I need devtools because I need the function install_github to install the non-CRAN package digitize here.
sudo apt-get install r-cran-robustbase
I did not install R's packages right away, as terdon's answer proposes, but I could correct the permissions:
sudo chmod 755 /usr/lib/R/site-library/
which I think is the default setting.
I then had to do as rcs' answer proposes, to successfully install
tpoisot/digitize but only with
sudo apt-get install libssl-dev sudo apt-get install libcurl4-openssl-dev R install.packages('httr') install.packages('git2r') install.packages('devtools') library(devtools) install.packages('readbitmap') install_github('tpoisot/digitize')
The output of the last command can be
Skipping install for github remote, the SHA1 (d16e28b9) has not changed since last install. Use `force = TRUE` to force installation
install_github('tpoisot/digitize', force = TRUE) but you may get
... '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL '/tmp/RtmpX8eOLX/devtools57475d25a113/tpoisot-digitize-d16e28b' \ --library='/usr/local/lib/R/site-library' --install-tests Error: ERROR: no permission to install to directory ‘/usr/local/lib/R/site-library’ Error: Command failed (1)
I could not find a way to install digitize without
sudo. So do
sudo R, and repeat the same and you get
... '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet \ CMD INSTALL '/tmp/RtmpAlAT4e/devtools57e864e8c490/tpoisot-digitize-d16e28b' \ --library='/usr/local/lib/R/site-library' --install-tests * installing *source* package ‘digitize’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (digitize)
masi to the existing group
staff to work without
R; which you need also in a fresh installation
sudo usermod -a -G staff masi
Tests of the installation
Select four points in the axes with mouse
cal = digitize::ReadAndCal('Rintro-snail1.jpg')
data.points = digitize::DigitData(col = 'red')and choose manually points which are your data points
I close the Plot window by doing second-click.
df = digitize::Calibrate(data.points, cal, 0.1, 0.4, 0.0, 0.6)and seeing
x y 1 71.50 NA 2 65.65 NA ... 24 26.80 NA
x y 1 71.50 NA 2 65.65 NA 3 64.60 NA 4 60.85 NA 5 59.05 NA 6 58.15 NA
> .Library  "/usr/lib/R/library" > > .libPaths()  "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"  "/usr/lib/R/library"
ls /usr/lib/R/library/which does not list
base compiler grid methods rpart survival boot datasets KernSmooth mgcv spatial tcltk class foreign lattice nlme splines tools cluster graphics MASS nnet stats translations codetools grDevices Matrix parallel stats4 utils
ls -la /usr/local/lib/R/
total 12 drwxrwsr-x 3 root staff 4096 touko 19 22:25 . drwxr-xr-x 5 root root 4096 touko 19 22:25 .. drwxrwsr-x 2 root staff 4096 touko 19 22:25 site-library
ls -la /usr/local/lib/
total 20 drwxr-xr-x 5 root root 4096 touko 19 22:25 . drwxr-xr-x 14 root root 4096 touko 19 22:13 .. drwxrwsr-x 4 root staff 4096 huhti 21 01:13 python2.7 drwxrwsr-x 3 root staff 4096 huhti 21 01:08 python3.5 drwxrwsr-x 3 root staff 4096 touko 19 22:25 R
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) ...
- This project is more popular and can work better https://github.com/markummitchell/engauge-digitizer
Reasons for previous bugs
- No clean system: systems which were upgraded from 14.04, 15.10, etc.
- Messed up permissions/owners because of the previous thing.
- Own mistakes in the process.
- No backups in the case of failure.
- missing docs
System: Ubuntu 16.04 64 bit in a clean installation
Hardware: Dell PC 2013, Macbook Air 2013-mid, ...