Compilation Errors on Travis (for R package)

[leeper]

I have an R package that imports feather. Builds on Travis are failing due feather failing to compile. Any ideas how to correct?

Here's the set of errors:

* installing *source* package ‘feather’ ...
** package ‘feather’ successfully unpacked and MD5 sums checked
** libs
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather-read.cpp -o feather-read.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather-types.cpp -o feather-types.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather-write.cpp -o feather-write.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather/buffer.cc -o feather/buffer.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather/feather-c.cc -o feather/feather-c.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather/io.cc -o feather/io.o
g++ -std=c++0x -I/home/travis/R-bin/lib/R/include -DNDEBUG -I. -I/home/travis/R-bin/include -I"/usr/local/lib/R/site-library/Rcpp/include"   -fpic  -g -O2 -c feather/metadata.cc -o feather/metadata.o
feather/metadata.cc:29:7: error: expected nested-name-specifier before ‘FBString’
feather/metadata.cc:29:7: error: ‘FBString’ has not been declared
feather/metadata.cc:29:16: error: expected ‘;’ before ‘=’ token
feather/metadata.cc:29:16: error: expected unqualified-id before ‘=’ token
feather/metadata.cc:32:7: error: expected nested-name-specifier before ‘ColumnVector’
feather/metadata.cc:32:7: error: ‘ColumnVector’ has not been declared
feather/metadata.cc:32:20: error: expected ‘;’ before ‘=’ token
feather/metadata.cc:32:20: error: expected unqualified-id before ‘=’ token
feather/metadata.cc:178:3: error: ‘ColumnVector’ does not name a type
feather/metadata.cc: In member function ‘feather::Status feather::metadata::TableBuilder::Impl::Finish()’:
feather/metadata.cc:146:5: error: ‘FBString’ was not declared in this scope
feather/metadata.cc:146:14: error: expected ‘;’ before ‘desc’
feather/metadata.cc:148:7: error: ‘desc’ was not declared in this scope
feather/metadata.cc:154:9: error: ‘desc’ was not declared in this scope
feather/metadata.cc:156:27: error: ‘columns_’ was not declared in this scope
feather/metadata.cc:157:34: error: unable to deduce ‘auto’ from ‘<expression error>’
feather/metadata.cc: In member function ‘void feather::metadata::TableBuilder::Impl::add_column(const flatbuffers::Offset<feather::fbs::Column>&)’:
feather/metadata.cc:173:5: error: ‘columns_’ was not declared in this scope
feather/metadata.cc: In constructor ‘feather::metadata::TableBuilder::TableBuilder()’:
feather/metadata.cc:190:5: error: type ‘feather::metadata::TableBuilder’ is not a direct base of ‘feather::metadata::TableBuilder’
make: *** [feather/metadata.o] Error 1
ERROR: compilation failed for package ‘feather’
* removing ‘/usr/local/lib/R/site-library/feather’

[hadley]

The problem is -std=c++0x - but I don't know why it wouldn't be picking up the SystemRequirements: C++11. Any ideas @jimhester ?

[jimhester]

I think the problem is the configure file, from https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-C_002b_002b11-code

If a package using C++11 has a configure script it is essential that it selects the correct compiler, via something like

CXX1X=`"${R_HOME}/bin/R" CMD config CXX1X`
CXX1XSTD=`"${R_HOME}/bin/R" CMD config CXX1XSTD`
CXX="$(CXX1X) $(CXX1XSTD)"
CXXFLAGS=`"${R_HOME}/bin/R" CMD config CXX1XFLAGS`
AC_LANG(C++)

I am trying to reproduce the error locally and will send a patch

[jimhester]

Actually I am mistaken, the gcc on travis is only 4.6.3, so you need to modify your .travis.yml to install at least gcc-4.9 in order to have -std=c++11

[jimhester]

So you have to install gcc-4.9 or greater and set CXX1X, CXX1XSTD in ~/.R/Makevars, e.g.

https://github.com/jimhester/rio/blob/9026180fd731aaed34f21cba3b5e207124618e5b/.travis.yml#L8-L20

Which allows you to build successfully, https://travis-ci.org/leeper/rio/builds/131807863#L1367-L1380

This is pretty painful, but I am not sure what can be done to avoid it unless travis updates their default gcc or ubuntu version...

[wesm]

is this resolved?

[leeper]

Yes, @jimhester's travis setup worked for me.

[maxheld83]

This fix would appear to cause other problems, though I am not sure whether this is actually an issue on feather's end.

If so, could this issue be reopened @leeper, @jimhester?

Once I add the above fix to my .travis.yml, travis fails on installing readxl, and doesn't even get to feather:

Installing readxl (0.1.1) ... 
Error: Command failed (1)

Failed to run system command:

	'/home/travis/R-bin/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmprmuGtQ/readxl' --library='/home/travis/build/maxheld83/goodlife/packrat/lib/x86_64-pc-linux-gnu/3.3.2' --install-tests --no-docs --no-multiarch --no-demo 

The command failed with output:
* installing *source* package 'readxl' ...
** package 'readxl' successfully unpacked and MD5 sums checked
** libs
g++ -I/home/travis/R-bin/lib/R/include -DNDEBUG -Iunix -I. -I/home/travis/R-bin/include -I"/home/travis/build/maxheld83/goodlife/packrat/lib/x86_64-pc-linux-gnu/3.3.2/Rcpp/include"  -DTINYFORMAT_NO_VARIADIC_TEMPLATES -std=c++11 -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
cc1plus: error: unrecognized command line option '-std=c++11'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package 'readxl'
* removing '/home/travis/build/maxheld83/goodlife/packrat/lib/x86_64-pc-linux-gnu/3.3.2/readxl'
Execution halted


The command "R -e "0" --args --bootstrap-packrat" failed and exited with 1 during .

Your build has been stopped.

I'm not sure what to do about that, but the problem seems to stem from the commands added as per the above fix.

Here's the complete .travis.yml:

language: r

sudo: false

install:
  - R -e "0" --args --bootstrap-packrat

warnings_are_errors: false

addons:
  apt:
    sources:
      - ubuntu-toolchain-r-test
    packages:
      - gcc-4.9
      - g++-4.9

before_install: |
  mkdir ~/.R
  cat <<EOF > ~/.R/Makevars
  CXX1X=g++-4.9
  CXX1XSTD=-std=c++11

cache:
  packages: true
  directories:
    - $TRAVIS_BUILD_DIR/_bookdown_files
    - $TRAVIS_BUILD_DIR/packrat/

before_script:
  - chmod +x ./_build.sh
  - chmod +x ./_deploy.sh

script:
  - ./_build.sh
  - ./_deploy.sh

notifications:
  email: false

[jimhester]

@maxheld83 I think that is actually a bug in readxl. It sets -std=c++11 but does not use the CXX1X compiler. Setting CXX=gcc-4.9 should fix the issue.

[maxheld83]

thanks @jimhester – is this the same issue as tidyverse/readxl#176 then?

Seems like it is, as per your discussion – I'll then continue the discussion there.

[maxheld83]

also here, FYI, just setting dist=trusty solves the problem, though I am not sure whether this is recommended.

language: r

sudo: false

dist: trusty

install:
  - R -e "0" --args --bootstrap-packrat

warnings_are_errors: false

cache:
  packages: true
  directories:
    - $TRAVIS_BUILD_DIR/_bookdown_files
    - $TRAVIS_BUILD_DIR/packrat/

before_script:
  - chmod +x ./_build.sh
  - chmod +x ./_deploy.sh

script:
  - ./_build.sh
  - ./_deploy.sh

notifications:
  email: false