EpiNow2 runntime errors

This runntime error seems to be just a warning, because Rt was still reported.  

https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup

Logging threshold set at INFO for the EpiNow2 logger

Writing EpiNow2 logs to the console and: /var/folders/bw/k6_tkc2142v1wh5r_1yhkqhc0000gp/T//Rtmpb4xcT4/regional-epinow/2020-10-27.log

Logging threshold set at INFO for the EpiNow2.epinow logger

Writing EpiNow2.epinow logs to the console and: /var/folders/bw/k6_tkc2142v1wh5r_1yhkqhc0000gp/T//Rtmpb4xcT4/epinow/2020-10-27.log

WARN [2021-11-09 19:42:32] epinow: There were 2 divergent transitions after warmup. See

http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup

to find out why this is a problem and how to eliminate them. - 

WARN [2021-11-09 19:42:32] epinow: Examine the pairs() plot to diagnose sampling problems

ts conda create condaR403

 # Hong will install anaconda R403 in a conda environment on ts117. This strategy worked. 

conda create --name condaR403

  environment location: /home/hqin/.conda/envs/condaR403

-bash-4.2$ conda activate condaR403

conda install -c r r-base #??

# which R shows an R403 inside an conda environment. 

R

install.packages('tidyverse') #this seems worked. 

install.packages('EpiNow2')  #this run for a while

non-zero exit again due to V8. 

(condaR403) -bash-4.2$ conda install -c conda-forge libv8

$ conda install -c conda-forge r-randomcolor

R

install.packages('EpiNow2') #this worked!!!!

> library(EpiNow2)

> 

module load sge

qsub epinow2.pbs #this runs!!!!

(condaR403) -bash-4.2$ cat epinow2.pbs

#!/bin/bash -l

#$ -S /bin/bash

#$ -N epinow_job

#$ -V

#$ -cwd

. /etc/profile.d/modules.sh

module load anaconda/5.2.0

source activate condaR403

R -f batch_Rt_by_county.R --args 900 901 1 4/1/2020 5/1/2020

ts conda tsR403, tidyverse, EpiNow2 installation

# THIS DID NOT WORK

-bash-4.2$ module load anaconda/5.2.0 

-bash-4.2$ conda create --name tsR403

Collecting package metadata: done

Solving environment: done

## Package Plan ##

  environment location: /home/hqin/.conda/envs/tsR403

Proceed ([y]/n)? y  

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

#

# To activate this environment, use

#

#     $ conda activate tsR403

#

# To deactivate an active environment, use

#

#     $ conda deactivate

-bash-4.2$ 

 -bash-4.2$ conda activate tsR403

(tsR403) -bash-4.2$ conda install -c conda-forge libv8

Collecting package metadata: done

Hong then run R

install.packages('tidyverse') #this seem to worked. 

-----------------------------[ ANTICONF ]-------------------------------

Configuration failed to find the libv8 engine library. Try installing:

 * deb: libv8-dev or libnode-dev (Debian / Ubuntu)

 * rpm: v8-devel (Fedora, EPEL)

 * brew: v8 (OSX)

 * csw: libv8_dev (Solaris)

To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:

R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'

---------------------------[ ERROR MESSAGE ]----------------------------

<stdin>:1:16: fatal error: v8.h: No such file or directory

compilation terminated.

-------------------------------------------------------

(tsR403) -bash-4.2$ conda install -c conda-forge r-randomcolor

Collecting package metadata: \ 

#this install many packages

Ref: https://github.com/iaconogi/bigSCale2/issues/19

I then tried:

R: install.packages('EpiNow2') #this seems to be running now. 

library(EpiNow2) #it worked!

install.packages('woldmet')

#The entire install seem to take almost 2 hours. 

Checked a few hour later, EpiNow2 installation did not work.