2ca5aae47a
## What changes were proposed in this pull request? This is to fix the code for the latest R changes in R-devel, when running CRAN check ``` checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'attach': attach Code: function(what, pos = 2L, name = deparse(substitute(what), backtick = FALSE), warn.conflicts = TRUE) Docs: function(what, pos = 2L, name = deparse(substitute(what)), warn.conflicts = TRUE) Mismatches in argument default values: Name: 'name' Code: deparse(substitute(what), backtick = FALSE) Docs: deparse(substitute(what)) Codoc mismatches from documentation object 'glm': glm Code: function(formula, family = gaussian, data, weights, subset, na.action, start = NULL, etastart, mustart, offset, control = list(...), model = TRUE, method = "glm.fit", x = FALSE, y = TRUE, singular.ok = TRUE, contrasts = NULL, ...) Docs: function(formula, family = gaussian, data, weights, subset, na.action, start = NULL, etastart, mustart, offset, control = list(...), model = TRUE, method = "glm.fit", x = FALSE, y = TRUE, contrasts = NULL, ...) Argument names in code not in docs: singular.ok Mismatches in argument names: Position: 16 Code: singular.ok Docs: contrasts Position: 17 Code: contrasts Docs: ... ``` With attach, it's pulling in the function definition from base::attach. We need to disable that but we would still need a function signature for roxygen2 to build with. With glm it's pulling in the function definition (ie. "usage") from the stats::glm function. Since this is "compiled in" when we build the source package into the .Rd file, when it changes at runtime or in CRAN check it won't match the latest signature. The solution is not to pull in from stats::glm since there isn't much value in doing that (none of the param we actually use, the ones we do use we have explicitly documented them) Also with attach we are changing to call dynamically. ## How was this patch tested? Manually. - [x] check documentation output - yes - [x] check help `?attach` `?glm` - yes - [x] check on other platforms, r-hub, on r-devel etc.. Author: Felix Cheung <felixcheung_m@hotmail.com> Closes #19557 from felixcheung/rattachglmdocerror.
65 lines
2.5 KiB
Bash
Executable file
65 lines
2.5 KiB
Bash
Executable file
#!/bin/bash
|
|
|
|
#
|
|
# Licensed to the Apache Software Foundation (ASF) under one or more
|
|
# contributor license agreements. See the NOTICE file distributed with
|
|
# this work for additional information regarding copyright ownership.
|
|
# The ASF licenses this file to You under the Apache License, Version 2.0
|
|
# (the "License"); you may not use this file except in compliance with
|
|
# the License. You may obtain a copy of the License at
|
|
#
|
|
# http://www.apache.org/licenses/LICENSE-2.0
|
|
#
|
|
# Unless required by applicable law or agreed to in writing, software
|
|
# distributed under the License is distributed on an "AS IS" BASIS,
|
|
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
# See the License for the specific language governing permissions and
|
|
# limitations under the License.
|
|
#
|
|
|
|
FWDIR="$(cd `dirname $0`; pwd)"
|
|
|
|
FAILED=0
|
|
LOGFILE=$FWDIR/unit-tests.out
|
|
rm -f $LOGFILE
|
|
|
|
SPARK_TESTING=1 NOT_CRAN=true $FWDIR/../bin/spark-submit --driver-java-options "-Dlog4j.configuration=file:$FWDIR/log4j.properties" --conf spark.hadoop.fs.defaultFS="file:///" $FWDIR/pkg/tests/run-all.R 2>&1 | tee -a $LOGFILE
|
|
FAILED=$((PIPESTATUS[0]||$FAILED))
|
|
|
|
NUM_TEST_WARNING="$(grep -c -e 'Warnings ----------------' $LOGFILE)"
|
|
|
|
# Also run the documentation tests for CRAN
|
|
CRAN_CHECK_LOG_FILE=$FWDIR/cran-check.out
|
|
rm -f $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]||$FAILED))
|
|
|
|
NUM_CRAN_WARNING="$(grep -c WARNING$ $CRAN_CHECK_LOG_FILE)"
|
|
NUM_CRAN_ERROR="$(grep -c ERROR$ $CRAN_CHECK_LOG_FILE)"
|
|
NUM_CRAN_NOTES="$(grep -c NOTE$ $CRAN_CHECK_LOG_FILE)"
|
|
HAS_PACKAGE_VERSION_WARN="$(grep -c "Insufficient package version" $CRAN_CHECK_LOG_FILE)"
|
|
|
|
if [[ $FAILED != 0 || $NUM_TEST_WARNING != 0 ]]; then
|
|
cat $LOGFILE
|
|
echo -en "\033[31m" # Red
|
|
echo "Had test warnings or failures; see logs."
|
|
echo -en "\033[0m" # No color
|
|
exit -1
|
|
else
|
|
# We have 2 NOTEs: for RoxygenNote and one in Jenkins only "No repository set"
|
|
# For non-latest version branches, one WARNING for package version
|
|
if [[ ($NUM_CRAN_WARNING != 0 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES -gt 2) &&
|
|
($HAS_PACKAGE_VERSION_WARN != 1 || $NUM_CRAN_WARNING != 1 || $NUM_CRAN_ERROR != 0 || $NUM_CRAN_NOTES -gt 1) ]]; then
|
|
cat $CRAN_CHECK_LOG_FILE
|
|
echo -en "\033[31m" # Red
|
|
echo "Had CRAN check errors; 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
|