downloading reverse dependencies ... downloading aroma.cn_1.7.1.tar.gz ... ok downloading aroma.core_3.3.1.tar.gz ... ok downloading EstMix_1.0.1.tar.gz ... ok downloading jointseg_1.0.2.tar.gz ... ok installing dependencies ‘acnr’, ‘aroma.core’, ‘aroma.light’, ‘expectile’, ‘GLAD’, ‘HaarSeg’, ‘mpcbs’, ‘PSCBS’, ‘R.filesets’, ‘sfit’ Warning: packages ‘sfit’, ‘expectile’, ‘HaarSeg’, ‘mpcbs’ are not available for this version of R Versions of these packages 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 ‘awsMethods’, ‘aws’ begin installing package ‘awsMethods’ begin installing package ‘aroma.light’ begin installing package ‘R.filesets’ begin installing package ‘acnr’ * installing *source* package ‘acnr’ ... ** this is package ‘acnr’ version ‘1.0.0’ ** package ‘acnr’ 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 (acnr) * installing *source* package ‘awsMethods’ ... ** this is package ‘awsMethods’ version ‘1.1-1’ ** package ‘awsMethods’ 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/RtmpWavCWS/R.INSTALL3694ab758e7096/awsMethods/src' gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c omp_funcs.c -o omp_funcs.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o awsMethods.so init.o omp_funcs.o -fopenmp -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpWavCWS/R.INSTALL3694ab758e7096/awsMethods/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-awsMethods/00new/awsMethods/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 (awsMethods) begin installing package ‘aws’ * installing *source* package ‘aroma.light’ ... ** this is package ‘aroma.light’ version ‘3.38.0’ ** 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 (aroma.light) begin installing package ‘PSCBS’ * installing *source* package ‘R.filesets’ ... ** this is package ‘R.filesets’ version ‘2.15.1’ ** package ‘R.filesets’ 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 (R.filesets) * installing *source* package ‘PSCBS’ ... ** this is package ‘PSCBS’ version ‘0.68.0’ ** 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 (PSCBS) begin installing package ‘aroma.core’ * installing *source* package ‘aws’ ... ** this is package ‘aws’ version ‘2.5-6’ ** package ‘aws’ 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/RtmpqHqRNz/R.INSTALL36953f9b36e8c/aws/src' gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ICIsmooth.f -o ICIsmooth.o gcc-14 -std=gnu23 -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 Rentries.c -o Rentries.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awslp.f -o awslp.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c awswghts.f -o awswghts.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c caws.f -o caws.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c cawsmask.f -o cawsmask.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c esiglike.f -o esiglike.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c estimateComplexSigma.f -o estimateComplexSigma.o gcc-14 -std=gnu23 -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 init.c -o init.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c misc.f -o misc.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c nlmeans.f -o nlmeans.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c pcaws.f -o pcaws.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c segment.f -o segment.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smooth3d.f -o smooth3d.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c smse3.f -o smse3.o gfortran-14 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c varest.f -o varest.o gcc-14 -std=gnu23 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o aws.so ICIsmooth.o Rentries.o awslp.o awswghts.o caws.o cawsmask.o esiglike.o estimateComplexSigma.o init.o misc.o nlmeans.o pcaws.o segment.o smooth3d.o smse3.o varest.o -fopenmp -llapack -L/home/hornik/tmp/R-d-gcc-14/lib -lRblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpqHqRNz/R.INSTALL36953f9b36e8c/aws/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-aws/00new/aws/libs ** 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 ** 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 (aws) begin installing package ‘GLAD’ * installing *source* package ‘GLAD’ ... ** this is package ‘GLAD’ version ‘2.72.0’ ** using staged installation checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... yes GSL has been found on the operating system operating system: Linux configure: creating ./config.status config.status: creating src/Makevars src/Makevars file PKG_LIBS = -lgsl -lgslcblas -lm PKG_CPPFLAGS = -I/usr/local/include ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-19) 14.2.0’ using C++ compiler: ‘g++-14 (Debian 14.2.0-19) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpdjB7vk/R.INSTALL3696411c0860bc/GLAD/src' g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c BkpInfo.cpp -o BkpInfo.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c HaarSeg.cpp -o HaarSeg.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c MoveBkp.cpp -o MoveBkp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c OutliersGNL.cpp -o OutliersGNL.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c chrBreakpoints.cpp -o chrBreakpoints.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cutree.cpp -o cutree.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c daglad.cpp -o daglad.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c distance.cpp -o distance.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c filterBkp.cpp -o filterBkp.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c findCluster.cpp -o findCluster.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c glad-utils.cpp -o glad-utils.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c hclust.cpp -o hclust.o gcc-14 -std=gnu23 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c laws.c -o laws.o g++-14 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c loopRemove.cpp -o loopRemove.o g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -lgsl -lgslcblas -lm -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpdjB7vk/R.INSTALL3696411c0860bc/GLAD/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-GLAD/00new/GLAD/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 (GLAD) * installing *source* package ‘aroma.core’ ... ** this is package ‘aroma.core’ version ‘3.3.1’ ** package ‘aroma.core’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning in setGenericS3.default(name, export = exportGeneric, envir = envir, : Renamed the preexisting function write to write.default, which was defined in environment aroma.core. ** 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 (aroma.core) checking PSCBS_0.68.0.tar.gz ... checking aroma.cn_1.7.1.tar.gz ... checking aroma.core_3.3.1.tar.gz ... checking EstMix_1.0.1.tar.gz ... checking jointseg_1.0.2.tar.gz ... Depends: Package: PSCBS Depends: R (>= 3.2.0) Imports: R.methodsS3 (>= 1.8.2), R.oo (>= 1.25.0), R.utils (>= 2.12.0), R.cache (>= 0.16.0), matrixStats (>= 0.62.0), aroma.light (>= 2.4.0), DNAcopy (>= 1.42.0), future (>= 1.28.0), parallel, graphics, grDevices, stats, utils Timings: user system elapsed PSCBS 148.511 7.867 161.722 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 1 3 Check results summary: PSCBS ... OK rdepends_aroma.cn ... OK rdepends_aroma.core ... NOTE * checking Rd cross-references ... NOTE rdepends_EstMix ... OK rdepends_jointseg ... OK