I am having some strange problems with missing execute permissions on some files when installing the latest miniconda. Does anyone see what the problem is?
I am installing on this Linux system:
-bash-4.2$ cat /etc/system-release
CentOS Linux release 7.9.2009 (Core)
-bash-4.2$ uname -a
Linux sad1.pp.rhul.ac.uk 3.10.0-1160.80.1.el7.x86_64 #1 SMP Tue Nov 8 15:48:59 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
I am following the instructions at conda.io
with PREFIX=/scratch4/george/miniconda
(which is an NFS-mounted area I have write access to)
When the installation finishes, apparently successfully, conda init fails:
installation finished.
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
Miniconda3-latest-Linux-x86_64.sh: line 524: /scratch4/george/miniconda/bin/conda: Permission denied
It turns out some key files do not have execute permissions set:
-bash-4.2$ find /scratch4/george/miniconda/bin \! -perm -u+x -ls
107602865387 8 -rw-r--r-- 1 george hep5 6748 Feb 3 11:56 /scratch4/george/miniconda/bin/c_rehash
107602865395 20 -rw-r--r-- 1 george hep5 17016 Feb 3 11:56 /scratch4/george/miniconda/bin/lzmainfo
107602865255 4 -rw-r--r-- 1 george hep5 116 Feb 3 11:56 /scratch4/george/miniconda/bin/idle3.10
107602865257 16860 -rw-r--r-- 1 george hep5 17263360 Feb 3 11:56 /scratch4/george/miniconda/bin/python3.10
107602865258 4 -rw-r--r-- 1 george hep5 3494 Feb 3 11:56 /scratch4/george/miniconda/bin/python3.10-config
107602865287 4 -rw-r--r-- 1 george hep5 527 Feb 3 11:56 /scratch4/george/miniconda/bin/conda
107602865289 4 -rw-r--r-- 1 george hep5 288 Feb 3 11:56 /scratch4/george/miniconda/bin/deactivate
If I set these x perms by hand, conda init then works, but when I go i=on to create new environments I have this problem repeatedly with the x permission not set on a subset of the files that need it, often causing the installation of the env to fail.