All Bioconda packages are generated with very specific channel priorities, namely conda-forge > bioconda > defaults and if one doesn't follow this, correct solving and dynamic library references cannot be guaranteed. So, a proper ad hoc installation command would be
conda install -c conda-forge -c bioconda -c defaults perl-bioperl=1.7.8
Encouraged Workflow
However, I would strongly encourage bioinformaticians (and other practitioners that value reproducible workflows) to not use ad hoc commands. Instead, adopt the practice of only working from YAML files to define software environments:
bioperl_1_7_8.yaml
name: bioperl_1_7_8
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- perl
- bioperl=1.7.8
Use this with conda env create -f bioperl_1_7_8.yaml.
All Bioconda packages are generated with very specific channel priorities, namely conda-forge > bioconda > defaults and if one doesn't follow this, correct solving and dynamic library references cannot be guaranteed. So, a proper ad hoc installation command would be
conda install -c conda-forge -c bioconda -c defaults perl-bioperl=1.7.8
Encouraged Workflow
However, I would strongly encourage bioinformaticians (and other practitioners that value reproducible workflows) to not use ad hoc commands. Instead, adopt the practice of only working from YAML files to define software environments:
bioperl_1_7_8.yaml
name: bioperl_1_7_8
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- perl
- bioperl=1.7.8
Use this with conda env create -f bioperl_1_7_8.yaml.
A workaround is to create a new environment with conda-forge as default channel (see also this answer) instead of installing into the base environment:
$ conda create --name perl
$ conda activate perl
$ conda config --add channels conda-forge
$ conda config --set channel_priority strict
$ conda install perl
$ conda install -c bioconda perl-bioperl=1.7.8
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.