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railorena / geneRFinder

A tool for prokaryotes gene prediction.
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not able to install R package 'caret' #2

Open chunlinxiao opened 1 year ago

chunlinxiao commented 1 year ago

Errors below:

Warning messages: 1: In install.packages("caret") : installation of package 'clock' had non-zero exit status 2: In install.packages("caret") : installation of package 'recipes' had non-zero exit status 3: In install.packages("caret") : installation of package 'caret' had non-zero exit status

In file included from /opt/gcc/7.3.0/include/c++/7.3.0/bits/localefwd.h:40:0, from /opt/gcc/7.3.0/include/c++/7.3.0/string:43, from /home/xi/R/R-4.2.2/library/cpp11/include/cpp11/declarations.hpp:4, from cpp11.cpp:5: /opt/gcc/7.3.0/include/c++/7.3.0/x86_64-redhat-linux-gnu/bits/c++locale.h:52:23: error: uselocale' was not declared in this scope extern "C" typeof(uselocale) uselocale; ^~~~~ /opt/gcc/7.3.0/include/c++/7.3.0/x86_64-redhat-linux-gnu/bits/c++locale.h:52:23: note: suggested alternative: 'timelocal' extern "C" typeof(uselocale) uselocale; ^~~~~ timelocal /opt/gcc/7.3.0/include/c++/7.3.0/x86_64-redhat-linux-gnu/bits/c++locale.h: In function 'int std::convert_from_v(locale_struct const&, char, int, const char*, ...)': /opt/gcc/7.3.0/include/c++/7.3.0/x86_64-redhat-linux-gnu/bits/c++locale.h:75:53: error: gnu_cxx::uselocale' cannot be used as a function c_locale old = gnu_cxx::uselocale(cloc); ^ /opt/gcc/7.3.0/include/c++/7.3.0/x86_64-redhat-linux-gnu/bits/c++locale.h:100:33: error:'gnu_cxx::uselocale' cannot be used as a function gnu_cxx::uselocale(old); ^ make: *** [cpp11.o] Error 1 ERROR: compilation failed for package 'clock'

any suggestion is appreciated.

railorena commented 1 year ago

Hi, Thank you for the contact! It looks like you are using Red Hat Linux, am I right? Caret needs the Clock package, and it looks like Clock package is not supported for Red Hat. You can try: install.packages("remotes") remotes::install_github("r-lib/clock") It will probably give an error, but I think it will show if you need to install some library for Linux. Maybe you need to install another C++ compiler.

chunlinxiao commented 1 year ago

Thank Raíssa for quick response.

Yes we use CentOS 7.9.2009. I tried remotes::install_github as you suggested, but got same errors.

I will see if having a newer c++ copiler would help.

also not sure if something relates to this post: https://stackoverflow.com/questions/32393098/cannot-compile-project-error-in-locale-h-file

railorena commented 1 year ago

Sorry, I couldn't find a solution to your problem. I hope you have found! If you have other questions, let me know.

chunlinxiao commented 1 year ago

thanks Raíssa f - I haven't got any solution yet.