units not working due to missing udunits C libraries

[dantonnoriega]

The package units depends on the packages udunits2. However, while the udunits2 package seems to successfully install after running install.packages('udunits2'), it doesn't actually work out-of-the-box. You can see this when you try to install it from from source.

I received the following error when I tried to install udunits2 from source...

> install.packages('udunits2', type = 'source')

[OMITTED]

-----Error: libudunits2 not found-----
     If the udunits2 library is installed in a non-standard location,
     use --configure-args='--with-udunits2-lib=/usr/local/lib' for example,
     or --configure-args='--with-udunits2-include=/usr/include/udunits2'
     replacing paths with appropriate values for your installation.
     You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIB
     environment variables.
     If udunits2 is not installed, please install it.
     It is required for this package.
ERROR: configuration failed for package ‘udunits2’
-----Error: libudunits2 not found-----
     If the udunits2 library is installed in a non-standard location,
     use --configure-args='--with-udunits2-lib=/usr/local/lib' for example,
     or --configure-args='--with-udunits2-include=/usr/include/udunits2'
     replacing paths with appropriate values for your installation.
     You can alternatively use the UDUNITS2_INCLUDE and UDUNITS2_LIB
     environment variables.
     If udunits2 is not installed, please install it.
     It is required for this package.
ERROR: configuration failed for package ‘udunits2’

Hence, what we need are these libraries.

Here is how I solved it on my mac using Homebrew.

1. In your Terminal.app, do the following:

brew install udunits

While I used Homebrew, it appears you can download the libraries here. I did not do it this way, but I'm assuming that if you do this successfully, then you should be able to do steps 2 and 3.

1. Once installed, go to R and install udunits2 from source...

install.packages('udunits2', type = 'source', repo = 'cran.rstudio.com')

1. Install units (I installed the development version).

devtools::install_github('edzer/units', type = 'source')

Or

install.packages('units', type = 'source')

DONE

[jameshiebert]

it doesn't actually work out-of-the-box

To be fair, the udunits2 R package does specifically declare a SystemRequirements which, by definition, has to be dealt with outside of the R packaging environment.

[edzer]

The problem is that this is left to the user, and many R users don't know what to do. Add a README.md to the Rudunits2 project, link from here? Where can windows binaries of udunits be found?

[krlmlr]

It may be just easiest to bundle libudunits2 with the udunits2 package. The rwinlib project offers quite a few libraries bundled for Windows, but I haven't found udunits2 there -- CC @gaborcsardi @jeroenooms.

[jeroen]

Why would windows users need to install from source? install.packages('udunits2') does work out of the box?

[krlmlr]

Oh, it does on my system, too. @ultinomics mentioned that "t doesn't actually work out-of-the-box"...

[jeroen]

I have added windows builds on rwinlib/udunits and also created a PR on the R package which automatically uses these builds when building the package from source on Windows: pacificclimate/Rudunits2#7

[edzer]

This is because on windows CRAN packages, external dependencies (SysRequirements) are linked statically to the shared library in the package. It seems this is also the case on mac -- @ultinomics installed from source. Thanks for the pointer to rwinlib!

[ginolhac]

just for the record, on mac and to complete the nice @ultinomics's answer
after installing udunits withbrew install udunits, I needed this to successfully compile:

install.packages('udunits2', type = 'source', repo = 'cran.rstudio.com', configure.args = "--with-udunits2-lib=/usr/local/Cellar/udunits/2.2.20/lib/")

[elbamos]

Is there a prospect for a near-term resolution of this? I'd like to add to my package a dependency on ggforce, which depends on units 0.4, but then the udunits issue breaks my travis builds.

[edzer]

Not sure if I understand your issue: have you seen this? Or are you trying a MacOSX flavor of travis?

[elbamos]

Yes, and both osx and linux.

Compare this: https://travis-ci.org/elbamos/largeVis/jobs/183274802 (OSX build works), with this https://travis-ci.org/elbamos/largeVis/jobs/183274804 (everything identical but using R-devel, build fails).

(A similar issue may be arising with Ubuntu and 64-bit builds, but I'm not yet sufficiently confident in the issue to report it. I'll know tonight.)

[edzer]

Well, it's your call that you want to do a macosx travis for r-devel, for which cran does not have binaries available: it means that you'll have to install udunits2 for this platform from source too. Although that is no problem at all in itself, IMHO you're overdoing your eagerness to check everything you can with this target: is it worth the effort?

[elbamos]

Hah! Well, cran requires it, and I've had so many issues of compilation problems on different platforms (my package makes extensive use of c++11, openmp, 64-but libraries etc.), that I feel a need to be thorough. I'm also checking with valgrind... id much rather find out from cran than get a moderately judgmental email from the cran maintainers. Not sure I understand why this would require a different installation of udunits. I'm installing the library with brew and the R package from source in both cases.

…

On Dec 12, 2016, at 11:07 AM, Edzer Pebesma ***@***.***> wrote: Well, it's your call that you want to do a macosx travis for r-devel, for which cran does not have binaries available: it means that you'll have to install udunits2 for this platform from source too. Although that is no problem at all in itself, IMHO you're overdoing your eagerness to check everything you can with this target: is it worth the effort? — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[edzer]

No, CRAN requires you test with r-devel, it doesn't specify on which platform. CRAN binary packages for MacOSX come with statically linked libraries, meaning the udunits2 C library is part of the udunits2 R package, and ignored by the R package. I don't think that your first travis build mentioned above installs source packages: extension .tgz indicates binary MacOSX packages, source pkgs have .tar.gz extension.

[jeroen]

There are no CRAN binary package for r-devel so on these targets you need to build from source and hence need to ensure that the system dependencies are available. Just add a line:

brew_packages: udunits

to the osx/r-devel entry in your travis build matrix.