[ Started: 2023-12-06 12:03:27 CET ] [ CARNIVAL v2.7.2 for BioC-3.17 from https://github.com/saezlab/CARNIVAL@master ] [1] "Libraries: " "/home/omnipath/local/R/4.3-3.17" [3] "/home/omnipath/local/R/4.3" "/usr/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/vroom_1.6.5.tar.gz' Content type 'application/x-gzip' length 750416 bytes (732 KB) ================================================== downloaded 732 KB * installing *source* package ‘vroom’ ... ** package ‘vroom’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Iconv.cpp -o Iconv.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c LocaleInfo.cpp -o LocaleInfo.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c altrep.cc -o altrep.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cpp11.cpp -o cpp11.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delimited_index.cc -o delimited_index.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c delimited_index_connection.cc -o delimited_index_connection.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fixed_width_index_connection.cc -o fixed_width_index_connection.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gen.cc -o gen.o gcc -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c grisu3.c -o grisu3.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c guess_type.cc -o guess_type.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c iconv_file.cc -o iconv_file.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c index_collection.cc -o index_collection.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom.cc -o vroom.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_big_int.cc -o vroom_big_int.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_chr.cc -o vroom_chr.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_date.cc -o vroom_date.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_dbl.cc -o vroom_dbl.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_dttm.cc -o vroom_dttm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_errors.cpp -o vroom_errors.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_fct.cc -o vroom_fct.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_fwf.cc -o vroom_fwf.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_int.cc -o vroom_int.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_num.cc -o vroom_num.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_rle.cc -o vroom_rle.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_time.cc -o vroom_time.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Imio/include -DWIN32_LEAN_AND_MEAN -Ispdlog/include -DFMT_HEADER_ONLY -I'/home/omnipath/local/R/4.3-3.17/cpp11/include' -I'/home/omnipath/local/R/4.3-3.17/progress/include' -I'/home/omnipath/local/R/4.3-3.17/tzdb/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c vroom_write.cc -o vroom_write.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o vroom.so Iconv.o LocaleInfo.o altrep.o cpp11.o delimited_index.o delimited_index_connection.o fixed_width_index_connection.o gen.o grisu3.o guess_type.o iconv_file.o index_collection.o vroom.o vroom_big_int.o vroom_chr.o vroom_date.o vroom_dbl.o vroom_dttm.o vroom_errors.o vroom_fct.o vroom_fwf.o vroom_int.o vroom_num.o vroom_rle.o vroom_time.o vroom_write.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-vroom/00new/vroom/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 (vroom) The downloaded source packages are in ‘/tmp/Rtmpp6kBak/downloaded_packages’ Bioconductor version '3.17' is out-of-date; the current release version '3.18' is available with R version '4.3'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Old packages: 'e1071', 'htmlwidgets', 'httpuv', 'later', 'sass', 'sets', 'xgboost' trying URL 'https://cloud.r-project.org/src/contrib/e1071_1.7-14.tar.gz' Content type 'application/x-gzip' length 326383 bytes (318 KB) ================================================== downloaded 318 KB trying URL 'https://cloud.r-project.org/src/contrib/htmlwidgets_1.6.4.tar.gz' Content type 'application/x-gzip' length 868895 bytes (848 KB) ================================================== downloaded 848 KB trying URL 'https://cloud.r-project.org/src/contrib/httpuv_1.6.13.tar.gz' Content type 'application/x-gzip' length 1879156 bytes (1.8 MB) ================================================== downloaded 1.8 MB trying URL 'https://cloud.r-project.org/src/contrib/later_1.3.2.tar.gz' Content type 'application/x-gzip' length 63597 bytes (62 KB) ================================================== downloaded 62 KB trying URL 'https://cloud.r-project.org/src/contrib/sass_0.4.8.tar.gz' Content type 'application/x-gzip' length 3025474 bytes (2.9 MB) ================================================== downloaded 2.9 MB trying URL 'https://cloud.r-project.org/src/contrib/sets_1.0-25.tar.gz' Content type 'application/x-gzip' length 275340 bytes (268 KB) ================================================== downloaded 268 KB trying URL 'https://cloud.r-project.org/src/contrib/xgboost_1.7.6.1.tar.gz' Content type 'application/x-gzip' length 1086571 bytes (1.0 MB) ================================================== downloaded 1.0 MB * installing *source* package ‘e1071’ ... ** package ‘e1071’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Rsvm.c -o Rsvm.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cmeans.c -o cmeans.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cshell.c -o cshell.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c floyd.c -o floyd.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c svm.cpp -o svm.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o e1071.so Rsvm.o cmeans.o cshell.o floyd.o init.o svm.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-e1071/00new/e1071/libs ** 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 ** 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 (e1071) * installing *source* package ‘htmlwidgets’ ... ** package ‘htmlwidgets’ 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 (htmlwidgets) * installing *source* package ‘later’ ... ** package ‘later’ successfully unpacked and MD5 sums checked ** using staged installation Running configure script -latomic linker flag not needed. ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callback_registry.cpp -o callback_registry.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c debug.cpp -o debug.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c later.cpp -o later.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c later_posix.cpp -o later_posix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c later_win32.cpp -o later_win32.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c timer_posix.cpp -o timer_posix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c timestamp_unix.cpp -o timestamp_unix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c timestamp_win32.cpp -o timestamp_win32.o gcc -I"/usr/share/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tinycthread.c -o tinycthread.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-later/00new/later/libs ** 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 ** 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 (later) * installing *source* package ‘sass’ ... ** package ‘sass’ successfully unpacked and MD5 sums checked ** using staged installation ** libs /usr/share/R/share/make/shlib.mk:18: warning: overriding recipe for target 'shlib-clean' Makevars:12: warning: ignoring old recipe for target 'shlib-clean' using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ /usr/share/R/share/make/shlib.mk:18: warning: overriding recipe for target 'shlib-clean' Makevars:12: warning: ignoring old recipe for target 'shlib-clean' gcc -I"/usr/share/R/include" -DNDEBUG -I./libsass/include -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compile.c -o compile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./libsass/include -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.cpp -o init.o MAKEFLAGS= CC="gcc" CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 " CXX="g++ -std=gnu++17" AR="ar" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro" make -C libsass make[1]: Entering directory '/tmp/RtmpsJdzy8/R.INSTALL2ab6525d765508/sass/src/libsass' gcc -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -I ./include -fPIC -c -o src/cencode.o src/cencode.c g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast.o src/ast.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_values.o src/ast_values.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_supports.o src/ast_supports.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_cmp.o src/ast_sel_cmp.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_unify.o src/ast_sel_unify.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_super.o src/ast_sel_super.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_sel_weave.o src/ast_sel_weave.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_selectors.o src/ast_selectors.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/context.o src/context.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/constants.o src/constants.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_utils.o src/fn_utils.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_miscs.o src/fn_miscs.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_maps.o src/fn_maps.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_lists.o src/fn_lists.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_colors.o src/fn_colors.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_numbers.o src/fn_numbers.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_strings.o src/fn_strings.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/fn_selectors.o src/fn_selectors.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/color_maps.o src/color_maps.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/environment.o src/environment.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast_fwd_decl.o src/ast_fwd_decl.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/bind.o src/bind.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/file.o src/file.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/util.o src/util.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/util_string.o src/util_string.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/json.o src/json.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/units.o src/units.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/values.o src/values.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/plugins.o src/plugins.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/source.o src/source.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/position.o src/position.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/lexer.o src/lexer.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/parser.o src/parser.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/parser_selectors.o src/parser_selectors.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/prelexer.o src/prelexer.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/eval.o src/eval.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/eval_selectors.o src/eval_selectors.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/expand.o src/expand.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/listize.o src/listize.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/cssize.o src/cssize.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/extender.o src/extender.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/extension.o src/extension.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/stylesheet.o src/stylesheet.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/output.o src/output.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/inspect.o src/inspect.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/emitter.o src/emitter.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/check_nesting.o src/check_nesting.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/remove_placeholders.o src/remove_placeholders.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass.o src/sass.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_values.o src/sass_values.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_context.o src/sass_context.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass_functions.o src/sass_functions.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/sass2scss.o src/sass2scss.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/backtrace.o src/backtrace.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/operators.o src/operators.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/ast2c.o src/ast2c.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/c2ast.o src/c2ast.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/to_value.o src/to_value.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/source_map.o src/source_map.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/error_handling.o src/error_handling.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/allocator.o src/memory/allocator.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/memory/shared_ptr.o src/memory/shared_ptr.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/utf8_string.o src/utf8_string.cpp g++ -std=gnu++17 -Wall -O2 -std=c++11 -I ./include -fPIC -c -o src/base64vlq.o src/base64vlq.cpp mkdir lib ar rcvs lib/libsass.a src/cencode.o src/ast.o src/ast_values.o src/ast_supports.o src/ast_sel_cmp.o src/ast_sel_unify.o src/ast_sel_super.o src/ast_sel_weave.o src/ast_selectors.o src/context.o src/constants.o src/fn_utils.o src/fn_miscs.o src/fn_maps.o src/fn_lists.o src/fn_colors.o src/fn_numbers.o src/fn_strings.o src/fn_selectors.o src/color_maps.o src/environment.o src/ast_fwd_decl.o src/bind.o src/file.o src/util.o src/util_string.o src/json.o src/units.o src/values.o src/plugins.o src/source.o src/position.o src/lexer.o src/parser.o src/parser_selectors.o src/prelexer.o src/eval.o src/eval_selectors.o src/expand.o src/listize.o src/cssize.o src/extender.o src/extension.o src/stylesheet.o src/output.o src/inspect.o src/emitter.o src/check_nesting.o src/remove_placeholders.o src/sass.o src/sass_values.o src/sass_context.o src/sass_functions.o src/sass2scss.o src/backtrace.o src/operators.o src/ast2c.o src/c2ast.o src/to_value.o src/source_map.o src/error_handling.o src/memory/allocator.o src/memory/shared_ptr.o src/utf8_string.o src/base64vlq.o a - src/cencode.o a - src/ast.o a - src/ast_values.o a - src/ast_supports.o a - src/ast_sel_cmp.o a - src/ast_sel_unify.o a - src/ast_sel_super.o a - src/ast_sel_weave.o a - src/ast_selectors.o a - src/context.o a - src/constants.o a - src/fn_utils.o a - src/fn_miscs.o a - src/fn_maps.o a - src/fn_lists.o a - src/fn_colors.o a - src/fn_numbers.o a - src/fn_strings.o a - src/fn_selectors.o a - src/color_maps.o a - src/environment.o a - src/ast_fwd_decl.o a - src/bind.o a - src/file.o a - src/util.o a - src/util_string.o a - src/json.o a - src/units.o a - src/values.o a - src/plugins.o a - src/source.o a - src/position.o a - src/lexer.o a - src/parser.o a - src/parser_selectors.o a - src/prelexer.o a - src/eval.o a - src/eval_selectors.o a - src/expand.o a - src/listize.o a - src/cssize.o a - src/extender.o a - src/extension.o a - src/stylesheet.o a - src/output.o a - src/inspect.o a - src/emitter.o a - src/check_nesting.o a - src/remove_placeholders.o a - src/sass.o a - src/sass_values.o a - src/sass_context.o a - src/sass_functions.o a - src/sass2scss.o a - src/backtrace.o a - src/operators.o a - src/ast2c.o a - src/c2ast.o a - src/to_value.o a - src/source_map.o a - src/error_handling.o a - src/memory/allocator.o a - src/memory/shared_ptr.o a - src/utf8_string.o a - src/base64vlq.o make[1]: Leaving directory '/tmp/RtmpsJdzy8/R.INSTALL2ab6525d765508/sass/src/libsass' g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sass.so compile.o init.o ./libsass/lib/libsass.a -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-sass/00new/sass/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 (sass) * installing *source* package ‘sets’ ... ** package ‘sets’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c closure.c -o closure.o gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o sets.so closure.o init.o -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-sets/00new/sets/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 (sets) * installing *source* package ‘xgboost’ ... ** package ‘xgboost’ successfully unpacked and MD5 sums checked ** using staged installation checking Backtrace lib... checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ -std=gnu++17 accepts -g... yes checking for g++ -std=gnu++17 option to enable C++11 features... none needed checking for backtrace in -lexecinfo... no checking endian... configure: creating ./config.status config.status: creating src/Makevars ** libs Makevars:17: -DXGBOOST_STRICT_R_MODE=1 Makevars:17: -DDMLC_LOG_BEFORE_THROW=0 Makevars:17: -DDMLC_ENABLE_STD_THREAD=1 Makevars:17: -DDMLC_DISABLE_STDIN=1 Makevars:17: -DDMLC_LOG_CUSTOMIZE=1 Makevars:17: -DXGBOOST_CUSTOMIZE_LOGGER=1 Makevars:17: -DRABIT_CUSTOMIZE_MSG_ using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++17 Makevars:17: -DXGBOOST_STRICT_R_MODE=1 Makevars:17: -DDMLC_LOG_BEFORE_THROW=0 Makevars:17: -DDMLC_ENABLE_STD_THREAD=1 Makevars:17: -DDMLC_DISABLE_STDIN=1 Makevars:17: -DDMLC_LOG_CUSTOMIZE=1 Makevars:17: -DXGBOOST_CUSTOMIZE_LOGGER=1 Makevars:17: -DRABIT_CUSTOMIZE_MSG_ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c xgboost_R.cc -o xgboost_R.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c xgboost_custom.cc -o xgboost_custom.o gcc -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/metric/metric.cc -o src/metric/metric.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/metric/elementwise_metric.cc -o src/metric/elementwise_metric.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/metric/multiclass_metric.cc -o src/metric/multiclass_metric.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/metric/rank_metric.cc -o src/metric/rank_metric.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/metric/auc.cc -o src/metric/auc.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/metric/survival_metric.cc -o src/metric/survival_metric.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/objective.cc -o src/objective/objective.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/regression_obj.cc -o src/objective/regression_obj.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/multiclass_obj.cc -o src/objective/multiclass_obj.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/rank_obj.cc -o src/objective/rank_obj.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/hinge.cc -o src/objective/hinge.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/aft_obj.cc -o src/objective/aft_obj.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/objective/adaptive.cc -o src/objective/adaptive.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gbm/gbm.cc -o src/gbm/gbm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gbm/gbtree.cc -o src/gbm/gbtree.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gbm/gbtree_model.cc -o src/gbm/gbtree_model.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gbm/gblinear.cc -o src/gbm/gblinear.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/gbm/gblinear_model.cc -o src/gbm/gblinear_model.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/simple_dmatrix.cc -o src/data/simple_dmatrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/data.cc -o src/data/data.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/sparse_page_raw_format.cc -o src/data/sparse_page_raw_format.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/ellpack_page.cc -o src/data/ellpack_page.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/gradient_index.cc -o src/data/gradient_index.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/gradient_index_page_source.cc -o src/data/gradient_index_page_source.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/gradient_index_format.cc -o src/data/gradient_index_format.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/sparse_page_dmatrix.cc -o src/data/sparse_page_dmatrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/proxy_dmatrix.cc -o src/data/proxy_dmatrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/data/iterative_dmatrix.cc -o src/data/iterative_dmatrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/predictor/predictor.cc -o src/predictor/predictor.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/predictor/cpu_predictor.cc -o src/predictor/cpu_predictor.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/constraints.cc -o src/tree/constraints.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/param.cc -o src/tree/param.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/tree_model.cc -o src/tree/tree_model.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/tree_updater.cc -o src/tree/tree_updater.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/updater_approx.cc -o src/tree/updater_approx.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/updater_colmaker.cc -o src/tree/updater_colmaker.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/updater_prune.cc -o src/tree/updater_prune.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/updater_quantile_hist.cc -o src/tree/updater_quantile_hist.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/updater_refresh.cc -o src/tree/updater_refresh.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/tree/updater_sync.cc -o src/tree/updater_sync.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/linear/linear_updater.cc -o src/linear/linear_updater.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/linear/updater_coordinate.cc -o src/linear/updater_coordinate.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/linear/updater_shotgun.cc -o src/linear/updater_shotgun.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/learner.cc -o src/learner.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/logging.cc -o src/logging.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/global_config.cc -o src/global_config.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/collective/communicator.cc -o src/collective/communicator.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/collective/socket.cc -o src/collective/socket.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/charconv.cc -o src/common/charconv.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/column_matrix.cc -o src/common/column_matrix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/common.cc -o src/common/common.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/hist_util.cc -o src/common/hist_util.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/host_device_vector.cc -o src/common/host_device_vector.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/io.cc -o src/common/io.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/json.cc -o src/common/json.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/numeric.cc -o src/common/numeric.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/pseudo_huber.cc -o src/common/pseudo_huber.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/quantile.cc -o src/common/quantile.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/random.cc -o src/common/random.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/survival_util.cc -o src/common/survival_util.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/threading_utils.cc -o src/common/threading_utils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/timer.cc -o src/common/timer.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/common/version.cc -o src/common/version.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/c_api/c_api.cc -o src/c_api/c_api.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c src/c_api/c_api_error.cc -o src/c_api/c_api_error.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c amalgamation/dmlc-minimum0.cc -o amalgamation/dmlc-minimum0.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rabit/src/engine.cc -o rabit/src/engine.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rabit/src/rabit_c_api.cc -o rabit/src/rabit_c_api.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -fvisibility=hidden -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rabit/src/allreduce_base.cc -o rabit/src/allreduce_base.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o xgboost.so ./xgboost_R.o ./xgboost_custom.o ./init.o ./src/metric/metric.o ./src/metric/elementwise_metric.o ./src/metric/multiclass_metric.o ./src/metric/rank_metric.o ./src/metric/auc.o ./src/metric/survival_metric.o ./src/objective/objective.o ./src/objective/regression_obj.o ./src/objective/multiclass_obj.o ./src/objective/rank_obj.o ./src/objective/hinge.o ./src/objective/aft_obj.o ./src/objective/adaptive.o ./src/gbm/gbm.o ./src/gbm/gbtree.o ./src/gbm/gbtree_model.o ./src/gbm/gblinear.o ./src/gbm/gblinear_model.o ./src/data/simple_dmatrix.o ./src/data/data.o ./src/data/sparse_page_raw_format.o ./src/data/ellpack_page.o ./src/data/gradient_index.o ./src/data/gradient_index_page_source.o ./src/data/gradient_index_format.o ./src/data/sparse_page_dmatrix.o ./src/data/proxy_dmatrix.o ./src/data/iterative_dmatrix.o ./src/predictor/predictor.o ./src/predictor/cpu_predictor.o ./src/tree/constraints.o ./src/tree/param.o ./src/tree/tree_model.o ./src/tree/tree_updater.o ./src/tree/updater_approx.o ./src/tree/updater_colmaker.o ./src/tree/updater_prune.o ./src/tree/updater_quantile_hist.o ./src/tree/updater_refresh.o ./src/tree/updater_sync.o ./src/linear/linear_updater.o ./src/linear/updater_coordinate.o ./src/linear/updater_shotgun.o ./src/learner.o ./src/logging.o ./src/global_config.o ./src/collective/communicator.o ./src/collective/socket.o ./src/common/charconv.o ./src/common/column_matrix.o ./src/common/common.o ./src/common/hist_util.o ./src/common/host_device_vector.o ./src/common/io.o ./src/common/json.o ./src/common/numeric.o ./src/common/pseudo_huber.o ./src/common/quantile.o ./src/common/random.o ./src/common/survival_util.o ./src/common/threading_utils.o ./src/common/timer.o ./src/common/version.o ./src/c_api/c_api.o ./src/c_api/c_api_error.o ./amalgamation/dmlc-minimum0.o ./rabit/src/engine.o ./rabit/src/rabit_c_api.o ./rabit/src/allreduce_base.o -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-xgboost/00new/xgboost/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 (xgboost) * installing *source* package ‘httpuv’ ... ** package ‘httpuv’ successfully unpacked and MD5 sums checked ** using staged installation ** Using bundled copy of libuv ** PKG_CFLAGS=-Ilibuv/include ** PKG_LIBS=./libuv/.libs/libuv.a ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callback.cpp -o callback.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c callbackqueue.cpp -o callbackqueue.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filedatasource-unix.cpp -o filedatasource-unix.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filedatasource-win.cpp -o filedatasource-win.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fs.cpp -o fs.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c gzipdatasource.cpp -o gzipdatasource.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c http.cpp -o http.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c httprequest.cpp -o httprequest.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c httpresponse.cpp -o httpresponse.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c httpuv.cpp -o httpuv.o gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c md5.c -o md5.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mime.cpp -o mime.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c socket.cpp -o socket.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c staticpath.cpp -o staticpath.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c thread.cpp -o thread.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c timegm.cpp -o timegm.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c utils.cpp -o utils.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c uvutil.cpp -o uvutil.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c webapplication.cpp -o webapplication.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-base.cpp -o websockets-base.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-hixie76.cpp -o websockets-hixie76.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-hybi03.cpp -o websockets-hybi03.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets-ietf.cpp -o websockets-ietf.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c websockets.cpp -o websockets.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c winutils.cpp -o winutils.o cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4 cd libuv; \ if ! command -v automake >/dev/null 2>&1 ; then \ echo "automake not found. Touching files so configure will not try to run automake."; \ touch aclocal.m4; \ touch -r aclocal.m4 configure Makefile.in; \ else \ echo "automake found. Running autoupdate and autogen.sh."; \ autoupdate; \ sh autogen.sh; \ fi; \ chmod +x configure; \ CC="gcc" CFLAGS="-g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fpic -fvisibility=hidden -DNDEBUG" CPPFLAGS="" AR="ar" RANLIB="ranlib" LDFLAGS="-Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro" ./configure "--quiet" automake found. Running autoupdate and autogen.sh. + libtoolize --copy + aclocal -I m4 + autoconf configure.ac:46: warning: $as_echo is obsolete; use AS_ECHO(["message"]) instead lib/m4sugar/m4sh.m4:692: _AS_IF_ELSE is expanded from... lib/m4sugar/m4sh.m4:699: AS_IF is expanded from... ./lib/autoconf/general.m4:2249: AC_CACHE_VAL is expanded from... ./lib/autoconf/general.m4:2270: AC_CACHE_CHECK is expanded from... m4/ax_pthread.m4:88: AX_PTHREAD is expanded from... configure.ac:46: the top level + automake --add-missing --copy make --directory=libuv \ HAVE_DTRACE=0 make[1]: Entering directory '/tmp/RtmpGimaJ4/R.INSTALL2ac16f7851b76a/httpuv/src/libuv' CC src/libuv_la-fs-poll.lo CC src/libuv_la-idna.lo CC src/libuv_la-inet.lo CC src/libuv_la-random.lo CC src/libuv_la-strscpy.lo CC src/libuv_la-threadpool.lo CC src/libuv_la-timer.lo CC src/libuv_la-uv-data-getter-setters.lo CC src/libuv_la-uv-common.lo CC src/libuv_la-version.lo CC src/unix/libuv_la-async.lo CC src/unix/libuv_la-core.lo CC src/unix/libuv_la-dl.lo CC src/unix/libuv_la-fs.lo CC src/unix/libuv_la-getaddrinfo.lo CC src/unix/libuv_la-getnameinfo.lo CC src/unix/libuv_la-loop-watcher.lo CC src/unix/libuv_la-loop.lo CC src/unix/libuv_la-pipe.lo CC src/unix/libuv_la-poll.lo CC src/unix/libuv_la-process.lo CC src/unix/libuv_la-random-devurandom.lo CC src/unix/libuv_la-signal.lo CC src/unix/libuv_la-stream.lo CC src/unix/libuv_la-tcp.lo CC src/unix/libuv_la-thread.lo src/unix/thread.c: In function ‘uv__thread_stack_size’: src/unix/thread.c:195:24: warning: comparison of integer expressions of different signedness: ‘rlim_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 195 | if (lim.rlim_cur >= PTHREAD_STACK_MIN) | ^~ src/unix/thread.c: In function ‘uv_thread_create_ex’: src/unix/thread.c:243:20: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 243 | if (stack_size < PTHREAD_STACK_MIN) | ^ CC src/unix/libuv_la-tty.lo CC src/unix/libuv_la-udp.lo CC src/unix/libuv_la-linux-core.lo CC src/unix/libuv_la-linux-inotify.lo CC src/unix/libuv_la-linux-syscalls.lo CC src/unix/libuv_la-procfs-exepath.lo CC src/unix/libuv_la-proctitle.lo CC src/unix/libuv_la-random-getrandom.lo CC src/unix/libuv_la-random-sysctl-linux.lo CC src/unix/libuv_la-epoll.lo CCLD libuv.la ar: `u' modifier ignored since `D' is the default (see `U') make[1]: Leaving directory '/tmp/RtmpGimaJ4/R.INSTALL2ac16f7851b76a/httpuv/src/libuv' gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c http-parser/http_parser.c -o http-parser/http_parser.o gcc -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sha1/sha1.c -o sha1/sha1.o g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -Ilibuv/include -pthread -I'/home/omnipath/local/R/4.3-3.17/later/include' -I'/home/omnipath/local/R/4.3-3.17/Rcpp/include' -fvisibility=hidden -DSTRICT_R_HEADERS -fpic -g -O2 -ffile-prefix-map=/build/r-base-MHXHhT/r-base-4.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c base64/base64.cpp -o base64/base64.o g++ -std=gnu++17 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -o httpuv.so RcppExports.o callback.o callbackqueue.o filedatasource-unix.o filedatasource-win.o fs.o gzipdatasource.o http.o httprequest.o httpresponse.o httpuv.o md5.o mime.o socket.o staticpath.o thread.o timegm.o utils.o uvutil.o webapplication.o websockets-base.o websockets-hixie76.o websockets-hybi03.o websockets-ietf.o websockets.o winutils.o ./libuv/.libs/libuv.a ./http-parser/http_parser.o ./sha1/sha1.o ./base64/base64.o -pthread -L/usr/lib/R/lib -lR installing to /home/omnipath/local/R/4.3-3.17/00LOCK-httpuv/00new/httpuv/libs ** R ** demo ** 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 (httpuv) The downloaded source packages are in ‘/tmp/Rtmpp6kBak/downloaded_packages’ 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cloud.r-project.org Bioconductor version 3.17 (BiocManager 1.30.22), R 4.3.1 (2023-06-16) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'BiocCheck' Skipping 1 packages ahead of CRAN: sass [ Finished: 2023-12-06 12:14:18 CET ]