how to install a R package from github manually or offline

Question

I try to download the tsdyn package from github (it is not yet updated on cran) but my proxy prevents me to connect to github.

library(devtools)
install_github("MatthieuStigler/tsDyn", ref="Dev94", subdir="tsDyn") 

Downloading github repo MatthieuStigler/tsDyn@Dev94
Erreur dans function (type, msg, asError = TRUE)  : 
Failed to connect to api.github.com port 443: Connection refused

Then I downloaded the .zip and tried to install package from .zip and got this error :

Erreur dans read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",     "Type")) : 
impossible d'ouvrir la connexion
De plus : Message d'avis :
In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
impossible d'ouvrir le fichier compressé 'tsDyn-master/DESCRIPTION', cause probable : 'No such file or directory' 

I don't understand since I can find the DESCRIPTION file in the repository. I Think it is trying to connect to internet which is not allowed by my professional connexion. I found that some people with Linux succeeded to have it downloaded by another port than 443 (port 8000 must be allowed I think but not sure) but I have windows 7. I have administrator credentials and it doesn't work either when I try to use R as an administrator. I really don't know anything about proxy configuration so if you have any idea, please try to be the more specific possible about the actions I should do.

Thanks a lot by advance !

Edit1 : I tried your proposal, and remove the unnecessary level in the file repository, I made a

Rscript -e "install.packages ('C:/Users/stephanie/Downloads/tsDyn.zip',repos=NULL) " 

and I got from the terminal "Installing package into 'C:/Users/stephanie/Documents/R/win-library/3.1' (as 'lib' is unspecified). It seemed to work but when I use the command library(tsDyn) in R I got "Erreur dans library(tsDyn), 'tsDyn' n'est pas un nom correct de package installé" (is not a proper name of installed package in english I guess). Though, the files exist in win-library but I noticed that the files MD5 and INDEX which are always present in the other package directories are not present here. An idea ?

Edit2 : I found a solution, removing as advised the unnecessary level, I used next the install function of devtools and it worked (offline)...

library(devtools)
install("C:/Users/stephanie/Downloads/tsDyn")

I really don't understand the difference with the terminal command so, if somebody can give me clue, I have solved my pb but I would be interested in understanding how !

Answer 1

You can avoid this by setting up proxy when working behind the firewall. The instructions to setup proxy from Rstudio are in this Link.

1. Check with your IT admin which proxy you should use to access anything HTTP/HTTPS while on the internal network? In most cases, it would be HTTP - http://proxy.companydomain:8080 HTTPS - https://proxy.companydomain:8080
2. Locate the Renviron.site file. One my windows 10, I located it in C:\Users\yourid\Documents\R\R-3.4.3\etc. In Linux it varies.

3. Open the Renviron.site using a text editor and paste your proxy. save the file and restart R

    options(Internet.info = 0)
    http_proxy=http://proxy.companydomain:8080/
    https_proxy=https://proxy.companydomain:8080/
   

4. In my case, I had another error after setting up the proxy, which is unsupported proxy ....libcurl is built without the HTTPS-proxy support.. Hence, I changed the second line to http:// instead of https://. This worked without any errors.

   https_proxy=http://proxy.companydomain:8080/
   

   Hope this helps. It is a bit easy to setup proxy, and let things go automatically.

Answer 2

Either move everything up one level so you don't have an intermediary folder called tsDyn and can then:

install_github("MatthieuStigler/tsDyn")

Or leave things as they are and

install_github("MatthieuStigler/tsDyn/tsDyn")

The proof is in the pudding

library(devtools)
install_github("MatthieuStigler/tsDyn/tsDyn")

    # Downloading github repo MatthieuStigler/tsDyn@master
# Installing tsDyn
# "C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL  \
#   "C:/Users/dominic/AppData/Local/Temp/RtmpiwFHUz/devtools30d0779d2870/MatthieuStigler-tsDyn-8048816/tsDyn"  \
#   --library="D:/Copy/R/win-library/3.1" --install-tests 
# 
# * installing *source* package 'tsDyn' ...
# ** libs
# 
# *** arch - i386
# gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c llar.c -o llar.o
# gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c misc.c -o misc.o
# gcc -m32 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c search.c -o search.o
# gcc -m32 -shared -s -static-libgcc -o tsDyn.dll tmp.def llar.o misc.o search.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/i386 -lR
# installing to D:/Copy/R/win-library/3.1/tsDyn/libs/i386
# 
# *** arch - x64
# gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c llar.c -o llar.o
# gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c misc.c -o misc.o
# gcc -m64 -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c search.c -o search.o
# gcc -m64 -shared -s -static-libgcc -o tsDyn.dll tmp.def llar.o misc.o search.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LC:/PROGRA~1/R/R-31~1.2/bin/x64 -lR
# installing to D:/Copy/R/win-library/3.1/tsDyn/libs/x64
# ** R
# ** data
# ** inst
# ** tests
# ** preparing package for lazy loading
# ** help
# *** installing help indices
# ** building package indices
# ** installing vignettes
# ** testing if installed package can be loaded
# *** arch - i386
# *** arch - x64
# * DONE (tsDyn)

library(tsDyn)
tsDyn::autopairs

# function (x, lag = 1, h, type = c("levels", "persp", "image", 
#     "lines", "points", "regression")) 
# {
#     panel <- list(levels = function() sm::sm.density(X, h = rep(h, 
#         2), xlab = xlab, ylab = ylab, main = "density", display = "slice"), 
#         persp = function() sm::sm.density(X, h = rep(h, 2), xlab = xlab, 
#             ylab = ylab, main = "density", display = "persp"), 
#         image = function() sm::sm.density(X, h = rep(h, 2), xlab = xlab, 
#             ylab = ylab, main = "density", display = "image"), 
#         lines = function() plot(X, xlab = xlab, ylab = ylab, 
#             main = "lines", type = "l"), points = function() plot(X, 
#             xlab = xlab, ylab = ylab, main = "scatter"), regression = function() sm::sm.regression(X[, 
#             1], X[, 2], h = h, xlab = xlab, ylab = ylab, main = "regression", 
#             ask = FALSE))
#     lags <- c(-lag, 0)
#     X <- embedd(x, lags = lags)
#     xlab <- paste("lag", lag)
#     ylab <- paste("lag", 0)
#     type <- match.arg(type)
#     if (missing(h)) {
#         h <- sm::hnorm(X)[1]
#     }
#     panel[[type]]()
# }
# <environment: namespace:tsDyn>