Merge pull request #2281 from infotroph/travis-multiR

Travis: Build against multiple R versions

.travis.yml

@@ -6,7 +6,9 @@
 
 language: r
 r:
-  - 3.5
+  - release
+  - devel
+  - oldrel
 
 # TRUSTY: Change version when 16.04 image is available.
 dist: trusty
@@ -19,6 +21,13 @@ env:
     # When Travis updates, check for Make 4 and add -O if available.
     - MAKEFLAGS="-j2"
     - PGHOST=localhost
+    - RGL_USE_NULL=TRUE # Keeps RGL from complaining it can't find X11
+
+matrix:
+  fast_finish: true
+  allow_failures:
+    - r: devel
+    - r: oldrel
 
 cache: 
   - directories:
@@ -43,7 +52,6 @@ addons:
       - libgmp-dev
       - libhdf5-dev
       - liblapack-dev
-      - libmagick++-dev
       - libnetcdf-dev
       - libproj-dev
       - libudunits2-dev
@@ -57,8 +65,10 @@ addons:
       - r-bioc-biocinstaller
       - r-cran-ape
       - r-cran-curl
+      - r-cran-data.table
       - r-cran-devtools
       - r-cran-dplyr
+      - r-cran-gap
       - r-cran-ggplot2
       - r-cran-httr
       - r-cran-igraph
@@ -71,7 +81,10 @@ addons:
       - r-cran-redland
       - r-cran-rncl
       - r-cran-roxygen2
+      - r-cran-rsqlite
+      - r-cran-sf
       - r-cran-shiny
+      - r-cran-sirt
       - r-cran-testthat
       - r-cran-tidyverse
       - r-cran-xml
@@ -105,8 +118,6 @@ install:
   - rm configure
   - R CMD INSTALL .
   - popd
-  # temporary until remotes 2.0.2 binary reaches C2D4U
-  - Rscript -e 'if(packageVersion("remotes") <= "2.0.1"){install.packages("remotes", repos = "http://cran.rstudio.com")}'
 
 before_script:
   - sudo service postgresql stop
@@ -128,17 +139,26 @@ before_script:
 
 script:
   - set -e
-  - echo 'Installing PEcAn packages'
   - Rscript scripts/generate_makefile_deps.R
+  - echo 'Installing PEcAn packages' && echo -en 'travis_fold:start:install_pkgs\\r'
   # TODO: Would probably be faster to use -j2 NCPUS=1 as for other steps,
   # but many dependency compilations seem not parallel-safe.
   # More debugging needed.
   - NCPUS=2 make -j1
-  - echo 'Testing PEcAn packages'
+  - echo -en 'travis_fold:end:install_pkgs\\r'
+  #
+  - echo 'Testing PEcAn packages' && echo -en 'travis_fold:start:test_pkgs\\r'
   - make test
-  - make check
-  - echo 'Testing Integration'
+  - echo -en 'travis_fold:end:test_pkgs\\r'
+  #
+  - echo 'Checking PEcAn packages' && echo -en 'travis_fold:start:check_pkgs\\r'
+  - REBUILD_DOCS=FALSE make check
+  - echo -en 'travis_fold:end:check_pkgs\\r'
+  #
+  - echo 'Testing Integration' && echo -en 'travis_fold:start:integration_test\\r'
   - ./tests/integration.sh travis
+  - echo -en 'travis_fold:end:integration_test\\r'
+  #
   - if [[ `git status -s` ]]; then 
       echo "These files were changed by the build process:";
       git status -s;

CHANGELOG.md

@@ -8,7 +8,10 @@ For more information about this file see also [Keep a Changelog](http://keepacha
 ## [Unreleased]
 
 ### Changed
-- Automatic build are currently done using R version 3.5 and most development will be done with version 3.5 as well. It still might be possible to use R version 3.4 however we will not guarantee future compatibility with 3.4.
+- Improved testing (#2281). Automatic Travis CI builds of PEcAn on are now run using three versions of R in parallel. This should mean fewer issues with new releases and better backwards compatibility, but note that we still only guarantee full compatibility with the current release version of R. The tested versions are:
+  - `release`, the current public release of R (currently R 3.5). Build failures in this version are fixed before merging the change that caused them. When we say PEcAn is fully tested and working, this is the build we mean.
+  - `devel`, the newest available development build of R. We will fix issues with this version before the next major R release.
+  - `oldrel`, the previous major release of R (currently R 3.4). We will fix issues with this version as time allows, but we do not guarantee that it will stay compatible.
 - Reverting back from PR #2137 to fix issues with MAAT wrappers.
 - Moved docker files for models into model specific folder, for example Dockerfile for sipnet now is in models/sipnet/Dockerfile.
 - `PEcAn.utils`

Makefile

@@ -103,9 +103,9 @@ depends_R_pkg = time Rscript -e " \
 	deps <- if (grepl('base/utils', '$(1)')) { c('Depends', 'Imports', 'LinkingTo') } else { TRUE }; \
 	devtools::install_deps('$(strip $(1))', Ncpus = ${NCPUS}, dependencies = deps);"
 install_R_pkg = time Rscript -e "devtools::install('$(strip $(1))', Ncpus = ${NCPUS});"
-check_R_pkg = Rscript scripts/check_with_errors.R $(strip $(1))
-test_R_pkg = Rscript -e "devtools::test('"$(strip $(1))"', stop_on_failure = TRUE, stop_on_warning = FALSE)" # TODO: Raise bar to stop_on_warning = TRUE when we can
-doc_R_pkg = Rscript -e "devtools::document('"$(strip $(1))"')"
+check_R_pkg = time Rscript scripts/check_with_errors.R $(strip $(1))
+test_R_pkg = time Rscript -e "devtools::test('"$(strip $(1))"', stop_on_failure = TRUE, stop_on_warning = FALSE)" # TODO: Raise bar to stop_on_warning = TRUE when we can
+doc_R_pkg = time Rscript -e "devtools::document('"$(strip $(1))"')"
 
 $(ALL_PKGS_I) $(ALL_PKGS_C) $(ALL_PKGS_T) $(ALL_PKGS_D): | .install/devtools .install/roxygen2 .install/testthat
 

scripts/check_with_errors.R

@@ -6,13 +6,15 @@ pkg <- arg[1]
 # check() sets its own values for `_R_CHECK_*` environment variables, without
 # checking whether any are already set. It winds up string-concatenating new
 # onto old (e.g. "FALSE TRUE") instead of either respecting or overriding them.
+# (Fixed in devtools 2.0.1.9000; remove these lines after next CRAN release)
 Sys.unsetenv(
     c('_R_CHECK_CRAN_INCOMING_',
     '_R_CHECK_CRAN_INCOMING_REMOTE_',
     '_R_CHECK_FORCE_SUGGESTS_'))
 
 log_level <- Sys.getenv('LOGLEVEL', unset = NA)
 die_level <- Sys.getenv('DIELEVEL', unset = NA)
+redocument <- as.logical(Sys.getenv('REBUILD_DOCS', unset = NA))
 
 # message('log_level = ', log_level)
 # message('die_level = ', die_level)
@@ -33,7 +35,7 @@ die_warn <- !is.na(die_level) && die_level == 'warn'
 
 log_notes <- !is.na(log_level) && log_level == 'all'
 
-chk <- devtools::check(pkg, quiet = TRUE, error_on = "never")
+chk <- devtools::check(pkg, quiet = TRUE, error_on = "never", document = redocument)
 
 errors <- chk[['errors']]
 n_errors <- length(errors)