Package management is a wonderful tool. If integrated with the operating system, it allows
us to install and upgrade components with great ease and reliability. It is also pleasant
at the application level: CRAN functions really well thanks to install.packages() and
update.packages() even though these are generally unaware of the host OS (which can lead
to occassional frustrations). The fact that the OS package management system and the
application package management system do not know about each other can lead to
occassional frictions.
There are two specific issues this package tries to help with. We discuss both below.
Say you just upgraded from Ubuntu 19.10 to Ubuntu 20.04, as I just did this week (in late
May of 2020). You may have a number of CRAN packages installed from source in
/usr/local/lib/R/site-library. All fine.
But apt and dpkg do not know about them. So it may remove libraries not knowing about
these implicit dependencies. Next time you try to load one of the affected packages, it
will fail.
Problem Illustration
R> library(git2r)
Error: package or namespace load failed for ‘git2r’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/git2r/libs/git2r.so':
libgit2.so.27: cannot open shared object file: No such file or directory
R> The chshli package can help here:
Example:
R> library(chshli)
Attaching chshli on ubuntu:20.04
R> checkSharedLibs(db="19.10")
Looking at libxml2.so.2 : libxml2
Looking at libapt-pkg.so.5.90 : libapt-pkg5.90
Looking at libgit2.so.27 : libgit2-27
NULL
R>This identifies libgit2 (likely via package git2r),
libapt-pkg (likely via RcppApt and
libxml2 (likely via xml2). All three R packages
can probably be fixed via a simple reinstallation from source.
Say you experiment with RSPM, for example via this Rocker
container which you can
pull via docker pull rocker/r-rspm:18.04. And you did just run
install.packages("xml2"). But maybe you cannot load it as the next example shows.
Problem Illustration
> install.packages("xml2")
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/latest/src/contrib/xml2_1.3.2.tar.gz'
Content type 'binary/octet-stream' length 519621 bytes (507 KB)
==================================================
downloaded 507 KB
* installing *binary* package ‘xml2’ ...
* DONE (xml2)
The downloaded source packages are in
‘/tmp/RtmpW0G7Mr/downloaded_packages’
> library(xml2)
Error: package or namespace load failed for ‘xml2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/xml2/libs/xml2.so':
libxml2.so.2: cannot open shared object file: No such file or directory
> Here RSPM helps us with a quick and painless download of a binary. Which we then cannot load as it depends on an OS-level package.
The chshli package can help here:
Example:
R> library(chshli)
Attaching chshli on ubuntu:18.04
R> checkSharedLibs()
Looking at libxml2.so.2 : libxml2
NULL
> and installing (at the system-level, i.e. as root) sudo apt install libxml2 will make your
package work. Which is a very nice complement to the nice and fast installation via RSPM.
(And we should note that we now add "a few" libraries to the aforementioned RSPM containers. So
xml2 will already be covered if you try to replicate this.)
For now from GitHub via remotes::install_github("eddelbuettel/chshli") or, if you have
littler, via installGithub eddelbuettel/chshli.
Note that you may need to provide the backend end file for your distribution. As these are large we
do not ship them. See inst/rawdata/ and inst/extdata in the source, and try to follow what I did
for Ubuntu if your system is different.
Dirk Eddelbuettel
GPL (>= 2)