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library(tidyverse)  # devtools::install_github('tidyverse/tidyverse')
#> -- Attaching packages -------------------------------------------------------------------------------- tidyverse 1.2.1 --
#> v ggplot2 2.2.1     v purrr   0.2.4
#> v tibble  1.3.4     v dplyr   0.7.4
#> v tidyr   0.7.2     v stringr 1.2.0
#> v readr   1.1.1     v forcats 0.2.0
#> -- Conflicts ----------------------------------------------------------------------------------- tidyverse_conflicts() --
#> x dplyr::filter() masks stats::filter()
#> x dplyr::lag()    masks stats::lag()

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#' ---
#' title: "Setup (with `{renv}`)"
#' author: "Corrado Lanera"
#' date: "`r date()`"
#' output:
#'   html_document:
#'     toc: true
#'     toc_float: true
#'     keep_md: true
#' ---

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# import os utilities
import os
import requests, zipfile, io

# import numpy
import numpy as np

# images
import skimage
from skimage import transform

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import types


def imports():
    for name, val in globals().items():
        if isinstance(val, types.ModuleType):
            yield val.__name__


print(list(imports()))

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sudo apt-get install libopenblas-base
sudo update-alternatives --config libblas.so.3-x86_64-linux-gnu # check openblas/libblas.so.3
sudo update-alternatives --config liblapack.so.3-x86_64-linux-gnu # select lapack/liblapack.so.3 

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R package tensorflow use the conda envirnment "r-tensorflow". hence I have to install my compiled version of tf within that environment

1. update system and python
```
sudo apt-get update
sudo apt-get upgrade
```

2. install and update conda, and anaconda
```

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# download tarbal from https://www.zotero.org/download/
# xvzf fro .bz, xvjf for .bz2
sudo tar xvjf Zotero-5.0.70_linux-x86_64.tar.bz2 -C /opt/
cd /opt/Zotero_linux-x86_64
sudo ./set_launcher_icon

# if not already present symlink to the menu
ln -s /opt/zotero/zotero.desktop ~/.local/share/applications/zotero.desktop

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# examples for R-4.0.2
sudo wget https://cran.r-project.org/src/base/R-4/R-4.0.2.tar.gz
sudo tar -xvzf R-4.0.2.tar.gz
cd R-4.0.2

# install in /opt/R to make it automatically discovered by RSSP
sudo ./configure --prefix=/opt/R/$(cat VERSION) --enable-memory-profiling --enable-R-shlib --with-blas --with-lapack
sudo make
sudo make install

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# CL personal adjustment form https://discourse.mc-stan.org/t/rstan-rstantools-travis/6102

language: R
sudo: true
cache: packages

env:
 - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"

r_packages:

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# R Benchmark 3.1 (05/2020) [Corrado Lanera]
# version 3.1 changed default random generator packages and functions
# given that the older ones are deprecated, R 4.0.0 @ Xeon 2.4GHz Ubuntu 10.04.4 LTS 

# R Benchmark 2.5 (06/2008) [Simon Urbanek]
# version 2.5: scaled to get roughly 1s per test, R 2.7.0 @ 2.6GHz Mac Pro
# R Benchmark 2.4 (06/2008) [Simon Urbanek]
# version 2.4 adapted to more recent Matrix package
# R Benchmark 2.3 (21 April 2004)
# Warning: changes are not carefully checked yet!