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Problem passing travis #69

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JMMaronge opened this issue Nov 10, 2018 · 13 comments
Closed

Problem passing travis #69

JMMaronge opened this issue Nov 10, 2018 · 13 comments

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@JMMaronge
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I'm getting this error when running travis:

Error in FUN(X[[i]], ...) : 
  Invalid comparison operator in dependency: >= 
Calls: install_missing_remote_deps ... remote_package_deps -> get_dep_table -> lapply -> FUN
Execution halted
The command "install_missing_remote_deps_all ${ants_user}/ANTsRCore ${ants_user}/ANTsR" failed and exited with 1 during .

The travis build is here.

Before the most recent commit to ANTsRCore, I had the same .travis file, but was able to install ANTsRCore, build is here.

My current .travis.yml file is:

 language: r
warnings_are_errors: true
sudo: false
cache: packages
use_bioc: true
bioc_required: true
r: release

os:
  - linux
  - osx

env:
  global: RGL_USE_NULL=TRUE

r_check_args: "--as-cran --install-args=--build"

before_install:
  - export PROJ_DIR=`basename $PWD`    
  - fname=travis_helpers.sh
  - wget -O ${fname} http://bit.ly/travis_helpers
  - cat ${fname}; source ${fname}; rm ${fname}  
  - cat DESCRIPTION
  - remove_neuroc_packages 
  - export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
  # does all the clang exports
  - x=`export_clang_cxx`; eval ${x}
  - echo "CC=${CC}, CXX=${CXX}, CXX1X=${CXX1X}"
  - echo "CXX1XSTD=${CXX1XSTD}, CXX11=${CXX11}"  
  - clang_cxx  
  - export cmake_version="3.11"
  - cmake --version
  - x=`cmake_setup`; echo "${x}"; eval ${x};
  - cmake --version
  - export ants_user=ANTsX
  - install_missing_remote_deps_all stnava/ITKR
  - install_missing_remote_deps_all ${ants_user}/ANTsRCore ${ants_user}/ANTsR
  - echo "Done Installing Missing Deps"
  - gh_binary_install stnava/ITKR
  - gh_binary_install ${ants_user}/ANTsRCore
  - gh_binary_install ${ants_user}/ANTsR  
  - cat DESCRIPTION
  - install_remotes_no_dep
  - cat DESCRIPTION
  - export PACKAGE_NAME=`package_name`# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r

Any suggestions?
@muschellij2
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I think this error may be whitespace after R (>= 2.10), which was my doing. I have patched it and please try again when a new release is built at https://github.com/ANTsX/ANTsRCore/releases/tag/v0.6.2.2.1

@avalcarcel9
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Still problems passing travis. I updated based on your new release with the patch and the previous error is fixed but there is a new similar error:

Downloading GitHub repo ANTsX/ANTsRCore@master Skipping ANTsRCore, it is already being installed Error in vapply(remotes, install_remote, ..., FUN.VALUE = character(1)) : values must be type 'character', but FUN(X[[4]]) result is type 'logical' . Error in FUN(X[[i]], ...) : Installing Remote: muschellij2/extrantsr failed! Calls: install_remotes_no_dep -> sapply -> lapply -> FUN

The travis build for mimosa is here

I can attach anything else you might need to debug.

@muschellij2
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muschellij2 commented Nov 12, 2018 via email

@muschellij2
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muschellij2 commented Nov 12, 2018 via email

@muschellij2
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This should work now, fixed bug in ghtravis. Try to rebuild

@adigherman
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Thanks John. You were fast. Just finished testing and was about to say that I was not able to replicate the issue: https://travis-ci.org/adigherman/mimosa/builds/454067476

@avalcarcel9
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Adi did I see you used the most recent git version of mimosa. Did you change anything before running travis? Are your compile settings or travis.yml different than mine? I have no idea why your version wouldn't replicate the issue other than some sort of different settings.

@adigherman
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Ali, I did use your most recent version of mimosa. I believe John fixed the ghtravis issue while I was testing.

@muschellij2
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muschellij2 commented Nov 12, 2018 via email

@avalcarcel9
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Last rebuild was last night but pushed the changes this morning. Are you both making changes today? Should I try to submit again?

@adigherman
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adigherman commented Nov 12, 2018 via email

@avalcarcel9
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The changes to ghtravis that John pushed worked! Now travis is passing again! Thanks so much for both of your help!

@JMMaronge
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Agreed, the changes result in passing travis for me as well. Thanks John and Adi.

@JMMaronge JMMaronge mentioned this issue Nov 13, 2018
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4 participants
@muschellij2 @JMMaronge @adigherman @avalcarcel9