[ Started: 2024-05-07 15:19:00 CEST ] [ CARNIVAL v2.7.2 for BioC-3.19 from https://github.com/saezlab/CARNIVAL@master (2b8887a 2023-12-06 13:18:32) ] [1] "Libraries: " "/home/omnipath/local/R/4.4-3.19" [3] "/home/omnipath/local/R/4.4" "/opt/R-alpha/lib/R/library" trying URL 'https://cran.uni-muenster.de/src/contrib/ragg_1.3.1.tar.gz' Content type 'application/x-gzip' length 430413 bytes (420 KB) ================================================== downloaded 420 KB trying URL 'https://cran.uni-muenster.de/src/contrib/stringi_1.8.4.tar.gz' Content type 'application/x-gzip' length 11917497 bytes (11.4 MB) ================================================== downloaded 11.4 MB trying URL 'https://cran.uni-muenster.de/src/contrib/tinytex_0.51.tar.gz' Content type 'application/x-gzip' length 34491 bytes (33 KB) ================================================== downloaded 33 KB * installing *source* package ‘ragg’ ... ** package ‘ragg’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu Using PKG_LIBS=-L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c capture_dev.cpp -o capture_dev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c jpeg_dev.cpp -o jpeg_dev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c png_dev.cpp -o png_dev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c ppm_dev.cpp -o ppm_dev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c tiff_dev.cpp -o tiff_dev.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_curves.cpp -o agg/src/agg_curves.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_font_freetype.cpp -o agg/src/agg_font_freetype.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_image_filters.cpp -o agg/src/agg_image_filters.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_trans_affine.cpp -o agg/src/agg_trans_affine.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_vcgen_dash.cpp -o agg/src/agg_vcgen_dash.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I./agg/include -I/usr/local/include/freetype2 -I/usr/include/harfbuzz -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/libpng16 -I/usr/include/x86_64-linux-gnu -I'/home/omnipath/local/R/4.4-3.19/systemfonts/include' -I'/home/omnipath/local/R/4.4-3.19/textshaping/include' -I/usr/local/include -fpic -g -O2 -c agg/src/agg_vcgen_stroke.cpp -o agg/src/agg_vcgen_stroke.o ar rcs agg/libstatagg.a agg/src/agg_curves.o agg/src/agg_font_freetype.o agg/src/agg_image_filters.o agg/src/agg_trans_affine.o agg/src/agg_vcgen_dash.o agg/src/agg_vcgen_stroke.o g++ -std=gnu++17 -shared -L/usr/local/lib -o ragg.so capture_dev.o init.o jpeg_dev.o png_dev.o ppm_dev.o tiff_dev.o -Lagg -lstatagg -L/usr/local/lib -lfreetype -lpng16 -lz -ltiff -ljpeg installing to /home/omnipath/local/R/4.4-3.19/00LOCK-ragg/00new/ragg/libs ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded from temporary location ** 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 (ragg) * installing *source* package ‘stringi’ ... ** package ‘stringi’ successfully unpacked and MD5 sums checked ** using staged installation checking for R_HOME... /opt/R-alpha/lib/R checking for R... /opt/R-alpha/lib/R/bin/R checking for endianness... little checking for cat... /usr/bin/cat 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 whether the C++ compiler supports the 'long long' type... yes checking whether the compiler implements namespaces... yes checking whether the compiler supports the Standard Template Library... yes checking whether std::map is available... yes checking for pkg-config... /usr/bin/pkg-config checking with 'pkg-config' for the system ICU4C (icu-i18n icu-uc)... 70.1 checking for ICU4C >= 61... yes checking for additional CPPFLAGS, LDFLAGS, and LIBS required... done checking whether an ICU4C-based project can be built... yes checking programmatically for sufficient U_ICU_VERSION_MAJOR_NUM... yes checking the capabilities of the ICU data library (ucnv, uloc, utrans)... yes checking the capabilities of the ICU data library (ucol)... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for elf.h... yes configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/uconfig_local.h config.status: creating src/install.libs.R *** stringi configure summary: ICU_FOUND=1 STRINGI_CXXSTD= STRINGI_CXXFLAGS= -fpic STRINGI_CPPFLAGS=-I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H STRINGI_LDFLAGS= -L/usr/lib/x86_64-linux-gnu STRINGI_LIBS= -licui18n -licuuc -licudata *** Compiler settings used: CXX=g++ -std=gnu++17 LD=g++ -std=gnu++17 CXXFLAGS=-g -O2 CPPFLAGS=-I/usr/local/include LDFLAGS= LIBS= ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_brkiter.cpp -o stri_brkiter.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_collator.cpp -o stri_collator.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_common.cpp -o stri_common.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_compare.cpp -o stri_compare.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_base.cpp -o stri_container_base.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_bytesearch.cpp -o stri_container_bytesearch.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_listint.cpp -o stri_container_listint.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_listraw.cpp -o stri_container_listraw.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_listutf8.cpp -o stri_container_listutf8.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_regex.cpp -o stri_container_regex.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_usearch.cpp -o stri_container_usearch.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_utf16.cpp -o stri_container_utf16.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_utf8.cpp -o stri_container_utf8.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_container_utf8_indexable.cpp -o stri_container_utf8_indexable.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_encoding_conversion.cpp -o stri_encoding_conversion.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_encoding_detection.cpp -o stri_encoding_detection.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_encoding_management.cpp -o stri_encoding_management.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_escape.cpp -o stri_escape.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_exception.cpp -o stri_exception.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_ICU_settings.cpp -o stri_ICU_settings.o In file included from stri_ICU_settings.cpp:37: uconfig_local.h:42: warning: "UCONFIG_USE_WINDOWS_LCID_MAPPING_API" redefined 42 | #define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 0 | In file included from /usr/include/unicode/platform.h:24, from /usr/include/unicode/ptypes.h:52, from stri_external.h:52, from stri_stringi.h:36, from stri_ICU_settings.cpp:33: /usr/include/unicode/uconfig.h:381: note: this is the location of the previous definition 381 | # define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 1 | g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_join.cpp -o stri_join.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_length.cpp -o stri_length.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_pad.cpp -o stri_pad.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_prepare_arg.cpp -o stri_prepare_arg.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_random.cpp -o stri_random.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_reverse.cpp -o stri_reverse.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_count.cpp -o stri_search_class_count.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_detect.cpp -o stri_search_class_detect.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_extract.cpp -o stri_search_class_extract.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_locate.cpp -o stri_search_class_locate.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_replace.cpp -o stri_search_class_replace.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_split.cpp -o stri_search_class_split.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_startsendswith.cpp -o stri_search_class_startsendswith.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_subset.cpp -o stri_search_class_subset.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_class_trim.cpp -o stri_search_class_trim.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_common.cpp -o stri_search_common.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_count.cpp -o stri_search_coll_count.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_detect.cpp -o stri_search_coll_detect.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_extract.cpp -o stri_search_coll_extract.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_locate.cpp -o stri_search_coll_locate.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_replace.cpp -o stri_search_coll_replace.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_split.cpp -o stri_search_coll_split.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_startsendswith.cpp -o stri_search_coll_startsendswith.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_coll_subset.cpp -o stri_search_coll_subset.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_count.cpp -o stri_search_boundaries_count.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_extract.cpp -o stri_search_boundaries_extract.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_locate.cpp -o stri_search_boundaries_locate.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_boundaries_split.cpp -o stri_search_boundaries_split.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_count.cpp -o stri_search_fixed_count.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_detect.cpp -o stri_search_fixed_detect.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_extract.cpp -o stri_search_fixed_extract.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_locate.cpp -o stri_search_fixed_locate.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_replace.cpp -o stri_search_fixed_replace.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_split.cpp -o stri_search_fixed_split.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_subset.cpp -o stri_search_fixed_subset.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_fixed_startsendswith.cpp -o stri_search_fixed_startsendswith.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_in.cpp -o stri_search_in.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_other_split.cpp -o stri_search_other_split.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_count.cpp -o stri_search_regex_count.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_detect.cpp -o stri_search_regex_detect.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_extract.cpp -o stri_search_regex_extract.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_locate.cpp -o stri_search_regex_locate.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_match.cpp -o stri_search_regex_match.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_replace.cpp -o stri_search_regex_replace.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_split.cpp -o stri_search_regex_split.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_search_regex_subset.cpp -o stri_search_regex_subset.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_sort.cpp -o stri_sort.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_sprintf.cpp -o stri_sprintf.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_stats.cpp -o stri_stats.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_string8.cpp -o stri_string8.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_stringi.cpp -o stri_stringi.o In file included from stri_stringi.cpp:39: uconfig_local.h:42: warning: "UCONFIG_USE_WINDOWS_LCID_MAPPING_API" redefined 42 | #define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 0 | In file included from /usr/include/unicode/platform.h:24, from /usr/include/unicode/ptypes.h:52, from stri_external.h:52, from stri_stringi.h:36, from stri_stringi.cpp:33: /usr/include/unicode/uconfig.h:381: note: this is the location of the previous definition 381 | # define UCONFIG_USE_WINDOWS_LCID_MAPPING_API 1 | g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_sub.cpp -o stri_sub.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_test.cpp -o stri_test.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_zone.cpp -o stri_time_zone.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_calendar.cpp -o stri_time_calendar.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_symbols.cpp -o stri_time_symbols.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_time_format.cpp -o stri_time_format.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_casemap.cpp -o stri_trans_casemap.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_other.cpp -o stri_trans_other.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_normalization.cpp -o stri_trans_normalization.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_trans_transliterate.cpp -o stri_trans_transliterate.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_ucnv.cpp -o stri_ucnv.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_uloc.cpp -o stri_uloc.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_utils.cpp -o stri_utils.o g++ -std=gnu++17 -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I. -UDEBUG -DNDEBUG -DU_HAVE_ELF_H -I/usr/local/include -fpic -fpic -g -O2 -c stri_wrap.cpp -o stri_wrap.o g++ -std=gnu++17 -shared -L/usr/local/lib -o stringi.so stri_brkiter.o stri_collator.o stri_common.o stri_compare.o stri_container_base.o stri_container_bytesearch.o stri_container_listint.o stri_container_listraw.o stri_container_listutf8.o stri_container_regex.o stri_container_usearch.o stri_container_utf16.o stri_container_utf8.o stri_container_utf8_indexable.o stri_encoding_conversion.o stri_encoding_detection.o stri_encoding_management.o stri_escape.o stri_exception.o stri_ICU_settings.o stri_join.o stri_length.o stri_pad.o stri_prepare_arg.o stri_random.o stri_reverse.o stri_search_class_count.o stri_search_class_detect.o stri_search_class_extract.o stri_search_class_locate.o stri_search_class_replace.o stri_search_class_split.o stri_search_class_startsendswith.o stri_search_class_subset.o stri_search_class_trim.o stri_search_common.o stri_search_coll_count.o stri_search_coll_detect.o stri_search_coll_extract.o stri_search_coll_locate.o stri_search_coll_replace.o stri_search_coll_split.o stri_search_coll_startsendswith.o stri_search_coll_subset.o stri_search_boundaries_count.o stri_search_boundaries_extract.o stri_search_boundaries_locate.o stri_search_boundaries_split.o stri_search_fixed_count.o stri_search_fixed_detect.o stri_search_fixed_extract.o stri_search_fixed_locate.o stri_search_fixed_replace.o stri_search_fixed_split.o stri_search_fixed_subset.o stri_search_fixed_startsendswith.o stri_search_in.o stri_search_other_split.o stri_search_regex_count.o stri_search_regex_detect.o stri_search_regex_extract.o stri_search_regex_locate.o stri_search_regex_match.o stri_search_regex_replace.o stri_search_regex_split.o stri_search_regex_subset.o stri_sort.o stri_sprintf.o stri_stats.o stri_string8.o stri_stringi.o stri_sub.o stri_test.o stri_time_zone.o stri_time_calendar.o stri_time_symbols.o stri_time_format.o stri_trans_casemap.o stri_trans_other.o stri_trans_normalization.o stri_trans_transliterate.o stri_ucnv.o stri_uloc.o stri_utils.o stri_wrap.o -L/usr/lib/x86_64-linux-gnu -licui18n -licuuc -licudata installing via 'install.libs.R' to /home/omnipath/local/R/4.4-3.19/00LOCK-stringi/00new/stringi ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (stringi) * installing *source* package ‘tinytex’ ... ** package ‘tinytex’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (tinytex) The downloaded source packages are in ‘/tmp/RtmpPfLF5V/downloaded_packages’ Warning message: package ‘remotes’ was built under R version 4.5.0 Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 alpha (2024-04-04 r86334) Old packages: 'SparseArray', 'wppi' trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/SparseArray_1.4.1.tar.gz' Content type 'application/x-gzip' length 373380 bytes (364 KB) ================================================== downloaded 364 KB trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/wppi_1.12.0.tar.gz' Content type 'application/x-gzip' length 661086 bytes (645 KB) ================================================== downloaded 645 KB * installing *source* package ‘SparseArray’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c ExtendableJaggedArray.c -o ExtendableJaggedArray.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c R_init_SparseArray.c -o R_init_SparseArray.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Rvector_summarization.c -o Rvector_summarization.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c Rvector_utils.c -o Rvector_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SBT_utils.c -o SBT_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SVT_SparseArray_class.c -o SVT_SparseArray_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Complex_methods.c -o SparseArray_Complex_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Math_methods.c -o SparseArray_Math_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_Ops_methods.c -o SparseArray_Ops_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_abind.c -o SparseArray_abind.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_aperm.c -o SparseArray_aperm.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_class.c -o SparseArray_class.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_dim_tuning.c -o SparseArray_dim_tuning.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subassignment.c -o SparseArray_subassignment.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_subsetting.c -o SparseArray_subsetting.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseArray_summarization.c -o SparseArray_summarization.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseMatrix_mult.c -o SparseMatrix_mult.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Arith.c -o SparseVec_Arith.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Compare.c -o SparseVec_Compare.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Logic.c -o SparseVec_Logic.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_Math.c -o SparseVec_Math.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c SparseVec_dotprod.c -o SparseVec_dotprod.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c XVector_stubs.c -o XVector_stubs.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c coerceVector2.c -o coerceVector2.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c leaf_utils.c -o leaf_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c matrixStats_methods.c -o matrixStats_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c randomSparseArray.c -o randomSparseArray.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c readSparseCSV.c -o readSparseCSV.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c rowsum_methods.c -o rowsum_methods.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c sparseMatrix_utils.c -o sparseMatrix_utils.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c test.c -o test.o gcc -I"/opt/R-alpha/lib/R/include" -DNDEBUG -I'/home/omnipath/local/R/4.4-3.19/S4Vectors/include' -I'/home/omnipath/local/R/4.4-3.19/IRanges/include' -I'/home/omnipath/local/R/4.4-3.19/XVector/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c thread_control.c -o thread_control.o gcc -shared -L/usr/local/lib -o SparseArray.so ExtendableJaggedArray.o IRanges_stubs.o R_init_SparseArray.o Rvector_summarization.o Rvector_utils.o S4Vectors_stubs.o SBT_utils.o SVT_SparseArray_class.o SparseArray_Complex_methods.o SparseArray_Math_methods.o SparseArray_Ops_methods.o SparseArray_abind.o SparseArray_aperm.o SparseArray_class.o SparseArray_dim_tuning.o SparseArray_subassignment.o SparseArray_subsetting.o SparseArray_summarization.o SparseMatrix_mult.o SparseVec_Arith.o SparseVec_Compare.o SparseVec_Logic.o SparseVec_Math.o SparseVec_dotprod.o XVector_stubs.o coerceVector2.o leaf_utils.o matrixStats_methods.o randomSparseArray.o readSparseCSV.o rowsum_methods.o sparseMatrix_utils.o test.o thread_control.o -fopenmp installing to /home/omnipath/local/R/4.4-3.19/00LOCK-SparseArray/00new/SparseArray/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning message: package ‘abind’ was built under R version 4.5.0 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: package ‘abind’ was built under R version 4.5.0 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: package ‘abind’ was built under R version 4.5.0 ** testing if installed package keeps a record of temporary installation path * DONE (SparseArray) * installing *source* package ‘wppi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading [2024-05-07 15:22:46] [INFO] [OmnipathR] Setting up new cache directory `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 15:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:46] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Contains 1 files. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 15:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-07 15:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-07 15:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-07 15:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-07 15:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:46] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-07 15:22:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:46] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2024-05-07 15:22:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 15:22:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:48] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:48] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-07 15:22:48] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:48] [TRACE] [OmnipathR] Contains 1 files. [2024-05-07 15:22:48] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-07 15:22:48] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 15:22:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:49] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-07 15:22:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-07 15:22:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-07 15:22:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-07 15:22:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:49] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-07 15:22:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:49] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-05-07 15:22:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 15:22:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:50] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Contains 1 files. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-07 15:22:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-07 15:22:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-07 15:22:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-07 15:22:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-07 15:22:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:50] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/local/R/4.4-3.19/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-07 15:22:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-07 15:22:50] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi) The downloaded source packages are in ‘/tmp/RtmpPfLF5V/downloaded_packages’ Bioconductor version 3.19 (BiocManager 1.30.23), R 4.4.0 alpha (2024-04-04 r86334) 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: BiocStyle [ Finished: 2024-05-07 15:22:53 CEST ]