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Package Installation

Source: vignettes/package-installation.Rmd
package-installation.Rmd

Installation

THIS VERSION: This is the recommended installation for the current release of nfportalutils that does not depend on synapser.

There will be a newer version of nfportalutils with synapser (i.e. see this issue on the roadmap), and instructions will be accordingly revised when the refactor is completed.

Make sure you are in a new R session (in RStudio, go to Session > Restart R if necessary). The trickiest part of the installation and package usage, for most R users, will be the Python interop.

Outside R

With R

  • Install remotes to help install other packages: install.packages("remotes").

  • Check that you have the correct reticulate version: packageVersion("reticulate").
    If the result is anything other than 1.28, then go to the reticulate install step, otherwise skip to nfportalutils install.

  • Install reticulate:

> remotes::install_github("rstudio/reticulate@v1.28")
Downloading GitHub repo rstudio/reticulate@v1.28
Running `R CMD build`...
* checking for file 'C:\Users\Erik\AppData\Local\Temp\Rtmporbql0\remotes322031ec7c50\rstudio-reticulate-3de77d1/DESCRIPTION' ... OK
* preparing 'reticulate':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building 'reticulate_1.28.tar.gz'
Installing package into ‘C:/Users/Erik/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
* installing *source* package 'reticulate' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c event_loop.cpp -o event_loop.o
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c libpython.cpp -o libpython.o
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c output.cpp -o output.o
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c python.cpp -o python.o
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c readline.cpp -o readline.o
g++ -std=gnu++17  -I"C:/PROGRA~1/R/R-43~1.2/include" -DNDEBUG  -I'C:/Users/Erik/AppData/Local/R/win-library/4.3/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c signals.cpp -o signals.o
g++ -std=gnu++17 -shared -s -static-libgcc -o reticulate.dll tmp.def RcppExports.o event_loop.o libpython.o output.o python.o readline.o signals.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LC:/PROGRA~1/R/R-43~1.2/bin/x64 -lR
installing to C:/Users/Erik/AppData/Local/R/win-library/4.3/00LOCK-reticulate/00new/reticulate/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (reticulate)
  • Install nfportalutils (choose option 3 - None):
> remotes::install_github("nf-osi/nfportalutils@v0.9500-presynapser")
Downloading GitHub repo nf-osi/nfportalutils@v0.9500-presynapser
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                               
2: CRAN packages only                
3: None                              
4: reticulate (1.28 -> 1.35.0) [CRAN]
Running `R CMD build`...
* checking for file 'C:\Users\Erik\AppData\Local\Temp\RtmpQzT2JT\remotes158c6d2c7833\nf-osi-nfportalutils-61636cd/DESCRIPTION' ... OK
* preparing 'nfportalutils':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted 'LazyData' from DESCRIPTION
* building 'nfportalutils_0.9500.tar.gz'
Installing package into ‘C:/Users/Erik/AppData/Local/R/win-library/4.3’
(as ‘lib’ is unspecified)
* installing *source* package 'nfportalutils' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nfportalutils)

Post-installation

It is recommended to set your Synapse authentication token as an environment variable that R can access. You can create an .Renviron in your home. For example, create ‘C:/Users/Erik/Documents/.Renviron’.

In the file, add

SYNAPSE_AUTH_TOKEN=xxx_your_token_here_xxx

Outside R

Outside R

With R

Test Your Installation

Restart R after adding your token. Then to test that your installation is working, load package and try to log in. If you have your authentication token set in the above recommended steps, you should be greeted accordingly. Without a token, you are logged in as “Anonymous” and functionality will be limited.

Login 

library(nfportalutils)
syn_login()