compilation failed for package ‘data.table’ on travis-ci

[twangxxx]

Hi, I got an error on Travis-CI build when I use 'data.table' as one of the dependency packages in my R package.

Almost the same code/configuration below passed the Travis build 3 days ago, however, I did some minor changes today in the documentation of my package and this data.table related error appeared in travis-ci build. I also notice you have a new release of data.table two days ago, so I was wondering if these two things are related.

Here is some information probably helpful:

1. Error message from Travis:

• installing source package ‘data.table’ ...
  ** package ‘data.table’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fopenmp -fPIC -Wall -g -O2 -c assign.c -o assign.o
  clang: error: unsupported option '-fopenmp'
  make: *** [assign.o] Error 1
  ERROR: compilation failed for package ‘data.table’
• removing ‘/Users/travis/R/Library/data.table’
• restoring previous ‘/Users/travis/R/Library/data.table’
  Error in i.p(...) :
  (converted from warning) installation of package ‘data.table’ had non-zero exit status
  Calls: ... with_rprofile_user -> with_envvar -> force -> force -> i.p
  Execution halted
  The command "Rscript travis_script.r" failed and exited with 1 during .

2. data.table is listed on my DESCRIPTION file under Imports part.

3. my travis build config file .travis.yml. :

language: R
r: bioc-release
sudo: true
cache: packages
os:

• osx

before_install:

• pip install --user -r requirements.txt

install:

• Rscript travis_script.r

script:

• travis_wait R CMD build .
• travis_wait R CMD check *tar.gz --no-manual

after_success:

• Rscript -e 'devtools::install_github("r-lib/covr");library(covr);codecov()'

4. And also my travis_script.r file, I use this to install all dependencies with my package.

install.packages("devtools")
library(devtools)

update.packages(ask = FALSE, checkBuilt = TRUE)
devtools::install_deps(dep = T)

Any advice or suggestions on how to solve this problem?

[mattdowle]

Thanks for the detailed info.

clang: error: unsupported option '-fopenmp'

That looks familiar on MacOS. But we're more used to seeing it on user machines rather than Travis. Please see: https://github.com/Rdatatable/data.table/wiki/Installation#openmp-enabled-compiler-for-mac

This one is Travis specific: #3331. See the sentence at the top "In order to compile data.table on Travis OSX, an OpenMP enabled compiler is required, so ..."

I've turned it back on here: #3941

[vincentvanhees]

Thanks Matt, that worked for me. To other people stumbling across the same issue and in need for a quick fix: Informed by Matt's reply above and #3331 I added the following lines to my own travis.yml file:

before_install:
  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install llvm &&
    export PATH="/usr/local/opt/llvm/bin:$PATH" &&
    export LDFLAGS="-L/usr/local/opt/llvm/lib" &&
    export CFLAGS="-I/usr/local/opt/llvm/include"; fi

As a result my R package (that imports data.table) builds again on Travis for both linux and osx.

[mattdowle]

Great. Thanks for the update. Thanks @MarcusKlik for the solution.

[jeroen]

Here is a solution that does not require custom compilers. Put this e.g. in your before_install:

sed -i.bak 's/-fopenmp//g' $(R RHOME)/etc/Makeconf

This modifies your R config to opt-out of OpenMP, so you can use standard xcode compilers.

[mattdowle]

@jeroen but that's not a solution if it disables openmp. Rather than the word 'custom' which implies something a little bit bad, I'd lean towards the words 'basic', 'limited' or even 'deficient' (in the sense of something missing) to descibe xcode compilers which lack openmp support by default, unlike windows and linux which support standard openmp built-in by default.