Reticulate unable to load conda environments with new (conda V4.4) startup method.

As of conda V4.4, the recommended way to add conda to your environment is to run conda.sh.

However, reticulate no longer works when I do that.

Problem

balter@balterbox:~$ R

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)

> library(reticulate)
> use_condaenv('microbiome')
> library(BiocStyle)
Error in library(BiocStyle) : there is no package called ‘BiocStyle’
>
Save workspace image? [y/n/c]: n
balter@balterbox:~$ conda activate microbiome
(microbiome) balter@balterbox:~$ R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

> library(BiocStyle)
>

Conda Info

(microbiome) balter@balterbox:~$ conda info

     active environment : microbiome
    active env location : /home/balter/conda/envs/microbiome
            shell level : 1
       user config file : /home/balter/.condarc
 populated config files : /home/balter/.condarc
          conda version : 4.5.9
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /home/balter/conda  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
                          https://conda.anaconda.org/anaconda/linux-64
                          https://conda.anaconda.org/anaconda/noarch
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
          package cache : /home/balter/conda/pkgs
                          /home/balter/.conda/pkgs
       envs directories : /home/balter/conda/envs
                          /home/balter/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.9 requests/2.19.1 CPython/3.6.5 Linux/4.15.0-29-generic ubuntu/18.04 glibc/2.27
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

System Info

(microbiome) balter@balterbox:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.04.1 LTS
Release:        18.04
Codename:       bionic

rstudio / reticulate

Reticulate unable to load conda environments with new (conda V4.4) startup method. #329