motus.org

Software Maintenance for the Motus Data-processing Server

The motus data processing server (hereinafter Server) is written mostly in R to reduce the maintenance burden and increase user transparency of the entire motus system; i.e. the client package and server package are in same language. It uses a fairly small subset of the R language, and only the recommended packages. There is no reason for the client and server target versions of R to be the same; on the server, stability is critical, while on the client side, tracking new upstream features might be given more weight.

The Server runs on debian linux 8.8

don't update R. This is almost always the right choice.
switching to a new X or Y from version X.Y.Z has a significant (Y) or highly significant (X) probability of breaking the Server
R does not (as of 2018-09) have "long-term-support" versions, a stable API, or apparently any governance procedures aimed at reducing the work of tracking upstream changes. There is nothing inherently wrong with using an older version under-the-hood in a production system (beyond what is wrong with using R at all for such purposes...)
the version of R used on the server is kept in a git repo at /home/sg/src/R-motus and upstream at https://github.com/jbrzusto/R-motus
if a hard-to-work-around bug in R is responsible for a problem with the Server, it is best to just patch R-motus with the minimal changeset that fixes the problem.
you will typically need to re-install packages, even if you've only rebuilt the R executable. This can take 30 minutes or more, requires that the Server not be running, and requies that upstream CRAN repositories still have the appropriate versions of packages needed by the version of R used on the Server.
however, as suggested here: http://zvfak.blogspot.com/2012/06/updating-r-but-keeping-your-installed.html we install non-bundled R packages to a separate directory, /home/sg/installed-R-packages so that if only a minor update/upgrade is made to R, the packages will be preserved and need not be reinstalled. This requires the file /home/sg/.Renviron with this line:

R_LIBS=/home/sg/installed-R-packages

Assuming you really need to update R:

make changes to the tree in /home/sg/src/R-motus
consult README.md in that tree to see the history of changes made for the Server's version of R
ensure a successful build with make:

cd /home/sg/src/R-motus
make

do some testing of the newly-built version before installing it system-wide:

cd /home/sg/src/R-motus
bin/R   ## will run the newly-built version
bin/R -d gdb ## will run the newly-built version with gdb for debugging

install the new version

cd /home/sg/src/R-motus
sudo make install

re-install required upstream packages; currently, this means:

install.packages(c('roxygen2', 'digest', 'dbplyr', 'dplyr', 'httr', 'jsonlite', 'lubridate', 'openssl', 'proto', 'RMySQL', 'RSQLite', 'sendmailR', 'stringi', 'XML'))

re-install the motusServer package:

cd /home/sg/src/motusServer
rpack -g .

restart all servers

## kill running servers gracefully, so that jobs
## will be resumed on restart
killAllMotusServers.sh -g
sleep 320 ## wait a bit over 5 minutes for graceful termination
runAllMotusServers.sh

document your changes in /home/sg/src/R-motus/README.md
if everything appears to be running correctly and your problem has been fixed, commit the changes to the R-motus repo and send a pull-request to the R-motus github repo maintainer
if you see repeated messages such as running server for queue 1 on your console, that means the servers are exiting with an error and then being automatically restarted. You can diagnose this with the error dumps in /sgm/logs/process1.txt, for example.