alpine / aports / problem installing R package : onbrand
I have attempted to install numerous R packages, some of which fail. Here's an example, with R REPL IO for R package, "onbrand", install, which installs without complaints on other OS's:
`` rlyeh:~$ R
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-musl (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
[Previously saved workspace restored]
install.packages("onbrand") Installing package into ‘/home/deepdark/R/x86_64-pc-linux-musl-library/4.2’ (as ‘lib’ is unspecified) --- Please select a CRAN mirror for use in this session --- Secure CRAN mirrors
1: 0-Cloud [https] 2: Australia (Canberra) [https] 3: Australia (Melbourne 1) [https] 4: Australia (Melbourne 2) [https] 5: Australia (Perth) [https] 6: Austria [https] 7: Belgium (Brussels) [https] 8: Brazil (PR) [https] 9: Brazil (RJ) [https] 10: Brazil (SP 1) [https] 11: Brazil (SP 2) [https] 12: Bulgaria [https] 13: Canada (MB) [https] 14: Canada (ON 3) [https] 15: Chile (Santiago) [https] 16: China (Beijing 2) [https] 17: China (Beijing 3) [https] 18: China (Hefei) [https] 19: China (Hong Kong) [https] 20: China (Guangzhou) [https] 21: China (Lanzhou) [https] 22: China (Nanjing) [https] 23: China (Shanghai 2) [https] 24: China (Shenzhen) [https] 25: Colombia (Cali) [https] 26: Costa Rica [https] 27: Cyprus [https] 28: Czech Republic [https] 29: Denmark [https] 30: East Asia [https] 31: Ecuador (Cuenca) [https] 32: Ecuador (Quito) [https] 33: Estonia [https] 34: France (Lyon 1) [https] 35: France (Lyon 2) [https] 36: France (Marseille) [https] 37: France (Paris 1) [https] 38: Germany (Erlangen) [https] 39: Germany (Leipzig) [https] 40: Germany (Göttingen) [https] 41: Germany (Münster) [https] 42: Germany (Regensburg) [https] 43: Greece [https] 44: Hungary [https] 45: Iceland [https] 46: Indonesia (Jakarta) [https] 47: Iran (Mashhad) [https] 48: Italy (Milano) [https] 49: Italy (Padua) [https] 50: Japan (Tokyo) [https] 51: Korea (Gyeongsan-si) [https] 52: Korea (Seoul 1) [https] 53: Korea (Ulsan) [https] 54: Malaysia [https] 55: Mexico (Mexico City) [https] 56: Morocco [https] 57: Netherlands [https] 58: New Zealand [https] 59: Norway [https] 60: South Africa (Johannesburg) [https] 61: Spain (A Coruña) [https] 62: Spain (Madrid) [https] 63: Sweden (Borås) [https] 64: Sweden (Umeå) [https] 65: Switzerland [https] 66: Taiwan (Taipei) [https] 67: Turkey (Denizli) [https] 68: Turkey (Istanbul) [https] 69: Turkey (Mersin) [https] 70: UK (Bristol) [https] 71: UK (London 1) [https] 72: USA (IA) [https] 73: USA (KS) [https] 74: USA (MI) [https] 75: USA (OH) [https] 76: USA (OR) [https] 77: USA (TN) [https] 78: USA (TX 1) [https] 79: Uruguay [https] 80: (other mirrors)
Selection: 77 also installing the dependencies ‘systemfonts’, ‘xml2’, ‘gdtools’, ‘flextable’, ‘officer’
https://mirrors.nics.utk.edu/cran/src/contrib/systemfonts_1.0.4.tar.gz' Content type 'application/x-gzip' length 81757 bytes (79 KB)
trying URL 'downloaded 79 KB
https://mirrors.nics.utk.edu/cran/src/contrib/xml2_1.3.3.tar.gz' Content type 'application/x-gzip' length 283965 bytes (277 KB)
trying URL 'downloaded 277 KB
https://mirrors.nics.utk.edu/cran/src/contrib/gdtools_0.2.4.tar.gz' Content type 'application/x-gzip' length 33426 bytes (32 KB)
trying URL 'downloaded 32 KB
https://mirrors.nics.utk.edu/cran/src/contrib/flextable_0.7.0.tar.gz' Content type 'application/x-gzip' length 764641 bytes (746 KB)
trying URL 'downloaded 746 KB
https://mirrors.nics.utk.edu/cran/src/contrib/officer_0.4.2.tar.gz' Content type 'application/x-gzip' length 692036 bytes (675 KB)
trying URL 'downloaded 675 KB
https://mirrors.nics.utk.edu/cran/src/contrib/onbrand_1.0.2.tar.gz' Content type 'application/x-gzip' length 3495184 bytes (3.3 MB)
trying URL 'downloaded 3.3 MB
- installing source package ‘systemfonts’ ... ** package ‘systemfonts’ successfully unpacked and MD5 sums checked ** using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/freetype2 -I/usr/include/libpng16 Using PKG_LIBS=-lfontconfig -lfreetype ** libs rm -f systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c caches.cpp -o caches.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c cpp11.cpp -o cpp11.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c dev_metrics.cpp -o dev_metrics.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c font_matching.cpp -o font_matching.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c font_registry.cpp -o font_registry.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c ft_cache.cpp -o ft_cache.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c string_shape.cpp -o string_shape.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c font_metrics.cpp -o font_metrics.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c font_fallback.cpp -o font_fallback.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c string_metrics.cpp -o string_metrics.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c emoji.cpp -o emoji.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c cache_store.cpp -o cache_store.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c init.cpp -o init.o g++ -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I/usr/include/freetype2 -I/usr/include/libpng16 -I'/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/cpp11/include' -O2 -fomit-frame-pointer -fpic -O2 -fomit-frame-pointer -D__MUSL__ -flto -c unix/FontManagerLinux.cpp -o unix/FontManagerLinux.o g++ -std=gnu++11 -shared -O2 -fomit-frame-pointer -D__MUSL__ -flto -fpic -L/usr/lib/R/lib -Wl,--as-needed,-O1,--sort-common -o systemfonts.so caches.o cpp11.o dev_metrics.o font_matching.o font_registry.o ft_cache.o string_shape.o font_metrics.o font_fallback.o string_metrics.o emoji.o cache_store.o init.o unix/FontManagerLinux.o -lfontconfig -lfreetype -L/usr/lib/R/lib -lR installing to /home/deepdark/R/x86_64-pc-linux-musl-library/4.2/00LOCK-systemfonts/00new/systemfonts/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 (systemfonts)
- installing source package ‘xml2’ ...
** package ‘xml2’ successfully unpacked and MD5 sums checked
** using staged installation
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing
libxml-2.0.pc' to the PKG_CONFIG_PATH environment variable Package 'libxml-2.0', required by 'virtual:world', not found Package libxml-2.0 was not found in the pkg-config search path. Perhaps you should add the directory containing
libxml-2.0.pc' to the PKG_CONFIG_PATH environment variable Package 'libxml-2.0', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-lxml2 ------------------------- ANTICONF ERROR --------------------------- Configuration failed because libxml-2.0 was not found. Try installing: - deb: libxml2-dev (Debian, Ubuntu, etc)
- rpm: libxml2-devel (Fedora, CentOS, RHEL)
- csw: libxml2_dev (Solaris) If libxml-2.0 is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
ERROR: configuration failed for package ‘xml2’
- removing ‘/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/xml2’
- installing source package ‘gdtools’ ...
** package ‘gdtools’ successfully unpacked and MD5 sums checked
** using staged installation
Package cairo was not found in the pkg-config search path.
Perhaps you should add the directory containing
cairo.pc' to the PKG_CONFIG_PATH environment variable Package 'cairo', required by 'virtual:world', not found Package cairo was not found in the pkg-config search path. Perhaps you should add the directory containing
cairo.pc' to the PKG_CONFIG_PATH environment variable Package 'cairo', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-lcairo -lfreetype -----------------------------[ ANTICONF ]------------------------------- Configuration failed to find libraries. Try installing: - deb: libcairo2-dev (Debian, Ubuntu)
- rpm: cairo-devel (Fedora, CentOS, RHEL)
- csw: libcairo_dev (Solaris)
- brew: cairo (OSX) If cairo freetype2 are already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a cairo freetype2.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' ---------------------------[ ERROR MESSAGE ]---------------------------- src/tests/sysdeps.c:1:10: fatal error: cairo-ft.h: No such file or directory 1 | #include <cairo-ft.h> | ^~~~~~~~~~~~ compilation terminated.
ERROR: configuration failed for package ‘gdtools’
- removing ‘/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/gdtools’ ERROR: dependency ‘xml2’ is not available for package ‘officer’
- removing ‘/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/officer’ ERROR: dependencies ‘officer’, ‘xml2’, ‘gdtools’ are not available for package ‘flextable’
- removing ‘/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/flextable’ ERROR: dependencies ‘flextable’, ‘officer’ are not available for package ‘onbrand’
- removing ‘/home/deepdark/R/x86_64-pc-linux-musl-library/4.2/onbrand’
The downloaded source packages are in ‘/tmp/RtmpfmaOgm/downloaded_packages’ Warning messages: 1: In install.packages("onbrand") : installation of package ‘xml2’ had non-zero exit status 2: In install.packages("onbrand") : installation of package ‘gdtools’ had non-zero exit status 3: In install.packages("onbrand") : installation of package ‘officer’ had non-zero exit status 4: In install.packages("onbrand") : installation of package ‘flextable’ had non-zero exit status 5: In install.packages("onbrand") : installation of package ‘onbrand’ had non-zero exit status
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