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joelostblom
joelostblom

Reputation: 49064

Errors building R-packages for conda

I am having a tough time installing R-packages that are not available in the Anaconda repositories. My attempts so far can be found here How to install R-packages not in the conda repositories?.

Currently, I am trying to build the R-package rafalib for conda by following the instructions from this article under the heading Building a conda R package.

The first part works fine.

conda skeleton cran rafalib

Out: 

Tip: install CacheControl to cache the CRAN metadata
Fetching metadata from http://cran.r-project.org/
Writing recipe for rafalib
Done

The build command runs into errors

conda build r-rafalib

Out:

Removing old build environment
Removing old work directory
BUILD START: r-rafalib-1.0.0-r3.2.2_0
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ......
Solving package specifications: .
Error:  Packages missing in current linux-64 channels: 
  - r 3.2.2*
  - r-rcolorbrewer

I have r 3.2.2-64bit installed via conda and it runs without problems. I also already have r-colorbrewer installed via conda and I can use that package without issues in R. Why am I getting these errors when trying to build a conda package?

I am on Linux (Antergos, an Arch derivative) with kernel 4.4.5-1-ARCH.

UPDATE 2015/04/19

Thanks to this answer, I found out that I could include the dependencies by building them separately in the same directory as the package I want to install. That didn't work for me, but I also read that I can include a channel in the build command with -c, just as when installing. So now I do:

conda build -c r r-rafalib

This gets passed all the dependency problems, but after fetching, extracting and linking packages, it fails. Here is the end of the error message.

Removing old work directory
Source cache directory is: /home/joel/anaconda2/conda-bld/src_cache
Downloading source to cache: rafalib_1.0.0.tar.gz
Downloading http://cran.r-project.org/src/contrib/rafalib_1.0.0.tar.gz
rafalib_1.0.0. 100% |#######################| Time: 0:00:00   4.87 MB/s
Success
Extracting download
Package: r-rafalib-1.0.0-r3.2.2_0
source tree in: /home/joel/anaconda2/conda-bld/work/rafalib
+ mv DESCRIPTION DESCRIPTION.old
+ grep -v '^Priority: ' DESCRIPTION.old
+ /home/joel/anaconda2/envs/_build/bin/R CMD INSTALL --build .
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Command failed: /bin/bash -x -e /home/joel/drafts/r-rafalib/build.sh

The error sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook is the same as I encounter when using install.packages() as reported here.

There is some related discussion in this thread. I have tried to get around this error by installing different versions of ncurses, including this patched version, and I have tried to link the readline libraries, as suggested here, but I keep running into the same error. I'm quite lost at this point and any help to solve this would be greatly appreciated.

Upvotes: 2

Views: 1571

Answers (1)

joelostblom
joelostblom

Reputation: 49064

Although I started out with a different problem, the final solution turned out to be the same as I posted elsewhere How to install R-packages not in the conda repositories?. I am adding it here for completeness.

In the end, I got around the rl_event_hookproblems by following the approach recommended here and symlinking anaconda's libreadline to the system one:

mv ~/anaconda3/lib/libreadline.s.6.2 ~/anaconda3/lib/libreadline.s.6.2.bak
ln -s /usr/lib/libreadline.so.6.3 ~/anaconda3/lib/libreadline.s.6.2

I am still having troubles installing some dependency heavy R-packages due to failure to load shared objects when using install.packages() from withing R. However, simpler packages work fine and I can get most of the dependency heavy packages from anacondas R-repositories.

Upvotes: 1

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