Libraries and programs for a generic datasciecne remote server to test data-science-related topics and setups.
- 1.1. How to use it
- 1.2. How it has been developed
intructions to come
All people will have their own credentials, sent to their email addresses.
Users will be in the sudoers group, so that you can run commands as root if your prepend those commands with sudo, as usual.
Use Anaconda as usual
Open the browser, and it will launch RStudio server in it by default (
You have R 3.6 installed.
Lubuntu GNU/Linux 18.04 (64 bits). Fetch iso from their website.
First enable "partners" repos.
## Uncomment the following two lines to add software from Canonical's ## 'partner' repository. ## This software is not part of Ubuntu, but is offered by Canonical and the ## respective vendors as a service to Ubuntu users. deb http://archive.canonical.com/ubuntu bionic partner deb-src http://archive.canonical.com/ubuntu bionic partner
sudo add-apt-repository -y ppa:nilarimogard/webupd8 # per a launchpadd-getkeys i altres sudo add-apt-repository -y ppa:utappia/stable # per a ucaresystem-core sudo add-apt-repository -y ppa:webupd8team/java # per a java propietari (on calgui) sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable # per a paquets d'analisi geoespacial sudo add-apt-repository -y 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' # main binary packages for R 3.5.x sudo add-apt-repository -y ppa:marutter/c2d4u3.5 # extra binary packages for R 3.5.x from the usual marruter repo
# Add the key for the new repo for R 3.6.x from cloud.r-project.org apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 # marutter apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 089EBE08314DF160 # ubuntugis-stable
Other general packages installed:
sudo apt install -y curl htop mc kupfer git cups-pdf parcellite
Launch parcellite and kupfer. Change parcellite to store 250 entries. And set kupfer to launch automatically on user login.
For demostration purposes, I'll add a full lubuntu desktop in this virtual machine
sudo apt-get install lubuntu-desktop
With X2Go (https://wiki.x2go.org) you can do so, from computers using GNU/Linux, Mac OSX or MS Windows
sudo add-apt-repository ppa:x2go/stable sudo apt-get update sudo apt-get install x2goserver x2goserver-xsession sudo apt-get install --no-install-recommends lxde sudo apt-get install x2golxdebindings
Connect with X2Go client to server
datascience.seeds4c.org , choosing as a session:
- Custom session:
lxsession -e LXDE -s Lubuntu
We add these repos to use the latest R versions released
Comandes i paquets lubuntu 18.04:
sudo apt-get install -y bwidget dos2unix freeglut3 freeglut3-dev git libc6 libcairo2-dev libcurl4-gnutls-dev libgdal-dev libgeos-dev libglpk-dev libgraphviz-dev libjq-dev libmagick++-dev libmpfr-dev libproj-dev libprotobuf-dev libssh2-1-dev libssl-dev libudunits2-dev libv8-dev libx11-dev libxml2 libxml2-dev libxml2:i386 libxt-dev pandoc protobuf-compiler r-cran-cairodevice r-cran-devtools r-cran-doparallel r-cran-geor r-cran-ggmap r-cran-ggplot2 r-cran-gstat r-cran-igraph r-cran-leaflet r-cran-lme4 r-cran-mapdata r-cran-maps r-cran-misc3d r-cran-ncdf4 r-cran-raster r-cran-rcolorbrewer r-cran-rgl r-cran-rglpk r-cran-rjags r-cran-rjava r-cran-rmio r-cran-rmysql r-cran-roxygen2 r-cran-snow r-cran-sp r-cran-xlsx r-cran-xml r-recommended subversion texlive-lang-spanish texlive-latex-extra texmaker tk-dev tk-table unaccent xvfb libssh2-1-dev ucaresystem-core libudunits2-dev gigolo filezilla openjdk-8-jre ibm-java80-jre sudo R CMD javareconf
Paquets de CRAN: posar dins de la comanda:
library(pacman) p_load("tidyverse", "caTools", "bitops", "httpuv", "devtools", "rpivotTable", "DT", "shiny", "magick", "rvg", "addinslist", "ff", "sparklyr", "data.table", "rio", "rpivotGadget", "radiant", "CRANsearcher", "regexplain", "rJava", "knitr", "rmarkdown", "webshot", "magick", "rsvg", "sf", "leaflet", "htmlwidgets")
Rstudio Addins: CRANsearcher, addinslist, regexplain
Paquets lubuntu 18.04: texstudio
Server version, to use through browser at
http://localhost:8787 from inside the X2Go session. Or directly from your remote local computer opening a browser at: http://datascience.seeds4c.org:8787
sudo apt-get install gdebi-core wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.3.959-amd64.deb sudo gdebi rstudio-server-1.3.959-amd64.deb
We will install anaconda on a system folder as
sudo mkdir /opt/py sudo chmod 777 /opt/py cd /tmp curl -O https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh bash Anaconda3-2019.03-Linux-x86_64.sh
datascience@datasciencepc:/tmp$ bash Anaconda3-2019.03-Linux-x86_64.sh Welcome to Anaconda3 2019.03 In order to continue the installation process, please review the license agreement. Please, press ENTER to continue >>> =================================== Anaconda End User License Agreement =================================== Copyright 2015, Anaconda, Inc. All rights reserved under the 3-clause BSD License: Redistribution and use in source and binary forms, with or without modification, are permitted provided that the fo llowing conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the followin g disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the follo wing disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Anaconda, Inc. ("Anaconda, Inc.") nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE D ISCLAIMED. IN NO EVENT SHALL ANACONDA, INC. BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DAT A, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Notice of Third Party Software Licenses ======================================= Anaconda Distribution contains open source software packages from third parties. These are available on an "as is" basis and subject to their individual license agreements. These licenses are available in Anaconda Distribution or at http://docs.anaconda.com/anaconda/pkg-docs. Any binary packages of these third party tools you obtain via Anacon da Distribution are subject to their individual licenses as well as the Anaconda license. Anaconda, Inc. reserves t he right to change which third party tools are provided in Anaconda Distribution. In particular, Anaconda Distribution contains re-distributable, run-time, shared-library files from the Intel(TM) M ath Kernel Library ("MKL binaries"). You are specifically authorized to use the MKL binaries with your installation of Anaconda Distribution. You are also authorized to redistribute the MKL binaries with Anaconda Distribution or i n the conda package that contains them. Use and redistribution of the MKL binaries are subject to the licensing ter ms located at https://software.intel.com/en-us/license/intel-simplified-software-license. If needed, instructions f or removing the MKL binaries after installation of Anaconda Distribution are available at http://www.anaconda.com. Anaconda Distribution also contains cuDNN software binaries from NVIDIA Corporation ("cuDNN binaries"). You are spe cifically authorized to use the cuDNN binaries with your installation of Anaconda Distribution. You are also author ized to redistribute the cuDNN binaries with an Anaconda Distribution package that contains them. If needed, instru ctions for removing the cuDNN binaries after installation of Anaconda Distribution are available at http://www.anac onda.com. Anaconda Distribution also contains Visual Studio Code software binaries from Microsoft Corporation ("VS Code"). Yo u are specifically authorized to use VS Code with your installation of Anaconda Distribution. Use of VS Code is sub ject to the licensing terms located at https://code.visualstudio.com/License. Cryptography Notice =================== This distribution includes cryptographic software. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to another country, of encryption software. BEFORE using any encry ption software, please check your country's laws, regulations and policies concerning the import, possession, or us e, and re-export of encryption software, to see if this is permitted. See the Wassenaar Arrangement http://www.wass enaar.org/ for more information. Anaconda, Inc. has self-classified this software as Export Commodity Control Number (ECCN) 5D992b, which includes m ass market information security software using or performing cryptographic functions with asymmetric algorithms. No license is required for export of this software to non-embargoed countries. In addition, the Intel(TM) Math Kernel Library contained in Anaconda, Inc.'s software is classified by Intel(TM) as ECCN 5D992b with no license required for export to non-embargoed countries and Microsoft's Visual Studio Code software is classified by Microsoft as ECC N 5D992.c with no license required for export to non-embargoed countries. The following packages are included in this distribution that relate to cryptography: openssl The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open So urce toolkit implementing the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols as well as a full-strength general purpose cryptography library. pycrypto A collection of both secure hash functions (such as SHA256 and RIPEMD160), and various encryption algorithms (A ES, DES, RSA, ElGamal, etc.). pyopenssl A thin Python wrapper around (a subset of) the OpenSSL library. kerberos (krb5, non-Windows platforms) A network authentication protocol designed to provide strong authentication for client/server applications by u sing secret-key cryptography. cryptography A Python library which exposes cryptographic recipes and primitives. Do you accept the license terms? [yes|no] [no] >>> yes Anaconda3 will now be installed into this location: /home/gid/anaconda3 - Press ENTER to confirm the location - Press CTRL-C to abort the installation - Or specify a different location below [/home/datascience/anaconda3] >>> /opt/py/anaconda3 ...
Paquets lubuntu 18.04:
sudo apt install -y python-numpy python-pandas python-matplotlib python-seaborn ipython-notebook ipython-doc