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I'm currently trying to set up continuous integration for a bookdown-project

The project bundles dependencies with packrat, so Travis CI needs to build the required packages from source. This seems to go okay for many packages, but the build is failing for data.table.

I am using the current version of data.table (1.11.8) and R (3.5.1)

Maybe I specified the wrong Version of C-compilers in my Makevars

What else could I check to get this working?

...
Installing curl (3.2) ... 
    OK (built source)
Installing data.table (1.11.8) ... 

[1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/home/travis/R-bin/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpiHzV25/data.table' --library='/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package 'data.table' ...\n** package 'data.table' successfully unpacked and MD5 sums checked\n** libs\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c assign.c -o assign.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c between.c -o between.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c bmerge.c -o bmerge.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c chmatch.c -o chmatch.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c dogroups.c -o dogroups.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fastmean.c -o fastmean.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fcast.c -o fcast.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fmelt.c -o fmelt.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c forder.c -o forder.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c frank.c -o frank.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fread.c -o fread.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c freadR.c -o freadR.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fsort.c -o fsort.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fwrite.c -o fwrite.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c fwriteR.c -o fwriteR.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c gsumm.c -o gsumm.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c ijoin.c -o ijoin.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c init.c -o init.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c inrange.c -o inrange.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c nqrecreateindices.c -o nqrecreateindices.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c openmp-utils.c -o openmp-utils.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c quickselect.c -o quickselect.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c rbindlist.c -o rbindlist.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c reorder.c -o reorder.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c shift.c -o shift.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c subset.c -o subset.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c transpose.c -o transpose.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c uniqlist.c -o uniqlist.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c vecseq.c -o vecseq.o\nclang -I\"/home/travis/R-bin/lib/R/include\" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c wrappers.c -o wrappers.o\nclang -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -o data.table.so assign.o between.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o freadR.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -fopenmp -L/home/travis/R-bin/lib/R/lib -lR\nmv data.table.so datatable.so\nif [ \"\" != \"Windows_NT\" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi\ninstalling to /home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1/data.table/libs\n** R\n** inst\n** tests\n** byte-compile and prepare package for lazy loading\n** help\n*** installing help indices\n** building package indices\n** installing vignettes\n** testing if installed package can be loaded\nError: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...):\n unable to load shared object '/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1/data.table/libs/datatable.so':\n  libomp.so: cannot open shared object file: No such file or directory\nError: loading failed\nExecution halted\nERROR: loading failed\n* removing '/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1/data.table'"
Error: Command failed (1)
Failed to run system command:
    '/home/travis/R-bin/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/RtmpiHzV25/data.table' --library='/home/travis/build/henningsway/Advanced-R-Solutions/packrat/lib/x86_64-pc-linux-gnu/3.5.1' --install-tests --no-docs --no-multiarch --no-demo 
The command failed with output:
* installing *source* package 'data.table' ...
** package 'data.table' successfully unpacked and MD5 sums checked
** libs
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c assign.c -o assign.o
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c between.c -o between.o
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c bmerge.c -o bmerge.o
clang -I"/home/travis/R-bin/lib/R/include" -DNDEBUG   -I/home/travis/R-bin/include  -fopenmp -fpic  -g -O2  -c chmatch.c -o chmatch.o
clang -I"/home/
Execution halted
The command "R -e "0" --args --bootstrap-packrat" failed and exited with 1 during .
Your build has been stopped.
stats-hb
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  • just set `CC=gcc` and it seems be working now... – stats-hb Oct 13 '18 at 09:33
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    Are you aware of [this installation instuction](https://github.com/Rdatatable/data.table/wiki/Installation#step-3)? – Jaap Oct 13 '18 at 10:06
  • @stats-hb If doing that solved your issue, I would suggest [answering your own question](https://stackoverflow.com/help/self-answer) – duckmayr Oct 13 '18 at 11:03
  • @Jaap Is there a continuous integration that I can use with GitLab while pushing Rshiny apps to the server ? Looks like Travis CI is for github ? – user5249203 Jan 10 '19 at 15:04

1 Answers1

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Setting CC=gcc actually solved the data.table-compilation problem for me.

(I think setting some other arguments for clang would have also been an option, as indicated in @jaaps comment above)

stats-hb
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