I set up travis for a rstan package however I get this clang error
Worker information
system_info
Build system information
docker_mtu
resolvconf
R for Travis-CI is not officially supported, but is community maintained.
Please file any issues at https://travis-ci.community/c/languages/r
and mention @jeroen and @jimhester in the issue
R-install
Installing R
apt
Adding APT Sources
git.checkout
3.66s$ git clone --depth=50 --branch=try-fix-old-release-5 https://github.com/stemangiola/ppcSeq.git stemangiola/ppcSeq
Setting environment variables from .travis.yml
$ export CXX_OLEVEL=2
$ export CXX=clang++
cache.1
Setting up build cache
package
Setting up package cache
R-session-info
R session information
before_install.1
1.61s$ sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
before_install.2
8.46s$ sudo apt-get update -q
before_install.3
0.00s$ mkdir -p ~/.R/
before_install.4
0.03s$ echo "CXX = `R CMD config CXX`" >> ~/.R/Makevars
before_install.5
0.03s$ echo "CXXFLAGS = `R CMD config CXXFLAGS` -pedantic -g0 -flto -stdlib=libc++" >> ~/.R/Makevars
before_install.6
0.00s$ echo "LDFLAGS += -flto -stdlib=libc++" >> ~/.R/Makevars
before_install.7
0.00s$ export CLANG_EXTRA_ARG=""
before_install.8
0.00s$ if [[ $CXX = "clang++" ]] ; then export CLANG_EXTRA_ARG=" -Qunused-arguments -fcolor-diagnostics " ; fi
before_install.9
0.00s$ sed -i.bak "s/ g++/ ${CXX}${CLANG_EXTRA_ARG}/" ~/.R/Makevars
before_install.10
0.00s$ sed -i.bak "s/O[0-3]/O$CXX_OLEVEL/" ~/.R/Makevars
Installing package dependencies
Installing R packages: remotes
4.00s$ Rscript -e 'install.packages(c("remotes"));if (!all(c("remotes") %in% installed.packages())) { q(status = 1, save = "no")}'
Installing package into ‘/home/travis/R/Library’
(as ‘lib’ is unspecified)
trying URL 'http://cloud.r-project.org/src/contrib/remotes_2.1.0.tar.gz'
Content type 'application/x-gzip' length 131622 bytes (128 KB)
==================================================
downloaded 128 KB
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (remotes)
The downloaded source packages are in
‘/tmp/Rtmpdljxpz/downloaded_packages’
34.10s$ Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'
Rcpp (NA -> 1.0.2 ) [CRAN]
rstan (NA -> 2.19.2 ) [CRAN]
rstantools (NA -> 1.5.1 ) [CRAN]
tibble (NA -> 2.1.3 ) [CRAN]
dplyr (NA -> 0.8.3 ) [CRAN]
magrittr (NA -> 1.5 ) [CRAN]
purrr (NA -> 0.3.2 ) [CRAN]
tidyr (NA -> 0.8.3 ) [CRAN]
ggplot2 (NA -> 3.2.1 ) [CRAN]
foreach (NA -> 1.4.7 ) [CRAN]
BH (NA -> 1.69.0-1 ) [CRAN]
RcppEigen (NA -> 0.3.3.5.0) [CRAN]
StanHeaders (NA -> 2.18.1-10) [CRAN]
inline (NA -> 0.3.15 ) [CRAN]
gridExtra (NA -> 2.3 ) [CRAN]
loo (NA -> 2.1.0 ) [CRAN]
pkgbuild (NA -> 1.0.5 ) [CRAN]
cli (NA -> 1.1.0 ) [CRAN]
crayon (NA -> 1.3.4 ) [CRAN]
fansi (NA -> 0.4.0 ) [CRAN]
pillar (NA -> 1.4.2 ) [CRAN]
pkgconfig (NA -> 2.0.2 ) [CRAN]
rlang (NA -> 0.4.0 ) [CRAN]
assertthat (NA -> 0.2.1 ) [CRAN]
glue (NA -> 1.3.1 ) [CRAN]
R6 (NA -> 2.4.0 ) [CRAN]
tidyselect (NA -> 0.2.5 ) [CRAN]
plogr (NA -> 0.2.0 ) [CRAN]
stringi (NA -> 1.4.3 ) [CRAN]
digest (NA -> 0.6.20 ) [CRAN]
gtable (NA -> 0.3.0 ) [CRAN]
lazyeval (NA -> 0.2.2 ) [CRAN]
reshape2 (NA -> 1.4.3 ) [CRAN]
scales (NA -> 1.0.0 ) [CRAN]
viridisLite (NA -> 0.3.0 ) [CRAN]
withr (NA -> 2.1.2 ) [CRAN]
iterators (NA -> 1.0.12 ) [CRAN]
plyr (NA -> 1.8.4 ) [CRAN]
stringr (NA -> 1.4.0 ) [CRAN]
labeling (NA -> 0.3 ) [CRAN]
munsell (NA -> 0.5.0 ) [CRAN]
RColorBrewer (NA -> 1.1-2 ) [CRAN]
colorspace (NA -> 1.4-1 ) [CRAN]
utf8 (NA -> 1.1.4 ) [CRAN]
vctrs (NA -> 0.2.0 ) [CRAN]
backports (NA -> 1.1.4 ) [CRAN]
ellipsis (NA -> 0.2.0.1 ) [CRAN]
zeallot (NA -> 0.1.0 ) [CRAN]
matrixStats (NA -> 0.54.0 ) [CRAN]
checkmate (NA -> 1.9.4 ) [CRAN]
callr (NA -> 3.3.1 ) [CRAN]
desc (NA -> 1.2.0 ) [CRAN]
prettyunits (NA -> 1.0.2 ) [CRAN]
rprojroot (NA -> 1.3-2 ) [CRAN]
processx (NA -> 3.4.1 ) [CRAN]
ps (NA -> 1.3.0 ) [CRAN]
Installing 56 packages: Rcpp, rstan, rstantools, tibble, dplyr, magrittr, purrr, tidyr, ggplot2, foreach, BH, RcppEigen, StanHeaders, inline, gridExtra, loo, pkgbuild, cli, crayon, fansi, pillar, pkgconfig, rlang, assertthat, glue, R6, tidyselect, plogr, stringi, digest, gtable, lazyeval, reshape2, scales, viridisLite, withr, iterators, plyr, stringr, labeling, munsell, RColorBrewer, colorspace, utf8, vctrs, backports, ellipsis, zeallot, matrixStats, checkmate, callr, desc, prettyunits, rprojroot, processx, ps
Installing packages into ‘/home/travis/R/Library’
(as ‘lib’ is unspecified)
trying URL 'http://cloud.r-project.org/src/contrib/Rcpp_1.0.2.tar.gz'
Content type 'application/x-gzip' length 3699570 bytes (3.5 MB)
==================================================
downloaded 3.5 MB
trying URL 'http://cloud.r-project.org/src/contrib/rstan_2.19.2.tar.gz'
Content type 'application/x-gzip' length 909934 bytes (888 KB)
==================================================
downloaded 888 KB
trying URL 'http://cloud.r-project.org/src/contrib/rstantools_1.5.1.tar.gz'
Content type 'application/x-gzip' length 63203 bytes (61 KB)
==================================================
downloaded 61 KB
trying URL 'http://cloud.r-project.org/src/contrib/tibble_2.1.3.tar.gz'
Content type 'application/x-gzip' length 310774 bytes (303 KB)
==================================================
downloaded 303 KB
trying URL 'http://cloud.r-project.org/src/contrib/dplyr_0.8.3.tar.gz'
Content type 'application/x-gzip' length 1173098 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'http://cloud.r-project.org/src/contrib/magrittr_1.5.tar.gz'
Content type 'application/x-gzip' length 200504 bytes (195 KB)
==================================================
downloaded 195 KB
trying URL 'http://cloud.r-project.org/src/contrib/purrr_0.3.2.tar.gz'
Content type 'application/x-gzip' length 373701 bytes (364 KB)
==================================================
downloaded 364 KB
trying URL 'http://cloud.r-project.org/src/contrib/tidyr_0.8.3.tar.gz'
Content type 'application/x-gzip' length 383932 bytes (374 KB)
==================================================
downloaded 374 KB
trying URL 'http://cloud.r-project.org/src/contrib/ggplot2_3.2.1.tar.gz'
Content type 'application/x-gzip' length 3204655 bytes (3.1 MB)
==================================================
downloaded 3.1 MB
trying URL 'http://cloud.r-project.org/src/contrib/foreach_1.4.7.tar.gz'
Content type 'application/x-gzip' length 359074 bytes (350 KB)
==================================================
downloaded 350 KB
trying URL 'http://cloud.r-project.org/src/contrib/BH_1.69.0-1.tar.gz'
Content type 'application/x-gzip' length 12378154 bytes (11.8 MB)
==================================================
downloaded 11.8 MB
trying URL 'http://cloud.r-project.org/src/contrib/RcppEigen_0.3.3.5.0.tar.gz'
Content type 'application/x-gzip' length 1633859 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'http://cloud.r-project.org/src/contrib/StanHeaders_2.18.1-10.tar.gz'
Content type 'application/x-gzip' length 1278878 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'http://cloud.r-project.org/src/contrib/inline_0.3.15.tar.gz'
Content type 'application/x-gzip' length 21455 bytes (20 KB)
==================================================
downloaded 20 KB
trying URL 'http://cloud.r-project.org/src/contrib/gridExtra_2.3.tar.gz'
Content type 'application/x-gzip' length 1062844 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
trying URL 'http://cloud.r-project.org/src/contrib/loo_2.1.0.tar.gz'
Content type 'application/x-gzip' length 2055775 bytes (2.0 MB)
==================================================
downloaded 2.0 MB
trying URL 'http://cloud.r-project.org/src/contrib/pkgbuild_1.0.5.tar.gz'
Content type 'application/x-gzip' length 29022 bytes (28 KB)
==================================================
downloaded 28 KB
trying URL 'http://cloud.r-project.org/src/contrib/cli_1.1.0.tar.gz'
Content type 'application/x-gzip' length 40232 bytes (39 KB)
==================================================
downloaded 39 KB
trying URL 'http://cloud.r-project.org/src/contrib/crayon_1.3.4.tar.gz'
Content type 'application/x-gzip' length 658694 bytes (643 KB)
==================================================
downloaded 643 KB
trying URL 'http://cloud.r-project.org/src/contrib/fansi_0.4.0.tar.gz'
Content type 'application/x-gzip' length 266123 bytes (259 KB)
==================================================
downloaded 259 KB
trying URL 'http://cloud.r-project.org/src/contrib/pillar_1.4.2.tar.gz'
Content type 'application/x-gzip' length 228815 bytes (223 KB)
==================================================
downloaded 223 KB
trying URL 'http://cloud.r-project.org/src/contrib/pkgconfig_2.0.2.tar.gz'
Content type 'application/x-gzip' length 6024 bytes
==================================================
downloaded 6024 bytes
trying URL 'http://cloud.r-project.org/src/contrib/rlang_0.4.0.tar.gz'
Content type 'application/x-gzip' length 859737 bytes (839 KB)
==================================================
downloaded 839 KB
trying URL 'http://cloud.r-project.org/src/contrib/assertthat_0.2.1.tar.gz'
Content type 'application/x-gzip' length 12742 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'http://cloud.r-project.org/src/contrib/glue_1.3.1.tar.gz'
Content type 'application/x-gzip' length 122950 bytes (120 KB)
==================================================
downloaded 120 KB
trying URL 'http://cloud.r-project.org/src/contrib/R6_2.4.0.tar.gz'
Content type 'application/x-gzip' length 31545 bytes (30 KB)
==================================================
downloaded 30 KB
trying URL 'http://cloud.r-project.org/src/contrib/tidyselect_0.2.5.tar.gz'
Content type 'application/x-gzip' length 21883 bytes (21 KB)
==================================================
downloaded 21 KB
trying URL 'http://cloud.r-project.org/src/contrib/plogr_0.2.0.tar.gz'
Content type 'application/x-gzip' length 7795 bytes
==================================================
downloaded 7795 bytes
trying URL 'http://cloud.r-project.org/src/contrib/stringi_1.4.3.tar.gz'
Content type 'application/x-gzip' length 7290890 bytes (7.0 MB)
==================================================
downloaded 7.0 MB
trying URL 'http://cloud.r-project.org/src/contrib/digest_0.6.20.tar.gz'
Content type 'application/x-gzip' length 135997 bytes (132 KB)
==================================================
downloaded 132 KB
trying URL 'http://cloud.r-project.org/src/contrib/gtable_0.3.0.tar.gz'
Content type 'application/x-gzip' length 368081 bytes (359 KB)
==================================================
downloaded 359 KB
trying URL 'http://cloud.r-project.org/src/contrib/lazyeval_0.2.2.tar.gz'
Content type 'application/x-gzip' length 83482 bytes (81 KB)
==================================================
downloaded 81 KB
trying URL 'http://cloud.r-project.org/src/contrib/reshape2_1.4.3.tar.gz'
Content type 'application/x-gzip' length 36405 bytes (35 KB)
==================================================
downloaded 35 KB
trying URL 'http://cloud.r-project.org/src/contrib/scales_1.0.0.tar.gz'
Content type 'application/x-gzip' length 299262 bytes (292 KB)
==================================================
downloaded 292 KB
trying URL 'http://cloud.r-project.org/src/contrib/viridisLite_0.3.0.tar.gz'
Content type 'application/x-gzip' length 44019 bytes (42 KB)
==================================================
downloaded 42 KB
trying URL 'http://cloud.r-project.org/src/contrib/withr_2.1.2.tar.gz'
Content type 'application/x-gzip' length 53578 bytes (52 KB)
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downloaded 52 KB
trying URL 'http://cloud.r-project.org/src/contrib/iterators_1.0.12.tar.gz'
Content type 'application/x-gzip' length 289201 bytes (282 KB)
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downloaded 282 KB
trying URL 'http://cloud.r-project.org/src/contrib/plyr_1.8.4.tar.gz'
Content type 'application/x-gzip' length 392451 bytes (383 KB)
==================================================
downloaded 383 KB
trying URL 'http://cloud.r-project.org/src/contrib/stringr_1.4.0.tar.gz'
Content type 'application/x-gzip' length 135777 bytes (132 KB)
==================================================
downloaded 132 KB
trying URL 'http://cloud.r-project.org/src/contrib/labeling_0.3.tar.gz'
Content type 'application/x-gzip' length 10722 bytes (10 KB)
==================================================
downloaded 10 KB
trying URL 'http://cloud.r-project.org/src/contrib/munsell_0.5.0.tar.gz'
Content type 'application/x-gzip' length 182653 bytes (178 KB)
==================================================
downloaded 178 KB
trying URL 'http://cloud.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz'
Content type 'application/x-gzip' length 11532 bytes (11 KB)
==================================================
downloaded 11 KB
trying URL 'http://cloud.r-project.org/src/contrib/colorspace_1.4-1.tar.gz'
Content type 'application/x-gzip' length 2152594 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'http://cloud.r-project.org/src/contrib/utf8_1.1.4.tar.gz'
Content type 'application/x-gzip' length 218882 bytes (213 KB)
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downloaded 213 KB
trying URL 'http://cloud.r-project.org/src/contrib/vctrs_0.2.0.tar.gz'
Content type 'application/x-gzip' length 668258 bytes (652 KB)
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downloaded 652 KB
trying URL 'http://cloud.r-project.org/src/contrib/backports_1.1.4.tar.gz'
Content type 'application/x-gzip' length 13859 bytes (13 KB)
==================================================
downloaded 13 KB
trying URL 'http://cloud.r-project.org/src/contrib/ellipsis_0.2.0.1.tar.gz'
Content type 'application/x-gzip' length 7045 bytes
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downloaded 7045 bytes
trying URL 'http://cloud.r-project.org/src/contrib/zeallot_0.1.0.tar.gz'
Content type 'application/x-gzip' length 32549 bytes (31 KB)
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downloaded 31 KB
trying URL 'http://cloud.r-project.org/src/contrib/matrixStats_0.54.0.tar.gz'
Content type 'application/x-gzip' length 183731 bytes (179 KB)
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downloaded 179 KB
trying URL 'http://cloud.r-project.org/src/contrib/checkmate_1.9.4.tar.gz'
Content type 'application/x-gzip' length 214038 bytes (209 KB)
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downloaded 209 KB
trying URL 'http://cloud.r-project.org/src/contrib/callr_3.3.1.tar.gz'
Content type 'application/x-gzip' length 94264 bytes (92 KB)
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downloaded 92 KB
trying URL 'http://cloud.r-project.org/src/contrib/desc_1.2.0.tar.gz'
Content type 'application/x-gzip' length 65612 bytes (64 KB)
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downloaded 64 KB
trying URL 'http://cloud.r-project.org/src/contrib/prettyunits_1.0.2.tar.gz'
Content type 'application/x-gzip' length 8262 bytes
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downloaded 8262 bytes
trying URL 'http://cloud.r-project.org/src/contrib/rprojroot_1.3-2.tar.gz'
Content type 'application/x-gzip' length 50414 bytes (49 KB)
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downloaded 49 KB
trying URL 'http://cloud.r-project.org/src/contrib/processx_3.4.1.tar.gz'
Content type 'application/x-gzip' length 123430 bytes (120 KB)
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downloaded 120 KB
trying URL 'http://cloud.r-project.org/src/contrib/ps_1.3.0.tar.gz'
Content type 'application/x-gzip' length 261887 bytes (255 KB)
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downloaded 255 KB
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -pedantic -g0 -flto -stdlib=libc++ -c api.cpp -o api.o
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -pedantic -g0 -flto -stdlib=libc++ -c attributes.cpp -o attributes.o
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -pedantic -g0 -flto -stdlib=libc++ -c barrier.cpp -o barrier.o
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -pedantic -g0 -flto -stdlib=libc++ -c date.cpp -o date.o
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -pedantic -g0 -flto -stdlib=libc++ -c module.cpp -o module.o
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -I"/home/travis/R-bin/lib/R/include" -DNDEBUG -I../inst/include/ -I/home/travis/R-bin/include -fpic -g -O2 -pedantic -g0 -flto -stdlib=libc++ -c rcpp_init.cpp -o rcpp_init.o
clang++ -Qunused-arguments -fcolor-diagnostics -std=gnu++11 -shared -L/home/travis/R-bin/lib/R/lib -L/home/travis/R-bin/lib -flto -stdlib=libc++ -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/home/travis/R-bin/lib/R/lib -lR
/usr/bin/ld: /usr/local/clang-7.0.0/bin/../lib/LLVMgold.so: error loading plugin: /usr/local/clang-7.0.0/bin/../lib/LLVMgold.so: cannot open shared object file: No such file or directory
clang-7: error: linker command failed with exit code 1 (use -v to see invocation)
/home/travis/R-bin/lib/R/share/make/shlib.mk:6: recipe for target 'Rcpp.so' failed
make: *** [Rcpp.so] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/travis/R/Library/Rcpp’
Error in i.p(...) :
(converted from warning) installation of package ‘Rcpp’ had non-zero exit status
Calls: <Anonymous> ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% installed.packages())) { message("missing: ", paste(setdiff(deps$package, installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 during .
Your build has been stopped.
This is my travis file (automatically generated by the last version of rstantools)
language: r
sudo: false
r: devel
cache: packages
latex: true
env:
matrix:
- CXX_OLEVEL=2 CXX=clang++
matrix:
include:
- os: linux
compiler: clang
addons:
apt:
sources: [ 'ubuntu-toolchain-r-test', 'llvm-toolchain-precise-5.0' ]
packages:
- llvm-5.0-dev
env:
- CXX_OLEVEL=2 CXX=clang++
before_install:
- sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
- sudo apt-get update -q
- mkdir -p ~/.R/
- echo "CXX = `R CMD config CXX`" >> ~/.R/Makevars
- echo "CXXFLAGS = `R CMD config CXXFLAGS` -pedantic -g0 -flto -stdlib=libc++" >> ~/.R/Makevars
- echo "LDFLAGS += -flto -stdlib=libc++" >> ~/.R/Makevars
- export CLANG_EXTRA_ARG=""
- if [[ $CXX = "clang++" ]] ; then export CLANG_EXTRA_ARG=" -Qunused-arguments -fcolor-diagnostics " ; fi
- sed -i.bak "s/ g++/ ${CXX}${CLANG_EXTRA_ARG}/" ~/.R/Makevars
- sed -i.bak "s/O[0-3]/O$CXX_OLEVEL/" ~/.R/Makevars
script:
- |
travis_wait 42 R CMD build .
travis_wait 59 R CMD check ppcSeq*tar.gz
after_script:
- tar -ztvf ppcSeq_*.tar.gz
- echo ${NOT_CRAN}
after_success:
- travis_wait 40 tar -C .. -xf $PKG_TARBALL
after_failure:
- cat ppcSeq.Rcheck/00*
Thanks!