O.rka O.rka - 1 month ago 28
R Question

R is broken with "dyld: Library not loaded: @rpath/libpcre.1.dylib"

I'm trying to follow Brew doctor: dyld: Library not loaded & Error: No available formula for zlib but it isn't helping. I had my

R
working earlier today but I installed
r-essentials
through
conda
(how my
R
was installed originally) and am now getting the following error:

$ which R
/Users/jespinoz/anaconda/bin/R

$ /Users/jespinoz/anaconda/bin/R
dyld: Library not loaded: @rpath/libpcre.1.dylib
Referenced from: /Users/jespinoz/anaconda/lib/R/lib/libR.dylib
Reason: image not found
Trace/BPT trap: 5

Answer

I ended up deleting my entire anaconda directory and reinstalling :(

In hindsight, I realized that I needed to make a shellscript just incase anything weird happened and I needed to reinstall everything again. Everytime I install a new module that I think will be useful I just add it to here.

Here's all my Python and R packages:

# Python
conda install xarray --yes
conda install holoviews --yes
conda install seaborn --yes
conda install scikit-learn --yes
conda install scikit-image --yes
conda install -c https://conda.anaconda.org/biocore scikit-bio --yes
conda install dill --yes
conda install pandas --yes
conda install numpy --yes
conda install networkx --yes
conda install scipy --yes
pip install fastcluster
conda install -c jjhelmus tensorflow=0.8.0rc0 --yes
conda install bokeh --yes
conda install BioPython --yes
conda install tqdm --yes
pip install git+https://github.com/pymc-devs/pymc3
conda install dask --yes
conda install numba --yes
pip install nbopen
pip install nbextensions
pip install https://github.com/ipython-contrib/IPython-notebook-extensions/tarball/master
conda install html5lib --yes
pip install selenium
conda install phantoms --yes
pip install pubchempy —yes
conda install --channel https://conda.anaconda.org/rdkit rdkit --yes
conda install --channel https://conda.anaconda.org/bioconda bioservices --yes
conda install --channel https://conda.anaconda.org/ales-erjavec orange-bioinformatics
pip install plotly
pip install ete3

# R
conda install -c r r --yes
conda install -c r r-essentials --yes
conda install -c r r-rserve --yes
conda install -c r r-devtools --yes
conda install -c r r-rcurl --yes
conda install -c r r-RJSONIO --yes
conda install -c r r-jpeg --yes
conda install -c r r-png --yes
conda install -c r r-roxygen2 --yes
conda install --channel https://conda.anaconda.org/bioconda bioconductor-edger --yes