The problem may be your /tmp is set to noexec in /etc/fstab. Verify with grep tmp /etc/fstab.
Run the installer with TMPDIR set to a directory you have write permissions to, on a file system with executable permission. i.e.:
Copymkdir /users/$USER/tmpconda
TMPDIR=/users/$USER/tmpconda bash Miniconda2-latest-Linux-x86_64.sh
Solution was found at Anaconda Issues 11587
A quick test of executability on a file system:
$ touch foo && chmod +x foo && ./foo
-bash: ./foo: Permission denied
noexec will cause "Permission denied" even if x is set on the file.
The problem may be your /tmp is set to noexec in /etc/fstab. Verify with grep tmp /etc/fstab.
Run the installer with TMPDIR set to a directory you have write permissions to, on a file system with executable permission. i.e.:
Copymkdir /users/$USER/tmpconda
TMPDIR=/users/$USER/tmpconda bash Miniconda2-latest-Linux-x86_64.sh
Solution was found at Anaconda Issues 11587
A quick test of executability on a file system:
$ touch foo && chmod +x foo && ./foo
-bash: ./foo: Permission denied
noexec will cause "Permission denied" even if x is set on the file.
I faced similar issue in Debian 10 and fixed the issue by exporting a writeable path to TMP environment variable.
Reference: https://github.com/ContinuumIO/anaconda-issues/issues/11154
I believe that the problem lies with the configuration of autotools in r-base>3.4.1b2, but I'm not competent to fix that. The plus side is that, although configure can't find zlib during the pre-installation, zlib is actually present in any Conda environment with r-base and can be linked during the actual installation. I filed an issue at Conda-Forge, but until and unless the issue is resolved in r-base, I made a fork of ShortRead which skips the check. It works for me with r-base=3.5.1.
tldr: remotes::install_github("brendanf/ShortRead")
I had the same error for the past week. I tried every thing that was mentioned regarding the zlib library on the internet. I couldn't fix it properly. I have the zlib installed as when I run: pkg-config zlib --libs; I get as output: -lz
$ pkg-config zlib --libs
-lz
I am running conda (v4.5.4). R version 3.4.3 and I have R as a conda environment. I think the problem is with multiple zlib libraries (ubuntu base and conda).
Somehow I just made this to work. What I did was to install R in ubuntu shell (i.e. outside conda) and install the ShortRead library there. There was no conflict/error with the zlib. After that I added the core Rlib directories to libPaths in conda.
$.libPaths(c('/home/aridaman/.conda/envs/rstudio/lib/R/library','/usr/local/lib/R/site-library/','/usr/lib/R/site-library','/usr/lib/R/site-library'))
This is not ideal but somehow worked for me. I would be glad to have a better conda based solution.