Rstudio and R source code install (20220105)

jsyu@Oreo:~$ sudo apt update

jsyu@Oreo:~$ sudo apt --fix-broken install

jsyu@Oreo:~$ sudo apt install xvfb xauth xfonts-base xorg-dev libtiff5 libtiff5-dev  libcairo2 libghc-cairo-dev texlive-latex-base gsfonts-x11 t1-xfree86-nonfree ttf-xfree86-nonfree ttf-xfree86-nonfree-syriac xfonts-75dpi xfonts-100dpi

jsyu@Oreo:~$ sudo apt install openssl libssl-dev xml2 libxml2-dev icu-devtools libicu-dev

For Ubuntu 18.04

jsyu@Oreo:~$ sudo apt install libreadline-dev libbz2-dev libpcre2 libpcre2-dev libpcre3-dev libpcre2-dev libcurl libcurl3 libcurl4 libcurl3-gnutls libcurl3-dev libcurl4-dev  libcurl4-gnutls-dev libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev texlive texlive-fonts-extra texlive-fonts-extra-doc html2ps texinfo   libclang-dev

For Ubuntu 20.04

jsyu@Oreo:~$ sudo apt install libreadline-dev libbz2-dev libpcre2-dev libpcre3-dev libpcre2-dev  libcurl3-gnutls libcurl3-dev libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev texlive texlive-fonts-extra texlive-fonts-extra-doc html2ps texinfo libclang-dev libpq5

jsyu@Oreo:~$ sudo apt install openjdk-11-jre openjdk-11-jdk libblas-dev g++ gfortran libicu66 make aglfn git tk-dev liblapack-dev libopenblas-dev

Check https://www.rstudio.com/products/rstudio/download/#download for the newest version of source code of RStudio

jsyu@Oreo:~$ wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-2021.09.1-372-amd64.deb

jsyu@Oreo:~$ sudo dpkg -i rstudio-2021.09.1-372-amd64.deb

(Reading database ... 156559 files and directories currently installed.)

Preparing to unpack rstudio-2021.09.1-372-amd64.deb ...

Unpacking rstudio (2021.09.1+372) over (2021.09.1+372) ...

dpkg: dependency problems prevent configuration of rstudio:

 rstudio depends on libclang-dev; however:

  Package libclang-dev is not installed.

 rstudio depends on libpq5; however:

  Package libpq5 is not installed.

dpkg: error processing package rstudio (--install):

 dependency problems - leaving unconfigured

Processing triggers for gnome-menus (3.36.0-1ubuntu1) ...

Processing triggers for desktop-file-utils (0.24-1ubuntu3) ...

Processing triggers for mime-support (3.64ubuntu1) ...

Processing triggers for hicolor-icon-theme (0.17-2) ...

Processing triggers for shared-mime-info (1.15-1) ...

Errors were encountered while processing:

 rstudio

Check dependency if installation failed. Install required packages and re-run

sudo dpkg -i rstudio-2021.09.1-372-amd64.deb 

again.

Check https://cran.r-project.org/sources.html for the newest version of source code of R

jsyu@Oreo:~$ wget https://cran.r-project.org/src/base/R-4/R-4.1.2.tar.gz

jsyu@Oreo:~$ ls -al / | grep rwt

drwxrwxrwt  19 root root              4096 Dec 29 17:40 tmp

jsyu@Oreo:~$ tar zxvf R-4.1.2.tar.gz -C /tmp

jsyu@Oreo:/tmp/R-4.1.2$ cd /tmp/R-4.1.2

jsyu@Oreo:/tmp/R-4.1.2$ ./configure --prefix=/usr/local/R-4.1.2 --with-x --with-cairo --with-libtiff --with-libpng --with-jpeglib --enable-R-shlib --enable-BLAS-shlib

R is now configured for x86_64-pc-linux-gnu

  Source directory:                .

  Installation directory:          /usr/local/R-4.1.2

  C compiler:                      gcc  -g -O2

  Fortran fixed-form compiler: gfortran -fno-optimize-sibling-calls -g -O2

  Default C++ compiler:            g++ -std=gnu++14  -g -O2

  C++11 compiler:                  g++ -std=gnu++11  -g -O2

  C++14 compiler:                  g++ -std=gnu++14  -g -O2

  C++17 compiler:                  g++ -std=gnu++17  -g -O2

  C++20 compiler:                  g++ -std=gnu++2a  -g -O2

  Fortran free-form compiler:  gfortran -fno-optimize-sibling-calls -g -O2

  Obj-C compiler:                

  Interfaces supported:            X11

  External libraries:              pcre2, readline, curl

  Additional capabilities:         PNG, JPEG, TIFF, NLS, cairo

  Options enabled:                 shared R library, shared BLAS, R profiling

  Capabilities skipped:            ICU

  Options not enabled:             memory profiling

  Recommended packages:            yes

 

jsyu@Oreo:/tmp/R-4.1.2$ make -j 2 | tee make.log       # starting 20:43–20:49

jsyu@Oreo:/tmp/R-4.1.2$ make -j 2 check | tee check.log      # 20:50–20:54

jsyu@Oreo:/tmp/R-4.1.2$ sudo make install

jsyu@Oreo:/tmp/R-4.1.2$ sudo ln -s /usr/local/R-4.1.2/bin/R /usr/bin

jsyu@Oreo:/tmp/R-4.1.2$ sudo ln -s /usr/local/R-4.1.2/bin/Rscript \ /usr/bin

jsyu@Oreo:/tmp/R-4.1.2$ lscpu

Architecture:                        x86_64

CPU op-mode(s):                      32-bit, 64-bit

Byte Order:                          Little Endian

Address sizes:                       39 bits physical, 48 bits virtual

CPU(s):                              4

On-line CPU(s) list:                 0-3

Thread(s) per core:                  2

Core(s) per socket:                  2

Socket(s):                           1

NUMA node(s):                        1

Vendor ID:                           GenuineIntel

CPU family:                          6

Model:                               142

Model name:                          Intel(R) Core(TM) i3-8109U CPU @ 3.00GHz

Stepping:                            10

CPU MHz:                             1128.259

CPU max MHz:                         3600.0000

CPU min MHz:                         400.0000

BogoMIPS:                            6000.00

Virtualization:                      VT-x

L1d cache:                           64 KiB

L1i cache:                           64 KiB

L2 cache:                            512 KiB

L3 cache:                            4 MiB

NUMA node0 CPU(s):                   0-3


Under R (Command line interface, CLI)

jsyu@Oreo:/tmp/R-4.1.2$ sudo R           # Install R packages for every user requires sudo

> sessionInfo()

R version 4.1.2 (2021-11-01)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 20.04.3 LTS

Matrix products: default

BLAS:   /usr/local/R-4.1.2/lib/R/lib/libRblas.so

LAPACK: /usr/local/R-4.1.2/lib/R/lib/libRlapack.so

locale:

 [1] LC_CTYPE=en_US.UTF-8        LC_NUMERIC=C                LC_TIME=en_US.UTF-8    

 [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=lzh_TW          LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=lzh_TW             LC_NAME=C                   LC_ADDRESS=C              

[10] LC_TELEPHONE=C              LC_MEASUREMENT=lzh_TW   LC_IDENTIFICATION=C    

attached base packages:

[1] stats         graphics  grDevices utils         datasets  methods   base        

loaded via a namespace (and not attached):

[1] compiler_4.1.2

> capabilities()

           jpeg             png            tiff           tcltk             X11            aqua

           TRUE            TRUE            TRUE           FALSE            TRUE           FALSE

   http/ftp         sockets          libxml            fifo          cledit           iconv

           TRUE            TRUE            TRUE            TRUE            TRUE            TRUE

            NLS           Rprof         profmem           cairo             ICU  long.double

           TRUE            TRUE           FALSE            TRUE           FALSE            TRUE

        libcurl

           TRUE

      # See below for aligned terms with screen capture.

> install.packages('extrafont')

       # Choose from source list [70] at https://cran.csie.ntu.edu.tw

> install.packages('ggplot2')

> install.packages("rJava")

> install.packages("xlsx")           # Read and export to Excel and XML formats

> install.packages("gdata")         # Read Excel file

> install.packages("devtools")  

> install.packages("gplots")

> install.packages("cowplot")

> install.packages("RColorBrewer")

> install.packages("reshape2")

> install.packages("plyr")

> install.packages("ggpubr")

> install.packages("circlize")

> install.packages("magrittr")

> install.packages("org.Hs.eg.db")   # Okay if fail, one of the following installs it too.

## Packages of R that have been utilized in our class this semester:

## Must run   install.packages("devtools")   first  

genefilter

geneplotter

DESeq2

tximportData

tximport

apeglm

clusterProfiler

enrichplot    

ChIPpeakAnno  

pathview  

ConsensusClusterPlus

ComplexHeatmap

org.Hs.eg.db ?

# Install above components colored in teal

> devtools::install_bioc("genefilter")  

> devtools::install_bioc("geneplotter")   

> devtools::install_bioc("DESeq2")    

> devtools::install_bioc("tximportData")

… …

> devtools::install_bioc("ComplexHeatmap")

> installed.packages()        

   # Check installed R packages

> library('xlsx','gdata')

> sessionInfo()

R version 4.1.2 (2021-11-01)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Ubuntu 20.04.3 LTS

Matrix products: default

BLAS:   /usr/local/R-4.1.2/lib/R/lib/libRblas.so

LAPACK: /usr/local/R-4.1.2/lib/R/lib/libRlapack.so

locale:

 [1] LC_CTYPE=en_US.UTF-8         LC_NUMERIC=C                 LC_TIME=en_US.UTF-8        

 [4] LC_COLLATE=en_US.UTF-8   LC_MONETARY=lzh_TW           LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=lzh_TW              LC_NAME=lzh_TW               LC_ADDRESS=lzh_TW          

[10] LC_TELEPHONE=lzh_TW          LC_MEASUREMENT=lzh_TW        LC_IDENTIFICATION=lzh_TW

attached base packages:

[1] stats         graphics  grDevices utils         datasets  methods   base        

other attached packages:

[1] xlsx_0.6.5  rJava_1.0-6

loaded via a namespace (and not attached):

[1] compiler_4.1.2 tools_4.1.2        xlsxjars_0.6.1

> q()               # Quit R.

jsyu@Oreo:/tmp/R-4.1.2$ du -sh /usr/local/R-4.1.2/lib

2.0G    /usr/local/R-4.1.2/lib

        # All of the above-installed R packages took about 2GB of disk space.