Closed Unaimend closed 12 months ago
Brief description of the problem Installing xml2 package results in following error.
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: /home/td/Projects/Aging/Baseline/GIN/MicrobiomeGS/community_modeling_coupling/.snakemake/conda/d02a769616c111eca43b9ae67bcda15f_/include/libxml2/libxml/xmlerror.h:898:57: note: initializing argument 2 of 'void xmlSetStructuredErrorFunc(void*, xmlStructuredErrorFunc)' 898 | xmlStructuredErrorFunc handler); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ make: *** [/home/td/Projects/Aging/Baseline/GIN/MicrobiomeGS/community_modeling_coupling/.snakemake/conda/d02a769616c111eca43b9ae67bcda15f_/lib/R/etc/Makeconf:200: xml2_init.o] Error 1 ERROR: compilation failed for package ‘xml2’ * removing ‘/home/td/Projects/Aging/Baseline/GIN/MicrobiomeGS/community_modeling_coupling/.snakemake/conda/d02a769616c111eca43b9ae67bcda15f_/lib/R/library/xml2’ The downloaded source packages are in ‘/tmp/RtmpBgSu61/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done
Libxml version: + libxml2 2.12.0 h232c23b_0 conda-forge/linux-64 Cached R version 4.3.2 (2023-10-31) -- "Eye Holes" OS: Ubuntu 22.04.2 LTS
Conda environment that was used to install R
R
name: MicrobiomeGS2 channels: - conda-forge dependencies: - glpk - r-base - r-rcurl
Not applicable
Until the fix gets merged, you can install with pak::pak("KNnut/xml2@fix-build") in R cmdline
pak::pak("KNnut/xml2@fix-build")
Brief description of the problem Installing xml2 package results in following error.
Libxml version: + libxml2 2.12.0 h232c23b_0 conda-forge/linux-64 Cached R version 4.3.2 (2023-10-31) -- "Eye Holes" OS: Ubuntu 22.04.2 LTS
Conda environment that was used to install
R