downloading reverse dependencies ‘bartMan’, ‘bartXViz’, ‘iBART’, ‘BayesTreePrior’, ‘condvis2’, ‘evalITR’, ‘MachineShop’, ‘SuperLearner’, ‘vivid’ trying URL 'file:///data/Repositories/CRAN/src/contrib/bartMan_0.2.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/bartXViz_1.0.9.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/iBART_1.0.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/BayesTreePrior_1.0.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/condvis2_0.1.2.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/evalITR_1.0.0.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/MachineShop_3.9.1.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/SuperLearner_2.0-40.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/vivid_0.3.0.tar.gz' installing dependencies ‘bartCause’, ‘bartMachine’, ‘BayesTree’, ‘biglasso’, ‘censored’, ‘condvis2’, ‘DendSer’, ‘flashlight’, ‘gggenes’, ‘glmnetUtils’, ‘LogicReg’, ‘lvplot’, ‘ParBayesianOptimization’, ‘rBayesianOptimization’, ‘rqPen’, ‘scagnostics’, ‘zenplots’ Warning: package ‘ParBayesianOptimization’ is not available for this version of R A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installing-packages also installing the dependencies ‘hqreg’, ‘hrqglas’, ‘MetricsWeighted’, ‘PairViz’ begin installing package ‘hqreg’ begin installing package ‘hrqglas’ begin installing package ‘MetricsWeighted’ begin installing package ‘PairViz’ begin installing package ‘DendSer’ begin installing package ‘lvplot’ begin installing package ‘gggenes’ begin installing package ‘BayesTree’ begin installing package ‘scagnostics’ begin installing package ‘glmnetUtils’ begin installing package ‘bartCause’ begin installing package ‘censored’ begin installing package ‘rBayesianOptimization’ begin installing package ‘biglasso’ begin installing package ‘LogicReg’ begin installing package ‘bartMachine’ * installing *source* package ‘MetricsWeighted’ ... ** this is package ‘MetricsWeighted’ version ‘1.0.4’ ** package ‘MetricsWeighted’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MetricsWeighted) begin installing package ‘flashlight’ * installing *source* package ‘rBayesianOptimization’ ... ** this is package ‘rBayesianOptimization’ version ‘1.2.2’ ** package ‘rBayesianOptimization’ 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 (rBayesianOptimization) * installing *source* package ‘scagnostics’ ... ** this is package ‘scagnostics’ version ‘0.2-6’ ** package ‘scagnostics’ 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 (scagnostics) * installing *source* package ‘DendSer’ ... ** this is package ‘DendSer’ version ‘1.0.2’ ** package ‘DendSer’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpHAUyoe/R.INSTALL2c3a184d685dc7/DendSer/src' gcc-15 -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 DendSer_init.c -o DendSer_init.o gcc-15 -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 carct.c -o carct.o gcc-15 -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 cbar.c -o cbar.o gcc-15 -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 clpl.c -o clpl.o gcc-15 -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 cpl.c -o cpl.o gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o DendSer.so DendSer_init.o carct.o cbar.o clpl.o cpl.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpHAUyoe/R.INSTALL2c3a184d685dc7/DendSer/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-DendSer/00new/DendSer/libs ** R ** demo ** byte-compile and prepare package for lazy loading Warning in seriation::set_criterion_method("dist", "BAR", criterion_method_dist_BAR, : Entry with name ‘BAR’ already exists! Modifying entry. ** 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 (DendSer) begin installing package ‘condvis2’ * installing *source* package ‘hqreg’ ... ** this is package ‘hqreg’ version ‘1.4-1’ ** package ‘hqreg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp9os6BY/R.INSTALL2c39ff3cee27f0/hqreg/src' gcc-15 -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 data_process.c -o data_process.o gcc-15 -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 hqreg.c -o hqreg.o gcc-15 -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-15 -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 ksav.c -o ksav.o gcc-15 -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 util.c -o util.o gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o hqreg.so data_process.o hqreg.o init.o ksav.o util.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp9os6BY/R.INSTALL2c39ff3cee27f0/hqreg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-hqreg/00new/hqreg/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hqreg) * installing *source* package ‘gggenes’ ... ** this is package ‘gggenes’ version ‘0.6.0’ ** package ‘gggenes’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (gggenes) * installing *source* package ‘bartCause’ ... ** this is package ‘bartCause’ version ‘1.0-10’ ** package ‘bartCause’ 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 (bartCause) * installing *source* package ‘PairViz’ ... ** this is package ‘PairViz’ version ‘1.3.6’ ** package ‘PairViz’ successfully unpacked and MD5 sums checked ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PairViz) begin installing package ‘zenplots’ * installing *source* package ‘hrqglas’ ... ** this is package ‘hrqglas’ version ‘1.1.2’ ** package ‘hrqglas’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp5RxX6O/R.INSTALL2c3a0615b010be/hrqglas/src' gcc-15 -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 hrqglas_init.c -o hrqglas_init.o gcc-15 -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 solveBeta.c -o solveBeta.o gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o hrqglas.so hrqglas_init.o solveBeta.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp5RxX6O/R.INSTALL2c3a0615b010be/hrqglas/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-hrqglas/00new/hrqglas/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (hrqglas) begin installing package ‘rqPen’ * installing *source* package ‘glmnetUtils’ ... ** this is package ‘glmnetUtils’ version ‘1.1.9’ ** package ‘glmnetUtils’ 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 (glmnetUtils) * installing *source* package ‘flashlight’ ... ** this is package ‘flashlight’ version ‘1.0.0’ ** package ‘flashlight’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (flashlight) * installing *source* package ‘bartMachine’ ... ** this is package ‘bartMachine’ version ‘1.4.1’ ** 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 (bartMachine) * installing *source* package ‘condvis2’ ... ** this is package ‘condvis2’ version ‘0.1.2’ ** package ‘condvis2’ 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 (condvis2) * installing *source* package ‘BayesTree’ ... ** this is package ‘BayesTree’ version ‘0.3-1.5’ ** package ‘BayesTree’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyvBN0q/R.INSTALL2c3a157127acd5/BayesTree/src' g++-15 -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 BirthDeath.cpp -o BirthDeath.o g++-15 -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 ChangeRule.cpp -o ChangeRule.o g++-15 -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 Funs.cpp -o Funs.o g++-15 -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 Lib.cpp -o Lib.o Lib.cpp: In static member function ‘static void Lib::sortedUnique(int, double*, Vec&)’: Lib.cpp:89:11: warning: unused variable ‘nu’ [-Wunused-variable] 89 | vec_sz nu = 1; | ^~ Lib.cpp: In static member function ‘static void Lib::acov(Vec&, int, Vec&, bool)’: Lib.cpp:114:32: warning: typedef ‘ST’ locally defined but not used [-Wunused-local-typedefs] 114 | typedef Vec::size_type ST; | ^~ g++-15 -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 Likelihood.cpp -o Likelihood.o g++-15 -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 List.cpp -o List.o g++-15 -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 MuS.cpp -o MuS.o g++-15 -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 Node.cpp -o Node.o Node.cpp: In member function ‘void Node::currentFits(MuS*, int, double**, double*, int, double**, double*, double**)’: Node.cpp:629:60: warning: ‘indPartTest’ may be used uninitialized [-Wmaybe-uninitialized] 629 | for(int j=1;j<=nTest;j++) {if(indPartTest[j]==i) fits[2][j]=nodeMu; } | ~~~~~~~~~~~~~^ Node.cpp:602:14: note: ‘indPartTest’ was declared here 602 | int* indPartTest; | ^~~~~~~~~~~ g++-15 -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 Prior.cpp -o Prior.o g++-15 -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 Rlob.cpp -o Rlob.o g++-15 -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 Swap.cpp -o Swap.o g++-15 -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 mbart.cpp -o mbart.o mbart.cpp: In function ‘void mbart(int*, int*, int*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, int*, int*, int*, int*, int*, int*, int*, int*, int*, double*, double*, double*, int*)’: mbart.cpp:386:10: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 386 | if(!binary) sdraw[scnt] = sd.getS(); scnt++; | ^~ mbart.cpp:386:47: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 386 | if(!binary) sdraw[scnt] = sd.getS(); scnt++; | ^~~~ mbart.cpp:300:11: warning: variable ‘alpha’ set but not used [-Wunused-but-set-variable] 300 | double alpha=0.0; | ^~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o BayesTree.so BirthDeath.o ChangeRule.o Funs.o Lib.o Likelihood.o List.o MuS.o Node.o Prior.o Rlob.o Swap.o mbart.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyvBN0q/R.INSTALL2c3a157127acd5/BayesTree/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-BayesTree/00new/BayesTree/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (BayesTree) * installing *source* package ‘LogicReg’ ... ** this is package ‘LogicReg’ version ‘1.6.6’ ** package ‘LogicReg’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ using Fortran compiler: ‘GNU Fortran (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdsZm2M/R.INSTALL2c3a262a846b4d/LogicReg/src' gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c Myownscoring.f -o Myownscoring.o gcc-15 -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 clogic.c -o clogic.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c external.f -o external.o gcc-15 -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 registerDynamicSymbol.c -o registerDynamicSymbol.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c sextra.f -o sextra.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c slogic.f -o slogic.o gcc-15 -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 swrite.c -o swrite.o gfortran-15 -fpic -g -O2 -Wall -pedantic -mtune=native -c trioLR.f -o trioLR.o gcc-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o LogicReg.so Myownscoring.o clogic.o external.o registerDynamicSymbol.o sextra.o slogic.o swrite.o trioLR.o -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdsZm2M/R.INSTALL2c3a262a846b4d/LogicReg/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-LogicReg/00new/LogicReg/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 (LogicReg) * installing *source* package ‘censored’ ... ** this is package ‘censored’ version ‘0.3.3’ ** package ‘censored’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** 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 (censored) * installing *source* package ‘zenplots’ ... ** this is package ‘zenplots’ version ‘1.0.7’ ** package ‘zenplots’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3hseaQ/R.INSTALL2c3d5b10b66868/zenplots/src' gcc-15 -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 col_split.c -o col_split.o gcc-15 -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-15 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o zenplots.so col_split.o init.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3hseaQ/R.INSTALL2c3d5b10b66868/zenplots/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-zenplots/00new/zenplots/libs ** R ** data ** demo ** 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 (zenplots) * installing *source* package ‘rqPen’ ... ** this is package ‘rqPen’ version ‘4.1.4’ ** package ‘rqPen’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpCA9gul/R.INSTALL2c3d883ec9c5b5/rqPen/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c RcppExports.cpp -o RcppExports.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c solvebetaRcpp.cpp -o solvebetaRcpp.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o rqPen.so RcppExports.o solvebetaRcpp.o -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpCA9gul/R.INSTALL2c3d883ec9c5b5/rqPen/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-rqPen/00new/rqPen/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 (rqPen) * installing *source* package ‘lvplot’ ... ** this is package ‘lvplot’ version ‘0.2.2’ ** package ‘lvplot’ 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 (lvplot) * installing *source* package ‘biglasso’ ... ** this is package ‘biglasso’ version ‘1.6.1’ ** package ‘biglasso’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-12) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-12) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp64Pcyd/R.INSTALL2c3a1d5e42b8b7/biglasso/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/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++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c binomial.cpp -o binomial.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from utilities.h:13, from binomial.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/current/armadillo:38, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:32, from utilities.h:12: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ binomial.cpp: In function ‘SEXPREC* cdfit_binomial_ssr_approx(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: binomial.cpp:694:34: warning: ‘sumS’ may be used uninitialized [-Wmaybe-uninitialized] 694 | violations = check_rest_set(e1, e2, z, xMat, row_idx, col_idx,center, scale, a, lambda[l], sumS, alpha, s, m, n, p); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ binomial.cpp:544:10: note: ‘sumS’ was declared here 544 | double sumS; // temp result sum of s | ^~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cox.cpp -o cox.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from utilities.h:13, from cox.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/current/armadillo:38, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:32, from utilities.h:12: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ cox.cpp: In function ‘_Z9safe_initRSt6vectorIdSaIdEEN4Rcpp4XPtrI9BigMatrixNS3_15PreserveStorageEXadL_ZNS3_25standard_delete_finalizerIS5_EEvPT_EELb0EEEPdSB_S2_iPiRS_IiSaIiEERNS3_6VectorILi14ES6_EESI_iiiSB_SB_SC_._omp_fn.0’: cox.cpp:92:26: warning: ‘xTy’ may be used uninitialized [-Wmaybe-uninitialized] 92 | if(y[i] > 0) xTy += xCol[row_idx[i]]; | ~~~~^~~~~~~~~~~~~~~~~~~ cox.cpp:78:10: note: ‘xTy’ was declared here 78 | double xTy = 0; | ^~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c gaussian.cpp -o gaussian.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from utilities.h:13, from gaussian.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/current/armadillo:38, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:32, from utilities.h:12: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c gaussian_simple.cpp -o gaussian_simple.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from utilities.h:13, from gaussian_simple.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/current/armadillo:38, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:32, from utilities.h:12: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ gcc-15 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/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 g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c mgaussian.cpp -o mgaussian.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from utilities.h:13, from mgaussian.cpp:1: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/current/armadillo:38, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:32, from utilities.h:12: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -I"/home/hornik/tmp/R/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/bigmemory/include' -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c utilities.cpp -o utilities.o In file included from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/shared_ptr.hpp:17, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/bigmemory/include/bigmemory/BigMatrix.h:10, from utilities.h:13, from utilities.cpp:10: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/detail/shared_count.hpp:294:33: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 294 | explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) | ^~~~~~~~ In file included from /usr/include/c++/15/memory:80, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/current/armadillo:38, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57, from /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/RcppArmadillo/include/RcppArmadillo.h:32, from utilities.h:12: /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:354:31: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 354 | explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:365:22: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 365 | shared_ptr( std::auto_ptr && r ): px(r.get()), pn() | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:423:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 423 | shared_ptr & operator=( std::auto_ptr & r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:430:34: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 430 | shared_ptr & operator=( std::auto_ptr && r ) | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/BH/include/boost/smart_ptr/shared_ptr.hpp:432:38: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 432 | this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); | ^~~~~~~~ /usr/include/c++/15/bits/unique_ptr.h:58:28: note: declared here 58 | template class auto_ptr; | ^~~~~~~~ g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R/lib -Wl,-O1 -o biglasso.so RcppExports.o binomial.o cox.o gaussian.o gaussian_simple.o init.o mgaussian.o utilities.o -fopenmp -llapack -L/home/hornik/tmp/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp64Pcyd/R.INSTALL2c3a1d5e42b8b7/biglasso/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-biglasso/00new/biglasso/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 (biglasso) checking bartMachine_1.4.1.tar.gz ... checking bartMan_0.2.1.tar.gz ... checking bartXViz_1.0.9.tar.gz ... checking iBART_1.0.0.tar.gz ... checking BayesTreePrior_1.0.1.tar.gz ... checking condvis2_0.1.2.tar.gz ... checking evalITR_1.0.0.tar.gz ... checking MachineShop_3.9.1.tar.gz ... checking SuperLearner_2.0-40.tar.gz ... checking vivid_0.3.0.tar.gz ... Depends: Package: bartMachine Depends: R (>= 2.14.0) Imports: bartMachineJARs (>= 1.2.2), rJava, randomForest, missForest, stats, ggplot2, grid, checkmate, matrixStats, grDevices Timings: user system elapsed bartMachine 66.686 6.992 76.473 Results: Check status summary: ERROR NOTE OK Source packages 0 1 0 Reverse depends 1 2 6 Check results summary: bartMachine ... NOTE * checking CRAN incoming feasibility ... [5s/7s] NOTE rdepends_bartMan ... OK rdepends_bartXViz ... OK rdepends_BayesTreePrior ... NOTE * checking Rd files ... [0s/0s] NOTE rdepends_condvis2 ... OK rdepends_evalITR ... OK rdepends_iBART ... ERROR * checking re-building of vignette outputs ... [33s/33s] ERROR rdepends_MachineShop ... NOTE * checking Rd cross-references ... NOTE rdepends_SuperLearner ... OK rdepends_vivid ... OK Check results changes: Package: BayesTreePrior Check: CRAN incoming feasibility Old result: NOTE Package: evalITR Check: CRAN incoming feasibility Old result: NOTE Package: iBART Check: CRAN incoming feasibility Old result: NOTE