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hmors

Member

Registered: 2018-07-04

Posts: 17

Problem compiling packages with gcc-conda

Hi,
I have been trying to compile several packages from AUR, in this case YAY, and I have few problems with gcc-conda.
I am not really sure if it is a conda problem but after the

 makepkg -si 

I obtain the message:

 x86_64-conda_cos6-linux-gnu-cc: error: unrecognized command line option '-fstack-clash-protection'; did you mean '-fstack-protector'? 

 x86_64-conda_cos6-linux-gnu-cc: error: unrecognized command line option '-fcf-protection'; did you mean '-fstack-protector'? 

I have been trying to change the  Makefile  or trying to use gcc without conda but I did not have any success.  I do not have a so much of experience using the gcc compiler so I am not really sure
how to proceed. Does anybody has a clue how to solve this problem. Thanks ins advance.

V1del

Forum Moderator

Registered: 2012-10-16

Posts: 25,292

Re: Problem compiling packages with gcc-conda

You shouldn't mix package managers and definitely not try to build what should end up as system packages in a conda environment.

What happens if you actually don't use the conda environment to actually build this (check your PATH, you shouldn't have a conda path as your first priority)

hmors

Member

Registered: 2018-07-04

Posts: 17

Re: Problem compiling packages with gcc-conda

HI.
thanks for your answer.
I have checked my PATH, but to be honest I am not really sure why conda has the priority. This is the output for printenv:

 PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/var/lib/flatpak/exports/bin:/usr/lib/jvm/default/bin:/usr/bin/site_perl:/usr/bin/vendor_perl:/usr/bin/core_perl:/home/hector/bin 

So, at the end I commented the code:

 # >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/hector/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/hector/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/hector/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/hector/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

in order to avoid to initialize conda. I know this is only a "partial solution" and I will have to uncomment the code every time I need to use jupyter notebook but I really needed to compile the packages.
I will try to change the priorities as your pointed out. Thanks again for your answer.

V1del

Forum Moderator

Registered: 2012-10-16

Posts: 25,292

Re: Problem compiling packages with gcc-conda

Afaik on a normal install this block should be able to remain, but only actually trigger and be relevant when you explicitly run conda init and only in the shell you run that in. Do you have conda init somewhere in your .bashrc? Other startup files?