Bioequivalence and Bioavailability Forum • Update R and its libraries

Update R and its libraries [🇷 for BE/BA]

posted by Helmut – Vienna, Austria, 2019-03-23 19:20 (2088 d 16:59 ago) – Posting: # 20071
Views: 4,502

Dear RUsers,

it is good practice to update R and its libraries regularly. Bugs are removed, new functions added, and performance improved (e.g., subject simulations in PowerTOST run now 100times faster than originally).

Novices please read only the 1^st section and ignore the other.

Download-links: Windows, Linux, OS X.
When asked which flavour (32-, 64-bit, both) to install, opt for the one matching your OS.
Copy the entire library-folder of the previous installation to the new one. If asked whether newer files should be overwritten, answer N!
Open the R-console and type update.packages(checkBuilt=TRUE, ask=FALSE). You can make package-maintainers happy when you select the first CRAN mirror (0-Cloud). If you want to be patriotic, select one of the local mirrors close to you.
That’s all.
Same as above. With 15,000+ packages on CRAN it takes a while till all are compiled (both 32- and 64-bit for Windows; on Linux and OS X one works with the sources anyway) – especially when a new release of R is rolled out. If you are a nerd, likely you have the Rtools and devtools on your machine. If some of your a libraries are not compiled yet, you may see sumfink like this:
There is a binary version available but the source version is later: binary source needs_compilation cairoDevice 2.25 2.26 TRUE
When asked for compilation you can chicken out (N) or bravely answer: Yes, I’m a nerd! This should work if you read all the small print (I didn’t).
- Rtools have to be installed in C:\Rtools (another location or a network drive is not allowed).
- Window’s path-variable has to be set appropriately: C:\Rtools\bin; must be the first line (even before C:\Windows;).
If you are fine with that, you’re done. Happy compiling!

However, the installer asks whether you want to install it somewhere else. Possible, but not without pitfalls.
Since you are a nerd, I bet you prefer to have operating system(s) on C, software on D, and data on yet other drive(s). If you installed it say on D (like I did) you will be punished. Though you adapted the path-variable, you are slapped in the face with sumfink like this:
* installing *source* package 'cairoDevice' ... ** package 'cairoDevice' successfully unpacked and MD5 sums checked ** libs c:/Rtools/mingw_64/bin/gcc -I"D:/PROGRA~2/R/R-35~1.3/include" -DNDEBUG -D_R_=1 -DUSE_R=1 -mms-bitfields -I/include/gtk-2.0 -I/lib/gtk-2.0/include -I/include/atk-1.0 -I/include/cairo -I/include/pango-1.0 -I/include/glib-2.0 -I/lib/glib-2.0/include -I/include/cairo -I/include/gdk-pixbuf-2.0 -I/include -ID:/PROGRA~2/R/R-35~1.3/include -O2 -Wall -std=gnu99 -mtune=generic -c R_init_cairoDevice.c -o R_init_cairoDevice.o sh: c:/Rtools/mingw_64/bin/gcc: No such file or directory make: *** [D:/PROGRA~2/R/R-35~1.3/etc/x64/Makeconf:208: R_init_cairoDevice.o] Error 127 ERROR: compilation failed for package 'cairoDevice' * removing 'D:/Program Files/R/R-3.5.3/library/cairoDevice' * restoring previous 'D:/Program Files/R/R-3.5.3/library/cairoDevice'
Why the heck? After discussions with the maintainer on GitHub it is clear that the paths to the two compilers are hardcoded (!) to C:/Rtools/mingw_$(WIN)/bin/. Hence, whatever I tried the last years was futile.
Solution:
- Delete everything (yes!) pointing to Rtools and its subfolders from the path-variable.
- Close all R-sessions and start a new one.
  remotes::install_github('jeroen/makeconf') library(makeconf) makeconf::rtools_setup()
  If you get errors, keep them…
Now compilation worked with one exception (cause I don’t have libgtk on my machine).
Checking the DESCRIPTION-file of library Matrix (the compiled version on CRAN is 1.2-16):
Version: 1.2-17 Date: 2019-03-11 NeedsCompilation: yes Packaged: 2019-03-20 21:37:04 UTC; maechler Date/Publication: 2019-03-22 22:56:52 UTC Built: R 3.5.3; x86_64-w64-mingw32; 2019-03-23 16:03:44 UTC; windows
Bingo!

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

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Complete thread:

Update R and its librariesHelmut 2019-03-23 18:20 [🇷 for BE/BA]
- Update R and its libraries yjlee168 2019-03-23 21:53
  - Update R and its libraries Helmut 2019-03-23 23:46