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jean997 / cause

R package for CAUSE
https://jean997.github.io/cause/
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Setup continuous integration builds for cause #3

Closed jdblischak closed 2 years ago

jdblischak commented 5 years ago

I configured the following CI builds:

I wasn't able to get the builds to install. I removed RcppParallel from NAMESPACE, since that caused R CMD check to throw an error.

You can see the build logs at:

https://circleci.com/gh/jdblischak/cause/5 https://travis-ci.com/jdblischak/cause/builds/118972693 https://ci.appveyor.com/project/jdblischak/cause/builds/25942955

Any ideas how I can fix the build? I can run R CMD build . on my local Ubuntu, but R CMD check fails during the installation check. The file 00install.out contains the following:

* installing *source* package ‘cause’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/root/R/Library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/root/R/Library/RcppParallel/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c log_likelihood_functions.cpp -o log_likelihood_functions.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o cause.so RcppExports.o log_likelihood_functions.o -L/usr/local/lib/R/lib -lR
installing to /root/project/cause.Rcheck/00LOCK-cause/00new/cause/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘cause’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/root/project/cause.Rcheck/00LOCK-cause/00new/cause/libs/cause.so':
  /root/project/cause.Rcheck/00LOCK-cause/00new/cause/libs/cause.so: undefined symbol: _ZTIN3tbb4taskE
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/root/project/cause.Rcheck/cause’

Note that after you merge this PR, you'll need to activate these 3rd-party services by logging in with your GitHub account.

jdblischak commented 5 years ago

After incorporating PR #4 from @CreRecombinase, the CI builds now pass on my fork:

https://circleci.com/gh/jdblischak/cause/8 https://ci.appveyor.com/project/jdblischak/cause/builds/26596803 https://travis-ci.com/jdblischak/cause/builds/122640276

There are still some warnings, but you can worry about these if you decide to submit to CRAN.

jdblischak commented 2 years ago

I don't recall the context for this PR. If you'd like help setting up CI for cause, please just let me know