking multiclassPairs_0.4.3.tar.gz ... checking visxhclust_1.1.0.tar.gz ... Depends: Timings: user system elapsed dunn.test 15.765 2.308 18.471 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 1 4 Check results summary: dunn.test ... NOTE * checking CRAN incoming feasibility ... [4s/5s] NOTE rdepends_AgroR ... OK rdepends_FSA ... NOTE * checking Rd files ... [1s/1s] NOTE rdepends_MultBiplotR ... OK rdepends_multiclassPairs ... OK rdepends_visxhclust ... OK