Rstudio and R-4.2.2 source code install (20221229)
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 libharfbuzz-dev libfribidi-dev
jsyu@Oreo:~$ sudo apt install rsem trimmomatic fastqc rna-star
Check https://www.rstudio.com/products/rstudio/download/#download for the newest version of the IDE of RStudio that fits your Linux distribution. In our cases of Ubuntu 18.04 and 20.04, choose RSTUDIO-2022.12.0-353-AMD64.DEB for Ubuntu 18+/Debian 10+.
jsyu@Oreo:~$ wget \ https://download1.rstudio.org/electron/bionic/amd64/rstudio-2022.12.0-353-amd64.deb
jsyu@Oreo:~$ sudo dpkg -i rstudio-2022.12.0-353-amd64.deb
(Reading database ... 388651 files and directories currently installed.) Preparing to unpack rstudio-2022.12.0-353-amd64.deb ... Unpacking rstudio (2022.12.0+353) over (2021.09.1+372) ... Setting up rstudio (2022.12.0+353) ... Processing triggers for gnome-menus (3.13.3-11ubuntu1) ... Processing triggers for desktop-file-utils (0.23-1ubuntu3.18.04.1) ... Processing triggers for mime-support (3.60ubuntu1) ... Processing triggers for hicolor-icon-theme (0.17-2) ... Processing triggers for shared-mime-info (1.9-2) ... |
This means installation successfully completed.
If you run into failure like the messages below:
(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 the above dependency if installation failed. Install required packages and re-run
sudo dpkg -i rstudio-2022.12.0-353-amd64.deb
again.
Check https://cran.r-project.org/sources.html for the newest version of source code of R (in our case, R-4.2.2)
jsyu@Oreo:~$ wget \
https://cran.r-project.org/src/base/R-4/R-4.2.2.tar.gz
jsyu@Oreo:~$ ls -al / | grep rwt
drwxrwxrwt 19 root root 4096 Dec 29 17:40 tmp
jsyu@Oreo:~$ tar zxvf R-4.2.2.tar.gz -C /tmp
jsyu@Oreo:/tmp/R-4.2.2$ cd /tmp/R-4.2.2
jsyu@Oreo:/tmp/R-4.2.2$ ./configure --prefix=/usr/local/R-4.2.2 --with-x \ --with-cairo --with-libtiff --with-libpng --with-jpeglib --enable-R-shlib \ --enable-BLAS-shlib --enable-memory-profiling
R is now configured for x86_64-pc-linux-gnu Source directory: . Installation directory: /usr/local/R-4.2.2 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: Fortran free-form compiler: gfortran -fno-optimize-sibling-calls -g -O2 Obj-C compiler: Interfaces supported: X11, tcltk External libraries: pcre2, readline, curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, shared BLAS, R profiling, memory profiling Capabilities skipped: Options not enabled: Recommended packages: yes |
jsyu@Oreo:/tmp/R-4.2.2$ make -j 2 | tee make.log
jsyu@Oreo:/tmp/R-4.2.2$ make check | tee check.log
jsyu@Oreo:/tmp/R-4.2.2$ sudo make install
jsyu@Oreo:/tmp/R-4.2.2$ sudo ln -s /usr/local/R-4.2.2/bin/R /usr/bin
jsyu@Oreo:/tmp/R-4.2.2$ sudo ln -s /usr/local/R-4.2.2/bin/Rscript /usr/bin
jsyu@Oreo:/tmp/R-4.2.2$ 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-4.2.2$ sudo R # Install R packages for every user requires sudo
> sessionInfo()
R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS Matrix products: default BLAS: /usr/local/R-4.2.2/lib/R/lib/libRblas.so LAPACK: /usr/local/R-4.2.2/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.utf8 [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_4.2.2 tools_4.2.2 |
> capabilities()
jpeg png tiff tcltk X11 aqua http/ftp TRUE TRUE TRUE TRUE TRUE FALSE TRUE sockets libxml fifo cledit iconv NLS Rprof TRUE FALSE TRUE TRUE TRUE TRUE TRUE profmem cairo ICU long.double libcurl TRUE TRUE TRUE TRUE TRUE |
# It seems normal that libxml fails to be built in R-4.2.2. Install it inside R.
# Aqua is for MacOS.
> install.packages('XML')
# Choose from source list 68: Taiwan (Taipei) [https]
> install.packages('extrafont')
> install.packages('ggplot2')
> install.packages("rJava")
> install.packages("xlsx") # To read and export into Excel and XML formats
> install.packages("gdata") # To read Excel files
> 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("nlme")
> install.packages("org.Hs.eg.db") # Okay if fail ; one of the following installs it too (likely clusterProfiler ).
## Packages of R that have been utilized in our class this semester: ## Must run install.packages("devtools") first genefilter geneplotter DESeq2 tximportData tximport apeglm enrichplot clusterProfiler 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 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.1 LTS Matrix products: default BLAS: /usr/local/R-4.2.2/lib/R/lib/libRblas.so LAPACK: /usr/local/R-4.2.2/lib/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.utf8 [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 loaded via a namespace (and not attached): [1] Rcpp_1.0.9 compiler_4.2.2 later_1.3.0 urlchecker_1.0.1 [5] prettyunits_1.1.1 profvis_0.3.7 remotes_2.4.2 tools_4.2.2 [9] digest_0.6.31 pkgbuild_1.4.0 pkgload_1.3.2 memoise_2.0.1 [13] lifecycle_1.0.3 rlang_1.0.6 shiny_1.7.4 cli_3.5.0 [17] curl_4.3.3 fastmap_1.1.0 rJava_1.0-6 withr_2.5.0 [21] stringr_1.5.0 xlsxjars_0.6.1 desc_1.4.2 fs_1.5.2 [25] htmlwidgets_1.6.0 vctrs_0.5.1 devtools_2.4.5 rprojroot_2.0.3 [29] glue_1.6.2 R6_2.5.1 processx_3.8.0 sessioninfo_1.2.2 [33] callr_3.7.3 purrr_1.0.0 magrittr_2.0.3 ps_1.7.2 [37] promises_1.2.0.1 ellipsis_0.3.2 htmltools_0.5.4 usethis_2.1.6 [41] mime_0.12 xtable_1.8-4 httpuv_1.6.7 stringi_1.7.8 [45] miniUI_0.1.1.1 cachem_1.0.6 crayon_1.5.2 |
> q() # Quit R.
jsyu@Oreo:/tmp/R-4.2.2$ du -sh /usr/local/R-4.2.2/lib
1.9G /usr/local/R-4.2.2/lib
# All of the above-installed R packages took about 2GB of disk space.