From 349d95d0ce933d6670d5326ab560ccef420b814e Mon Sep 17 00:00:00 2001
From: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Date: Sun, 21 Aug 2016 13:43:15 -0700
Subject: [PATCH 1/5] Add CRAN documentation checks to run-tests.sh

---
 R/check-cran.sh |  2 +-
 R/run-tests.sh  | 22 +++++++++++++++++++---
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/R/check-cran.sh b/R/check-cran.sh
index 5c90fd07f28e4..8cbec038a686e 100755
--- a/R/check-cran.sh
+++ b/R/check-cran.sh
@@ -47,6 +47,6 @@ $FWDIR/create-docs.sh
 
 VERSION=`grep Version $FWDIR/pkg/DESCRIPTION | awk '{print $NF}'`
 
-"$R_SCRIPT_PATH/"R CMD check --as-cran SparkR_"$VERSION".tar.gz
+"$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS --as-cran SparkR_"$VERSION".tar.gz
 
 popd > /dev/null
diff --git a/R/run-tests.sh b/R/run-tests.sh
index 9dcf0ace7d97e..5a422f28de4e7 100755
--- a/R/run-tests.sh
+++ b/R/run-tests.sh
@@ -26,6 +26,14 @@ rm -f $LOGFILE
 SPARK_TESTING=1 $FWDIR/../bin/spark-submit --driver-java-options "-Dlog4j.configuration=file:$FWDIR/log4j.properties" --conf spark.hadoop.fs.default.name="file:///" $FWDIR/pkg/tests/run-all.R 2>&1 | tee -a $LOGFILE
 FAILED=$((PIPESTATUS[0]||$FAILED))
 
+# Also run the documentation tests for CRAN
+CRAN_CHECK_LOG_FILE=$FWDIR/cran-check.out
+rm -f $CRAN_CHECK_LOG_FILE
+CRAN_CHECK_OPTIONS="--no-tests --no-manual" $FWDIR/check-cran.sh 2>&1 | tee -a $CRAN_CHECK_LOG_FILE
+FAILED=$((PIPESTATUS[0]||$FAILED))
+
+HAS_CRAN_WARNING="$(grep -c WARNING $CRAN_CHECK_LOG_FILE)"
+
 if [[ $FAILED != 0 ]]; then
     cat $LOGFILE
     echo -en "\033[31m"  # Red
@@ -33,7 +41,15 @@ if [[ $FAILED != 0 ]]; then
     echo -en "\033[0m"  # No color
     exit -1
 else
-    echo -en "\033[32m"  # Green
-    echo "Tests passed."
-    echo -en "\033[0m"  # No color
+    if [[ $HAS_CRAN_WARNING != 0 ]]; then
+      cat $CRAN_CHECK_LOG_FILE
+      echo -en "\033[31m"  # Red
+      echo "Had CRAN check warnings; see logs."
+      echo -en "\033[0m"  # No color
+      exit -1
+    else
+      echo -en "\033[32m"  # Green
+      echo "Tests passed."
+      echo -en "\033[0m"  # No color
+    fi
 fi

From 96216ac20d4a77810ce957c15fabb9266028fe98 Mon Sep 17 00:00:00 2001
From: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Date: Mon, 22 Aug 2016 12:46:23 -0700
Subject: [PATCH 2/5] Remove e1071 to make Jenkins work for now

---
 R/pkg/DESCRIPTION | 1 -
 1 file changed, 1 deletion(-)

diff --git a/R/pkg/DESCRIPTION b/R/pkg/DESCRIPTION
index 357ab007931f5..6e73243cd67de 100644
--- a/R/pkg/DESCRIPTION
+++ b/R/pkg/DESCRIPTION
@@ -10,7 +10,6 @@ Depends:
     methods
 Suggests:
     testthat,
-    e1071,
     survival
 Description: The SparkR package provides an R frontend for Apache Spark.
 License: Apache License (== 2.0)

From 9de5e5974b5d596865adeba912c4c7c3f26809e0 Mon Sep 17 00:00:00 2001
From: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Date: Mon, 22 Aug 2016 14:00:44 -0700
Subject: [PATCH 3/5] Revert change to DESCRIPTION

---
 R/pkg/DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/pkg/DESCRIPTION b/R/pkg/DESCRIPTION
index 6e73243cd67de..357ab007931f5 100644
--- a/R/pkg/DESCRIPTION
+++ b/R/pkg/DESCRIPTION
@@ -10,6 +10,7 @@ Depends:
     methods
 Suggests:
     testthat,
+    e1071,
     survival
 Description: The SparkR package provides an R frontend for Apache Spark.
 License: Apache License (== 2.0)

From 5df8936651fb3a51fdc785740cdd27afd1c51171 Mon Sep 17 00:00:00 2001
From: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Date: Mon, 22 Aug 2016 14:01:11 -0700
Subject: [PATCH 4/5] ALso check for errors, notes. Refactor options

---
 R/check-cran.sh | 18 +++++++++++++++---
 R/run-tests.sh  | 12 ++++++++----
 2 files changed, 23 insertions(+), 7 deletions(-)

diff --git a/R/check-cran.sh b/R/check-cran.sh
index 8cbec038a686e..bb331466ae931 100755
--- a/R/check-cran.sh
+++ b/R/check-cran.sh
@@ -43,10 +43,22 @@ $FWDIR/create-docs.sh
 "$R_SCRIPT_PATH/"R CMD build $FWDIR/pkg
 
 # Run check as-cran.
-# TODO(shivaram): Remove the skip tests once we figure out the install mechanism
-
 VERSION=`grep Version $FWDIR/pkg/DESCRIPTION | awk '{print $NF}'`
 
-"$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS --as-cran SparkR_"$VERSION".tar.gz
+CRAN_CHECK_OPTIONS="--as-cran"
+
+if [ -n "$NO_TESTS" ]
+then
+  CRAN_CHECK_OPTIONS=$CRAN_CHECK_OPTIONS" --no-tests"
+fi
+
+if [ -n "$NO_MANUAL" ]
+then
+  CRAN_CHECK_OPTIONS=$CRAN_CHECK_OPTIONS" --no-manual"
+fi
+
+echo "Running CRAN check with $CRAN_CHECK_OPTIONS options"
+
+"$R_SCRIPT_PATH/"R CMD check $CRAN_CHECK_OPTIONS SparkR_"$VERSION".tar.gz
 
 popd > /dev/null
diff --git a/R/run-tests.sh b/R/run-tests.sh
index 5a422f28de4e7..eb5cc4c2ed0a6 100755
--- a/R/run-tests.sh
+++ b/R/run-tests.sh
@@ -29,10 +29,13 @@ FAILED=$((PIPESTATUS[0]||$FAILED))
 # Also run the documentation tests for CRAN
 CRAN_CHECK_LOG_FILE=$FWDIR/cran-check.out
 rm -f $CRAN_CHECK_LOG_FILE
-CRAN_CHECK_OPTIONS="--no-tests --no-manual" $FWDIR/check-cran.sh 2>&1 | tee -a $CRAN_CHECK_LOG_FILE
+
+NO_TESTS=1 NO_MANUAL=1 $FWDIR/check-cran.sh 2>&1 | tee -a $CRAN_CHECK_LOG_FILE
 FAILED=$((PIPESTATUS[0]||$FAILED))
 
-HAS_CRAN_WARNING="$(grep -c WARNING $CRAN_CHECK_LOG_FILE)"
+NUM_CRAN_WARNING="$(grep -c WARNING$ $CRAN_CHECK_LOG_FILE)"
+NUM_CRAN_ERROR="$(grep -c ERROR$ $CRAN_CHECK_LOG_FILE)"
+NUM_CRAN_NOTES="$(grep -c NOTE$ $CRAN_CHECK_LOG_FILE)"
 
 if [[ $FAILED != 0 ]]; then
     cat $LOGFILE
@@ -41,10 +44,11 @@ if [[ $FAILED != 0 ]]; then
     echo -en "\033[0m"  # No color
     exit -1
 else
-    if [[ $HAS_CRAN_WARNING != 0 ]]; then
+    # We have 2 existing NOTEs for new maintainer, attach()
+    if [[ $NUM_CRAN_WARNING != 0 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES != 2 ]]; then
       cat $CRAN_CHECK_LOG_FILE
       echo -en "\033[31m"  # Red
-      echo "Had CRAN check warnings; see logs."
+      echo "Had CRAN check errors; see logs."
       echo -en "\033[0m"  # No color
       exit -1
     else

From 2bde2b41f3d69a76acb09bca046ca21bfdbd7b28 Mon Sep 17 00:00:00 2001
From: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Date: Mon, 22 Aug 2016 15:04:37 -0700
Subject: [PATCH 5/5] Handle extra NOTE in Jenkins

---
 R/run-tests.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/run-tests.sh b/R/run-tests.sh
index eb5cc4c2ed0a6..1a1e8ab9ffe18 100755
--- a/R/run-tests.sh
+++ b/R/run-tests.sh
@@ -45,7 +45,8 @@ if [[ $FAILED != 0 ]]; then
     exit -1
 else
     # We have 2 existing NOTEs for new maintainer, attach()
-    if [[ $NUM_CRAN_WARNING != 0 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES != 2 ]]; then
+    # We have one more NOTE in Jenkins due to "No repository set"
+    if [[ $NUM_CRAN_WARNING != 0 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES -gt 3 ]]; then
       cat $CRAN_CHECK_LOG_FILE
       echo -en "\033[31m"  # Red
       echo "Had CRAN check errors; see logs."