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Install R and RStudio on Ubuntu 18.04 with essential libraries for data science. Based on pachamaltese/r_ubuntu_17_10.sh (for Ubuntu 17.10). Note: You need to make sure the default library location - /usr/local/lib/R/site-packages - is writable .
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| # Install R | |
| sudo apt update | |
| sudo apt install gdebi libxml2-dev libssl-dev libcurl4-openssl-dev libopenblas-dev r-base r-base-dev | |
| # Install RStudio | |
| cd ~/Downloads | |
| wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5001-amd64.deb | |
| sudo gdebi rstudio-1.2.5001-amd64.deb | |
| printf '\nexport QT_STYLE_OVERRIDE=gtk\n' | sudo tee -a ~/.profile | |
| # Install common packages | |
| R --vanilla << EOF | |
| install.packages(c("tidyverse","data.table","dtplyr","devtools","roxygen2","bit64","readr"), repos = "https://cran.rstudio.com/") | |
| q() | |
| EOF | |
| # Install TDD packages | |
| R --vanilla << EOF | |
| install.packages("testthis") | |
| q() | |
| EOF | |
| # Export to HTML/Excel | |
| R --vanilla << EOF | |
| install.packages(c("htmlTable","openxlsx"), repos = "https://cran.rstudio.com/") | |
| q() | |
| EOF | |
| # Blog tools | |
| R --vanilla << EOF | |
| install.packages(c("knitr","rmarkdown"), repos='http://cran.us.r-project.org') | |
| q() | |
| EOF | |
| sudo apt install python-pip | |
| sudo apt install python3-pip | |
| sudo -H pip install markdown rpy2==2.7.1 pelican==3.7.1 | |
| sudo -H pip3 install markdown rpy2==2.9.3 pelican==3.7.1 | |
| # PDF extraction tools | |
| sudo apt install libpoppler-cpp-dev default-jre default-jdk r-cran-rjava | |
| sudo R CMD javareconf | |
| R --vanilla << EOF | |
| library(devtools) | |
| install.packages("pdftools", repos = "https://cran.rstudio.com/") | |
| install_github("ropensci/tabulizer") | |
| q() | |
| EOF | |
| # TTF/OTF fonts usage | |
| sudo apt install libfreetype6-dev | |
| R --vanilla << EOF | |
| install.packages("showtext", repos = "https://cran.rstudio.com/") | |
| q() | |
| EOF | |
| # Cairo for graphic devices | |
| sudo apt install libgtk2.0-dev libxt-dev libcairo2-dev | |
| R --vanilla << EOF | |
| install.packages("Cairo", repos = "https://cran.rstudio.com/") | |
| q() | |
| EOF | |
| # Texlive for Latex/knitr | |
| sudo apt -y install texlive | |
| sudo apt -y install texlive-latex-recommended texlive-pictures texlive-latex-extra |
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Hi everyone! I have install R with the code above but when I tried to install the pacages Rcmdr, it doesn't work!
install.packages("Rcmdr")
Installing package into ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘pillar’, ‘tidyr’, ‘ggplot2’, ‘viridis’, ‘forcats’, ‘hms’, ‘readr’, ‘tibble’, ‘tidyselect’, ‘vctrs’, ‘cellranger’, ‘progress’, ‘broom’, ‘dplyr’, ‘Hmisc’, ‘haven’, ‘readxl’, ‘pbkrtest’, ‘rio’, ‘RcppEigen’, ‘RcmdrMisc’, ‘car’, ‘effects’, ‘lme4’
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/pillar_1.6.1.tar.gz'
Content type 'application/x-gzip' length 1111747 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/tidyr_1.1.3.tar.gz'
Content type 'application/x-gzip' length 707909 bytes (691 KB)
downloaded 691 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/ggplot2_3.3.5.tar.gz'
Content type 'application/x-gzip' length 3063309 bytes (2.9 MB)
downloaded 2.9 MB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/viridis_0.6.1.tar.gz'
Content type 'application/x-gzip' length 3054905 bytes (2.9 MB)
downloaded 2.9 MB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/forcats_0.5.1.tar.gz'
Content type 'application/x-gzip' length 258301 bytes (252 KB)
downloaded 252 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/hms_1.1.0.tar.gz'
Content type 'application/x-gzip' length 43142 bytes (42 KB)
downloaded 42 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/readr_1.4.0.tar.gz'
Content type 'application/x-gzip' length 488946 bytes (477 KB)
downloaded 477 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/tibble_3.1.2.tar.gz'
Content type 'application/x-gzip' length 686145 bytes (670 KB)
downloaded 670 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/tidyselect_1.1.1.tar.gz'
Content type 'application/x-gzip' length 92088 bytes (89 KB)
downloaded 89 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/vctrs_0.3.8.tar.gz'
Content type 'application/x-gzip' length 782608 bytes (764 KB)
downloaded 764 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/cellranger_1.1.0.tar.gz'
Content type 'application/x-gzip' length 63857 bytes (62 KB)
downloaded 62 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/progress_1.2.2.tar.gz'
Content type 'application/x-gzip' length 29506 bytes (28 KB)
downloaded 28 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/broom_0.7.8.tar.gz'
Content type 'application/x-gzip' length 632611 bytes (617 KB)
downloaded 617 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/dplyr_1.0.7.tar.gz'
Content type 'application/x-gzip' length 852103 bytes (832 KB)
downloaded 832 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/Hmisc_4.5-0.tar.gz'
Content type 'application/x-gzip' length 775444 bytes (757 KB)
downloaded 757 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/haven_2.4.1.tar.gz'
Content type 'application/x-gzip' length 282833 bytes (276 KB)
downloaded 276 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/readxl_1.3.1.tar.gz'
Content type 'application/x-gzip' length 2056165 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/pbkrtest_0.5.1.tar.gz'
Content type 'application/x-gzip' length 246327 bytes (240 KB)
downloaded 240 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/rio_0.5.27.tar.gz'
Content type 'application/x-gzip' length 444681 bytes (434 KB)
downloaded 434 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/RcppEigen_0.3.3.9.1.tar.gz'
Content type 'application/x-gzip' length 1633360 bytes (1.6 MB)
downloaded 1.4 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://www.stats.bris.ac.uk/R/src/contrib/RcppEigen_0.3.3.9.1.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 1430194 != reported length 1633360
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://www.stats.bris.ac.uk/R/src/contrib/RcppEigen_0.3.3.9.1.tar.gz': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘RcppEigen’ failed
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/RcmdrMisc_2.7-1.tar.gz'
Content type 'application/x-gzip' length 38408 bytes (37 KB)
downloaded 37 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/car_3.0-11.tar.gz'
Content type 'application/x-gzip' length 490173 bytes (478 KB)
downloaded 478 KB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/effects_4.2-0.tar.gz'
Content type 'application/x-gzip' length 2256933 bytes (2.2 MB)
downloaded 2.2 MB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/lme4_1.1-27.1.tar.gz'
Content type 'application/x-gzip' length 3311365 bytes (3.2 MB)
downloaded 3.2 MB
trying URL 'https://www.stats.bris.ac.uk/R/src/contrib/Rcmdr_2.7-1.tar.gz'
Content type 'application/x-gzip' length 4817926 bytes (4.6 MB)
downloaded 4.5 MB
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://www.stats.bris.ac.uk/R/src/contrib/Rcmdr_2.7-1.tar.gz' failed
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
downloaded length 4732786 != reported length 4817926
2: In download.file(url, destfile, method, mode = "wb", ...) :
URL 'https://www.stats.bris.ac.uk/R/src/contrib/Rcmdr_2.7-1.tar.gz': status was 'Failure when receiving data from the peer'
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘Rcmdr’ failed
ERROR: failed to lock directory ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6’ for modifying
Try removing ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-vctrs’
ERROR: dependency ‘RcppEigen’ is not available for package ‘lme4’
ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
ERROR: dependency ‘vctrs’ is not available for package ‘hms’
ERROR: dependency ‘vctrs’ is not available for package ‘tidyselect’
ERROR: dependency ‘lme4’ is not available for package ‘effects’
ERROR: dependencies ‘pillar’, ‘vctrs’ are not available for package ‘tibble’
ERROR: dependency ‘hms’ is not available for package ‘progress’
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
ERROR: dependency ‘tibble’ is not available for package ‘forcats’
ERROR: dependencies ‘hms’, ‘tibble’ are not available for package ‘readr’
ERROR: dependency ‘tibble’ is not available for package ‘cellranger’
ERROR: dependencies ‘tibble’, ‘tidyselect’, ‘vctrs’, ‘pillar’ are not available for package ‘dplyr’
ERROR: dependencies ‘dplyr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘tidyr’
ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
ERROR: dependencies ‘forcats’, ‘hms’, ‘readr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘haven’
ERROR: dependencies ‘cellranger’, ‘tibble’, ‘progress’ are not available for package ‘readxl’
ERROR: dependencies ‘dplyr’, ‘tibble’, ‘tidyr’ are not available for package ‘broom’
ERROR: dependencies ‘ggplot2’, ‘viridis’ are not available for package ‘Hmisc’
ERROR: dependencies ‘haven’, ‘readxl’, ‘tibble’ are not available for package ‘rio’
ERROR: dependencies ‘lme4’, ‘broom’, ‘dplyr’ are not available for package ‘pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘rio’, ‘lme4’ are not available for package ‘car’
ERROR: dependencies ‘car’, ‘Hmisc’, ‘haven’, ‘readxl’ are not available for package ‘RcmdrMisc’
The downloaded source packages are in
‘/tmp/RtmpCxgScz/downloaded_packages’
There were 23 warnings (use warnings() to see them)
trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.6.1.tar.gz'
Content type 'application/x-gzip' length 1111747 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/tidyr_1.1.3.tar.gz'
Content type 'application/x-gzip' length 707909 bytes (691 KB)
downloaded 691 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.3.5.tar.gz'
Content type 'application/x-gzip' length 3063309 bytes (2.9 MB)
downloaded 2.9 MB
trying URL 'https://cran.rstudio.com/src/contrib/viridis_0.6.1.tar.gz'
Content type 'application/x-gzip' length 3054905 bytes (2.9 MB)
downloaded 2.9 MB
trying URL 'https://cran.rstudio.com/src/contrib/forcats_0.5.1.tar.gz'
Content type 'application/x-gzip' length 258301 bytes (252 KB)
downloaded 252 KB
trying URL 'https://cran.rstudio.com/src/contrib/hms_1.1.0.tar.gz'
Content type 'application/x-gzip' length 43142 bytes (42 KB)
downloaded 42 KB
trying URL 'https://cran.rstudio.com/src/contrib/readr_1.4.0.tar.gz'
Content type 'application/x-gzip' length 488946 bytes (477 KB)
downloaded 477 KB
trying URL 'https://cran.rstudio.com/src/contrib/tibble_3.1.2.tar.gz'
Content type 'application/x-gzip' length 686145 bytes (670 KB)
downloaded 670 KB
trying URL 'https://cran.rstudio.com/src/contrib/tidyselect_1.1.1.tar.gz'
Content type 'application/x-gzip' length 92088 bytes (89 KB)
downloaded 89 KB
trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.3.8.tar.gz'
Content type 'application/x-gzip' length 782608 bytes (764 KB)
downloaded 764 KB
trying URL 'https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz'
Content type 'application/x-gzip' length 63857 bytes (62 KB)
downloaded 62 KB
trying URL 'https://cran.rstudio.com/src/contrib/progress_1.2.2.tar.gz'
Content type 'application/x-gzip' length 29506 bytes (28 KB)
downloaded 28 KB
trying URL 'https://cran.rstudio.com/src/contrib/broom_0.7.8.tar.gz'
Content type 'application/x-gzip' length 632611 bytes (617 KB)
downloaded 617 KB
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_1.0.7.tar.gz'
Content type 'application/x-gzip' length 852103 bytes (832 KB)
downloaded 832 KB
trying URL 'https://cran.rstudio.com/src/contrib/Hmisc_4.5-0.tar.gz'
Content type 'application/x-gzip' length 775444 bytes (757 KB)
downloaded 757 KB
trying URL 'https://cran.rstudio.com/src/contrib/haven_2.4.1.tar.gz'
Content type 'application/x-gzip' length 282833 bytes (276 KB)
downloaded 276 KB
trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.3.1.tar.gz'
Content type 'application/x-gzip' length 2056165 bytes (2.0 MB)
downloaded 2.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.5.1.tar.gz'
Content type 'application/x-gzip' length 246327 bytes (240 KB)
downloaded 240 KB
trying URL 'https://cran.rstudio.com/src/contrib/rio_0.5.27.tar.gz'
Content type 'application/x-gzip' length 444681 bytes (434 KB)
downloaded 434 KB
trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.3.9.1.tar.gz'
Content type 'application/x-gzip' length 1633360 bytes (1.6 MB)
downloaded 1.6 MB
trying URL 'https://cran.rstudio.com/src/contrib/RcmdrMisc_2.7-1.tar.gz'
Content type 'application/x-gzip' length 38408 bytes (37 KB)
downloaded 37 KB
trying URL 'https://cran.rstudio.com/src/contrib/car_3.0-11.tar.gz'
Content type 'application/x-gzip' length 490173 bytes (478 KB)
downloaded 478 KB
trying URL 'https://cran.rstudio.com/src/contrib/effects_4.2-0.tar.gz'
Content type 'application/x-gzip' length 2256933 bytes (2.2 MB)
downloaded 2.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-27.1.tar.gz'
Content type 'application/x-gzip' length 3311365 bytes (3.2 MB)
downloaded 3.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/Rcmdr_2.7-1.tar.gz'
Content type 'application/x-gzip' length 4817926 bytes (4.6 MB)
downloaded 4.6 MB
ERROR: failed to lock directory ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6’ for modifying
Try removing ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-vctrs’
ERROR: failed to lock directory ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6’ for modifying
Try removing ‘/home/alain/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-RcppEigen’
ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
ERROR: dependency ‘vctrs’ is not available for package ‘hms’
ERROR: dependency ‘vctrs’ is not available for package ‘tidyselect’
ERROR: dependency ‘RcppEigen’ is not available for package ‘lme4’
ERROR: dependencies ‘pillar’, ‘vctrs’ are not available for package ‘tibble’
ERROR: dependency ‘hms’ is not available for package ‘progress’
ERROR: dependency ‘lme4’ is not available for package ‘effects’
ERROR: dependency ‘tibble’ is not available for package ‘ggplot2’
ERROR: dependency ‘tibble’ is not available for package ‘forcats’
ERROR: dependencies ‘hms’, ‘tibble’ are not available for package ‘readr’
ERROR: dependency ‘tibble’ is not available for package ‘cellranger’
ERROR: dependencies ‘tibble’, ‘tidyselect’, ‘vctrs’, ‘pillar’ are not available for package ‘dplyr’
ERROR: dependencies ‘dplyr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘tidyr’
ERROR: dependency ‘ggplot2’ is not available for package ‘viridis’
ERROR: dependencies ‘forcats’, ‘hms’, ‘readr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘haven’
ERROR: dependencies ‘cellranger’, ‘tibble’, ‘progress’ are not available for package ‘readxl’
ERROR: dependencies ‘dplyr’, ‘tibble’, ‘tidyr’ are not available for package ‘broom’
ERROR: dependencies ‘ggplot2’, ‘viridis’ are not available for package ‘Hmisc’
ERROR: dependencies ‘haven’, ‘readxl’, ‘tibble’ are not available for package ‘rio’
ERROR: dependencies ‘lme4’, ‘broom’, ‘dplyr’ are not available for package ‘pbkrtest’
ERROR: dependencies ‘pbkrtest’, ‘rio’, ‘lme4’ are not available for package ‘car’
ERROR: dependencies ‘car’, ‘Hmisc’, ‘haven’, ‘readxl’ are not available for package ‘RcmdrMisc’
ERROR: dependencies ‘RcmdrMisc’, ‘car’, ‘effects’, ‘lme4’ are not available for package ‘Rcmdr’
The downloaded source packages are in
‘/tmp/RtmpCxgScz/downloaded_packages’
There were 25 warnings (use warnings() to see them)