Bsrgvty

I am trying to install the HMSC R package into RStudio Version 1.2.1335 and R version 3.6.1 (2019-07-05) -- "Action of the Toes" on a Linux Ubuntu
18.04.2 LTS System

The code to install through R is as follows

library(devtools)
install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')
install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))

When installing BayesLogit_0.6.tar.gz I get the following error

/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lblas
/home/barefootbushman/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -llapack
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'BayesLogit.so' failed
make: *** [BayesLogit.so] Error 1
ERROR: compilation failed for package ‘BayesLogit’
* removing ‘/home/barefootbushman/R/x86_64-pc-linux-gnu-library/3.6/BayesLogit’
Error in i.p(...) : 
 (converted from warning) installation of package ‘/tmp/RtmpL8qXxH/file18aa17542138/BayesLogit_0.6.tar.gz’ had non-zero exit status

I have checked for the installation of -lblas and -lapack using

sudo apt-get update

Hit:1 http://nz.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://nz.archive.ubuntu.com/ubuntu bionic-updates InRelease 
Hit:3 http://nz.archive.ubuntu.com/ubuntu bionic-backports InRelease 
Hit:4 https://repo.skype.com/deb stable InRelease 
Hit:5 https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ InRelease 
Get:6 https://desktop-download.mendeley.com/download/apt stable InRelease [2,456 B] 
Ign:7 http://dl.bintray.com/basespace/BaseMount-DEB saucy InRelease 
Ign:8 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy InRelease 
Hit:9 http://security.ubuntu.com/ubuntu bionic-security InRelease 
Hit:10 http://ppa.launchpad.net/inkscape.dev/stable/ubuntu bionic InRelease
Get:11 http://dl.bintray.com/basespace/BaseMount-DEB saucy Release [1,838 B] 
Get:12 http://dl.bintray.com/basespace/BaseSpaceFS-DEB saucy Release [1,837 B] 
Hit:13 http://ppa.launchpad.net/marutter/rrutter/ubuntu bionic InRelease 
Fetched 6,131 B in 2s (4,067 B/s) 
Reading package lists... Done

Followed by

sudo apt-get install libblas-dev liblapack-dev

Reading package lists... Done
Building dependency tree 
Reading state information... Done
libblas-dev is already the newest version (3.7.1-4ubuntu1).
liblapack-dev is already the newest version (3.7.1-4ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 28 not upgraded.

However, I still get the same error when attempting to install BayesLogit in R.

Any help on how to overcome this error would be appreciated.
Chris

To install the HMISC R package in all currently supported versions of Ubuntu open the terminal and type:

sudo apt install r-cran-hmisc 

The r-cran-hmisc package does not depend on either libblas-dev or liblapack-dev, so you won't get a cannot find -lblas or
cannot find -llapack error message when trying to install r-cran-hmisc.

The error message that you got when trying to install the HMISC R package is Anaconda's fault for sure, but I don't know where the culprit Anaconda file is located in your system. Usually when a path is borked by Anaconda you can symbolic link it back to the appropriate Ubuntu executable. If Anaconda has messed up too many paths in your system, the only way you're going to get rid of the mess is by completely uninstalling and purging Anaconda.