diff options
| -rw-r--r-- | R/CRAN_RELEASE.md | 91 | ||||
| -rw-r--r-- | R/README.md | 8 | ||||
| -rwxr-xr-x | R/check-cran.sh | 33 | ||||
| -rwxr-xr-x | R/create-docs.sh | 19 | ||||
| -rw-r--r-- | R/pkg/DESCRIPTION | 9 | ||||
| -rw-r--r-- | R/pkg/vignettes/sparkr-vignettes.Rmd | 9 |
6 files changed, 134 insertions, 35 deletions
diff --git a/R/CRAN_RELEASE.md b/R/CRAN_RELEASE.md new file mode 100644 index 0000000000..bea8f9fbe4 --- /dev/null +++ b/R/CRAN_RELEASE.md @@ -0,0 +1,91 @@ +# SparkR CRAN Release + +To release SparkR as a package to CRAN, we would use the `devtools` package. Please work with the +`dev@spark.apache.org` community and R package maintainer on this. + +### Release + +First, check that the `Version:` field in the `pkg/DESCRIPTION` file is updated. Also, check for stale files not under source control. + +Note that while `check-cran.sh` is running `R CMD check`, it is doing so with `--no-manual --no-vignettes`, which skips a few vignettes or PDF checks - therefore it will be preferred to run `R CMD check` on the source package built manually before uploading a release. + +To upload a release, we would need to update the `cran-comments.md`. This should generally contain the results from running the `check-cran.sh` script along with comments on status of all `WARNING` (should not be any) or `NOTE`. As a part of `check-cran.sh` and the release process, the vignettes is build - make sure `SPARK_HOME` is set and Spark jars are accessible. + +Once everything is in place, run in R under the `SPARK_HOME/R` directory: + +```R +paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::release(); .libPaths(paths) +``` + +For more information please refer to http://r-pkgs.had.co.nz/release.html#release-check + +### Testing: build package manually + +To build package manually such as to inspect the resulting `.tar.gz` file content, we would also use the `devtools` package. + +Source package is what get released to CRAN. CRAN would then build platform-specific binary packages from the source package. + +#### Build source package + +To build source package locally without releasing to CRAN, run in R under the `SPARK_HOME/R` directory: + +```R +paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::build("pkg"); .libPaths(paths) +``` + +(http://r-pkgs.had.co.nz/vignettes.html#vignette-workflow-2) + +Similarly, the source package is also created by `check-cran.sh` with `R CMD build pkg`. + +For example, this should be the content of the source package: + +```sh +DESCRIPTION R inst tests +NAMESPACE build man vignettes + +inst/doc/ +sparkr-vignettes.html +sparkr-vignettes.Rmd +sparkr-vignettes.Rman + +build/ +vignette.rds + +man/ + *.Rd files... + +vignettes/ +sparkr-vignettes.Rmd +``` + +#### Test source package + +To install, run this: + +```sh +R CMD INSTALL SparkR_2.1.0.tar.gz +``` + +With "2.1.0" replaced with the version of SparkR. + +This command installs SparkR to the default libPaths. Once that is done, you should be able to start R and run: + +```R +library(SparkR) +vignette("sparkr-vignettes", package="SparkR") +``` + +#### Build binary package + +To build binary package locally, run in R under the `SPARK_HOME/R` directory: + +```R +paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); devtools::build("pkg", binary = TRUE); .libPaths(paths) +``` + +For example, this should be the content of the binary package: + +```sh +DESCRIPTION Meta R html tests +INDEX NAMESPACE help profile worker +``` diff --git a/R/README.md b/R/README.md index 932d5272d0..47f9a86dfd 100644 --- a/R/README.md +++ b/R/README.md @@ -6,7 +6,7 @@ SparkR is an R package that provides a light-weight frontend to use Spark from R Libraries of sparkR need to be created in `$SPARK_HOME/R/lib`. This can be done by running the script `$SPARK_HOME/R/install-dev.sh`. By default the above script uses the system wide installation of R. However, this can be changed to any user installed location of R by setting the environment variable `R_HOME` the full path of the base directory where R is installed, before running install-dev.sh script. -Example: +Example: ```bash # where /home/username/R is where R is installed and /home/username/R/bin contains the files R and RScript export R_HOME=/home/username/R @@ -46,7 +46,7 @@ Sys.setenv(SPARK_HOME="/Users/username/spark") # This line loads SparkR from the installed directory .libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths())) library(SparkR) -sc <- sparkR.init(master="local") +sparkR.session() ``` #### Making changes to SparkR @@ -54,11 +54,11 @@ sc <- sparkR.init(master="local") The [instructions](https://cwiki.apache.org/confluence/display/SPARK/Contributing+to+Spark) for making contributions to Spark also apply to SparkR. If you only make R file changes (i.e. no Scala changes) then you can just re-install the R package using `R/install-dev.sh` and test your changes. Once you have made your changes, please include unit tests for them and run existing unit tests using the `R/run-tests.sh` script as described below. - + #### Generating documentation The SparkR documentation (Rd files and HTML files) are not a part of the source repository. To generate them you can run the script `R/create-docs.sh`. This script uses `devtools` and `knitr` to generate the docs and these packages need to be installed on the machine before using the script. Also, you may need to install these [prerequisites](https://github.com/apache/spark/tree/master/docs#prerequisites). See also, `R/DOCUMENTATION.md` - + ### Examples, Unit tests SparkR comes with several sample programs in the `examples/src/main/r` directory. diff --git a/R/check-cran.sh b/R/check-cran.sh index bb331466ae..c5f042848c 100755 --- a/R/check-cran.sh +++ b/R/check-cran.sh @@ -36,11 +36,27 @@ if [ ! -z "$R_HOME" ] fi echo "USING R_HOME = $R_HOME" -# Build the latest docs +# Build the latest docs, but not vignettes, which is built with the package next $FWDIR/create-docs.sh -# Build a zip file containing the source package -"$R_SCRIPT_PATH/"R CMD build $FWDIR/pkg +# Build source package with vignettes +SPARK_HOME="$(cd "${FWDIR}"/..; pwd)" +. "${SPARK_HOME}"/bin/load-spark-env.sh +if [ -f "${SPARK_HOME}/RELEASE" ]; then + SPARK_JARS_DIR="${SPARK_HOME}/jars" +else + SPARK_JARS_DIR="${SPARK_HOME}/assembly/target/scala-$SPARK_SCALA_VERSION/jars" +fi + +if [ -d "$SPARK_JARS_DIR" ]; then + # Build a zip file containing the source package with vignettes + SPARK_HOME="${SPARK_HOME}" "$R_SCRIPT_PATH/"R CMD build $FWDIR/pkg + + find pkg/vignettes/. -not -name '.' -not -name '*.Rmd' -not -name '*.md' -not -name '*.pdf' -not -name '*.html' -delete +else + echo "Error Spark JARs not found in $SPARK_HOME" + exit 1 +fi # Run check as-cran. VERSION=`grep Version $FWDIR/pkg/DESCRIPTION | awk '{print $NF}'` @@ -54,11 +70,16 @@ fi if [ -n "$NO_MANUAL" ] then - CRAN_CHECK_OPTIONS=$CRAN_CHECK_OPTIONS" --no-manual" + CRAN_CHECK_OPTIONS=$CRAN_CHECK_OPTIONS" --no-manual --no-vignettes" fi echo "Running CRAN check with $CRAN_CHECK_OPTIONS options" -"$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz - +if [ -n "$NO_TESTS" ] && [ -n "$NO_MANUAL" ] +then + "$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz +else + # This will run tests and/or build vignettes, and require SPARK_HOME + SPARK_HOME="${SPARK_HOME}" "$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz +fi popd > /dev/null diff --git a/R/create-docs.sh b/R/create-docs.sh index 69ffc5f678..84e6aa928c 100755 --- a/R/create-docs.sh +++ b/R/create-docs.sh @@ -20,7 +20,7 @@ # Script to create API docs and vignettes for SparkR # This requires `devtools`, `knitr` and `rmarkdown` to be installed on the machine. -# After running this script the html docs can be found in +# After running this script the html docs can be found in # $SPARK_HOME/R/pkg/html # The vignettes can be found in # $SPARK_HOME/R/pkg/vignettes/sparkr_vignettes.html @@ -52,21 +52,4 @@ Rscript -e 'libDir <- "../../lib"; library(SparkR, lib.loc=libDir); library(knit popd -# Find Spark jars. -if [ -f "${SPARK_HOME}/RELEASE" ]; then - SPARK_JARS_DIR="${SPARK_HOME}/jars" -else - SPARK_JARS_DIR="${SPARK_HOME}/assembly/target/scala-$SPARK_SCALA_VERSION/jars" -fi - -# Only create vignettes if Spark JARs exist -if [ -d "$SPARK_JARS_DIR" ]; then - # render creates SparkR vignettes - Rscript -e 'library(rmarkdown); paths <- .libPaths(); .libPaths(c("lib", paths)); Sys.setenv(SPARK_HOME=tools::file_path_as_absolute("..")); render("pkg/vignettes/sparkr-vignettes.Rmd"); .libPaths(paths)' - - find pkg/vignettes/. -not -name '.' -not -name '*.Rmd' -not -name '*.md' -not -name '*.pdf' -not -name '*.html' -delete -else - echo "Skipping R vignettes as Spark JARs not found in $SPARK_HOME" -fi - popd diff --git a/R/pkg/DESCRIPTION b/R/pkg/DESCRIPTION index 5a83883089..fe41a9e7da 100644 --- a/R/pkg/DESCRIPTION +++ b/R/pkg/DESCRIPTION @@ -1,8 +1,8 @@ Package: SparkR Type: Package Title: R Frontend for Apache Spark -Version: 2.0.0 -Date: 2016-08-27 +Version: 2.1.0 +Date: 2016-11-06 Authors@R: c(person("Shivaram", "Venkataraman", role = c("aut", "cre"), email = "shivaram@cs.berkeley.edu"), person("Xiangrui", "Meng", role = "aut", @@ -18,7 +18,9 @@ Depends: Suggests: testthat, e1071, - survival + survival, + knitr, + rmarkdown Description: The SparkR package provides an R frontend for Apache Spark. License: Apache License (== 2.0) Collate: @@ -48,3 +50,4 @@ Collate: 'utils.R' 'window.R' RoxygenNote: 5.0.1 +VignetteBuilder: knitr diff --git a/R/pkg/vignettes/sparkr-vignettes.Rmd b/R/pkg/vignettes/sparkr-vignettes.Rmd index 80e876027b..73a5e26a3b 100644 --- a/R/pkg/vignettes/sparkr-vignettes.Rmd +++ b/R/pkg/vignettes/sparkr-vignettes.Rmd @@ -1,12 +1,13 @@ --- title: "SparkR - Practical Guide" output: - html_document: - theme: united + rmarkdown::html_vignette: toc: true toc_depth: 4 - toc_float: true - highlight: textmate +vignette: > + %\VignetteIndexEntry{SparkR - Practical Guide} + %\VignetteEngine{knitr::rmarkdown} + \usepackage[utf8]{inputenc} --- ## Overview |