Error installing xml2 in Rstudio - Archlinux

[aoramos]

Brief description of the problem Installing xml2 package results in following error:

install.packages("xml2") Installing package into ‘/home/user/R/x86_64-pc-linux-gnu-library/4.3’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.3.5.tar.gz' Content type 'application/x-gzip' length 272664 bytes (266 KB)

downloaded 266 KB

• installing source package ‘xml2’ ... package ‘xml2’ successfully unpacked and MD5 sums checked using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/libxml2 Using PKG_LIBS=-lxml2 -lz -llzma -licui18n -licuuc -licudata -lm * libs using C compiler: ‘gcc (GCC) 13.2.1 20230801’ using C++ compiler: ‘g++ (GCC) 13.2.1 20230801’ g++ -std=gnu++17 -I"/usr/include/R/" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -c connection.cpp -o connection.o gcc -I"/usr/include/R/" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -I/usr/local/include -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -c init.c -o init.o g++ -std=gnu++17 -I"/usr/include/R/" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -c xml2_doc.cpp -o xml2_doc.o g++ -std=gnu++17 -I"/usr/include/R/" -DNDEBUG -I../inst/include -I/usr/include/libxml2 -DUCHAR_TYPE=wchar_t -DU_SHOW_CPLUSPLUS_API=0 -I/usr/local/include -fvisibility=hidden -fpic -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security -fstack-clash-protection -fcf-protection -Wp,-D_GLIBCXX_ASSERTIONS -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects -c xml2_init.cpp -o xml2_init.o xml2_init.cpp: In function ‘SEXPREC init_libxml2()’: xml2_init.cpp:46:35: error: invalid conversion from ‘void ()(void, xmlError)’ {aka ‘void ()(void, _xmlError)’} to ‘xmlStructuredErrorFunc’ {aka ‘void ()(void, const _xmlError*)’} [-fpermissive] 46	xmlSetStructuredErrorFunc(NULL, handleStructuredError);	^~~~~
  void ()(void, xmlError) {aka void ()(void, _xmlError)}

  In file included from xml2_init.cpp:8: /usr/include/libxml2/libxml/xmlerror.h:898:57: note: initializing argument 2 of ‘void xmlSetStructuredErrorFunc(void*, xmlStructuredErrorFunc)’ 898 | xmlStructuredErrorFunc handler); | ~~~~~^~~~~ make: *** [/usr/lib64/R/etc/Makeconf:200: xml2_init.o] Error 1 ERROR: compilation failed for package ‘xml2’

• removing ‘/home/user/R/x86_64-pc-linux-gnu-library/4.3/xml2’ Warning in install.packages : installation of package ‘xml2’ had non-zero exit status

The downloaded source packages are in ‘/tmp/Rtmpj1A2Pb/downloaded_packages’

libxml2 version 2.12.0-1 OS: Arch Linux x86_64 Kernel: 6.1.63-1-lts R version: 4.3.2 Rstudio 2023.09.1 Build 494

[carolinkun]

Hello, I'm having the same problem! Have you found any workarounds or fixes?

[aoramos]

Hi, I have done the following (see Error during installation of xml2 #418 ): "Until the fix gets merged, you can install with pak::pak("KNnut/xml2@fix-build") in R cmdline" and it worked!

[hadley]

Fixed by #417