downloading reverse dependencies ‘tepr’, ‘gap’ trying URL 'file:///data/Repositories/CRAN/src/contrib/tepr_1.1.12.tar.gz' trying URL 'file:///data/Repositories/CRAN/src/contrib/gap_1.6.tar.gz' installing dependencies ‘BradleyTerry2’, ‘cpp11bigwig’, ‘DOT’, ‘genetics’, ‘manhattanly’, ‘pedigree’, ‘pedigreemm’, ‘valr’ Warning: package ‘manhattanly’ 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 dependency ‘HaploSim’ begin installing package ‘HaploSim’ begin installing package ‘cpp11bigwig’ begin installing package ‘BradleyTerry2’ begin installing package ‘DOT’ begin installing package ‘genetics’ begin installing package ‘pedigreemm’ * installing *source* package ‘DOT’ ... ** this is package ‘DOT’ version ‘0.1’ ** package ‘DOT’ 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 (DOT) * installing *source* package ‘HaploSim’ ... ** this is package ‘HaploSim’ version ‘1.8.4.2’ ** package ‘HaploSim’ 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 (HaploSim) begin installing package ‘pedigree’ * installing *source* package ‘genetics’ ... ** this is package ‘genetics’ version ‘1.3.8.1.3’ ** package ‘genetics’ 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 ** 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 (genetics) * installing *source* package ‘BradleyTerry2’ ... ** this is package ‘BradleyTerry2’ version ‘1.1.3’ ** package ‘BradleyTerry2’ 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 (BradleyTerry2) * installing *source* package ‘pedigreemm’ ... ** this is package ‘pedigreemm’ version ‘0.3-5’ ** package ‘pedigreemm’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3omE3N/R.INSTALL11824557c3a3f5/pedigreemm/src' gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/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-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pedigree.c -o pedigree.o gcc-15 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o pedigreemm.so init.o pedigree.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3omE3N/R.INSTALL11824557c3a3f5/pedigreemm/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigreemm/00new/pedigreemm/libs ** 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 ** 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 (pedigreemm) * installing *source* package ‘pedigree’ ... ** this is package ‘pedigree’ version ‘1.4.2’ ** package ‘pedigree’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-15 (Debian 15.2.0-9) 15.2.0’ using C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpDFk8TD/R.INSTALL11833e65457b09/pedigree/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c Pedigree.cpp -o Pedigree.o gcc-15 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c pedigree_init.c -o pedigree_init.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o pedigree.so Pedigree.o pedigree_init.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpDFk8TD/R.INSTALL11833e65457b09/pedigree/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-pedigree/00new/pedigree/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 (pedigree) * installing *source* package ‘cpp11bigwig’ ... ** this is package ‘cpp11bigwig’ version ‘0.1.2’ ** package ‘cpp11bigwig’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpU3Xn8Q/R.INSTALL11824d7267dfd5/cpp11bigwig/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cpp11.cpp -o cpp11.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cpp11bigwig.cpp -o cpp11bigwig.o (cd libBigWig; make) make[2]: Entering directory '/home/hornik/tmp/scratch/RtmpU3Xn8Q/R.INSTALL11824d7267dfd5/cpp11bigwig/src/libBigWig' gcc -c -Wall -O3 -DNOCURL -fpic bwRead.c -o bwRead.o gcc -c -Wall -O3 -DNOCURL -fpic bwStats.c -o bwStats.o gcc -c -Wall -O3 -DNOCURL -fpic bwValues.c -o bwValues.o gcc -c -Wall -O3 -DNOCURL -fpic bwWrite.c -o bwWrite.o gcc -c -Wall -O3 -DNOCURL -fpic io.c -o io.o ar rcs libBigWig.a bwRead.o bwStats.o bwValues.o bwWrite.o io.o make[2]: Leaving directory '/home/hornik/tmp/scratch/RtmpU3Xn8Q/R.INSTALL11824d7267dfd5/cpp11bigwig/src/libBigWig' g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o cpp11bigwig.so cpp11.o cpp11bigwig.o -L./libBigWig -lBigWig -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpU3Xn8Q/R.INSTALL11824d7267dfd5/cpp11bigwig/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-cpp11bigwig/00new/cpp11bigwig/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 (cpp11bigwig) begin installing package ‘valr’ * installing *source* package ‘valr’ ... ** this is package ‘valr’ version ‘0.9.0’ ** using staged installation ** libs using C++ compiler: ‘g++-15 (Debian 15.2.0-9) 15.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpyZ18bp/R.INSTALL11844046ef826/valr/src' g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c bed12toexons.cpp -o bed12toexons.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c closest.cpp -o closest.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c complement.cpp -o complement.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c coverage.cpp -o coverage.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c cpp11.cpp -o cpp11.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c dist.cpp -o dist.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c flank.cpp -o flank.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c gcoverage.cpp -o gcoverage.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c intersect.cpp -o intersect.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c makewindows.cpp -o makewindows.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c merge.cpp -o merge.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c partition.cpp -o partition.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c random.cpp -o random.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c shuffle.cpp -o shuffle.o g++-15 -std=gnu++17 -I"/home/hornik/tmp/R-d-gcc-15/include" -DNDEBUG -I../inst/include -I'/home/hornik/lib/R/Library/4.6/x86_64-linux-gnu/cpp11/include' -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -pedantic -mtune=native -c subtract.cpp -o subtract.o g++-15 -std=gnu++17 -shared -L/home/hornik/tmp/R-d-gcc-15/lib -Wl,-O1 -o valr.so bed12toexons.o closest.o complement.o coverage.o cpp11.o dist.o flank.o gcoverage.o intersect.o makewindows.o merge.o partition.o random.o shuffle.o subtract.o -L/home/hornik/tmp/R-d-gcc-15/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpyZ18bp/R.INSTALL11844046ef826/valr/src' installing to /home/hornik/tmp/CRAN_recheck/Library/00LOCK-valr/00new/valr/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (valr) checking valr_0.9.0.tar.gz ... checking tepr_1.1.12.tar.gz ... checking gap_1.6.tar.gz ... Depends: Package: valr Depends: R (>= 4.0.0) Imports: broom, cli, cpp11bigwig, dplyr (>= 0.8.0), ggplot2, lifecycle, readr, rlang, stringr, tibble (>= 1.4.2) LinkingTo: cpp11 Timings: user system elapsed valr 170.819 13.671 173.641 Results: Check status summary: NOTE OK Source packages 1 0 Reverse depends 0 2 Check results summary: valr ... NOTE * checking CRAN incoming feasibility ... [6s/8s] NOTE rdepends_gap ... OK rdepends_tepr ... OK