GH-16177: Validate h2o 3 package on r 4 4 and add test image to jenkins (#16291)

* Add update dependencies for R 4.4.0

* Enable R 4.4.0 image

* Fix runit_GBM_weight_gamma.R

* Deal with .checkFieldsInMethod warning

* Add html tidy to the R image for CRAN check

* Fix runit_coxph_concordance.R test

* Fix runit_coxph_concordance_heart.R test

* Fix runit_coxph_predict.R

* Fix runit_pubdev_8945_coxph_all_interactions_mojo.R

* Fix runit_GBM_ecology.R

* Install uplift package even if it was archived

* Fix runit_GLM_libR_airlines.R

* Fix runit_GLM_offset.R

* Fix runit_PUBDEV_6037_fractionalbinomial_mojo.R

* Fix runit_PUBDEV_8638_bodyfat_RID_Binomial_compareR_test.R

* Fix runit_glrm_PUBDEV_3788_loss_by_col_err.R

* Fix runit_isofor_accuracy.R

* Fix runit_PUBDEV_8235_modelselection_gaussian_validation.R

* Fix runit_OLD_1079_airlines.R

* Fix runit_pubdev_6817_noK_PCA.R

* Fix runit_pca_5_golden.R

* Fix javapredict

* Fix runit_head_tail.R

* Fix runit_relevel.R

* Fix runit_import_upload_singlequoted.R

* Fix runit_ifelse.R

* Fix runit_h2oconfig.R and .parse.h2oconfig in config.R

* Fix runit_as.h2o_sparse.R

* Fix runit_pubdev_8218.R

* Fix runit_PUBDEV_7362_merge_duplicate_others.R

* Fix runit_pubdev_1654.R

* Fix runit_pubdev_1398.R

* Fix runit_pubdev_1383.R

* Fix runit_hexdev_29_categorical_continuous.R

* Fix runit_GLM_offset.R for R 3.5

* Add DT to R 4.4 image

* Do not set options(stringsAsFactors=TRUE) in the tests

* Fix runit_as.h2o_sparse.R

* Add new cran messages to validate_r_cmf_check_output.py

* More changes to the validate_r_cmd_check_output.py

Author: tomasfryda

docker/Jenkinsfile-build-docker

@@ -22,7 +22,7 @@ IMAGE_NAME_PREFIX = 'harbor.h2o.ai/opsh2oai/h2o-3'
 JDK_VERSIONS = ['8', '10', '11', '12', '13', '14', '15', '16', '17']
 JDK_VERSIONS_PY_R = ['8', '11', '17'] // stable, last-supported, latest
 PYTHON_VERSIONS = ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
-R_VERSION = ['3.3.3', '3.4.1', '3.5.3', '3.6.2', '4.0.2']
+R_VERSION = ['3.3.3', '3.4.1', '3.5.3', '3.6.2', '4.0.2', '4.4.0']
 
 def pipelineContext
 

docker/Makefile

@@ -276,6 +276,22 @@ ifeq ($(shell echo $(PUSH) | tr [:upper:] [:lower:] ),true)
 	docker push harbor.h2o.ai/opsh2oai/h2o-3/dev-r-4.0.2-jdk-$*:$(VERSION)
 endif
 
+ifneq ($(CI), 1)
+dev-r-4.4.0-jdk-%: dev-r-4.4.0
+endif
+dev-r-4.4.0-jdk-%:
+	docker build -t harbor.h2o.ai/opsh2oai/h2o-3/dev-r-4.4.0-jdk-$*:$(VERSION) \
+		$(NO_CACHE) \
+		-f jenkins-images/Dockerfile-jdk-others \
+		--build-arg FROM_VERSION=$(VERSION) \
+		--build-arg FROM_IMAGE=harbor.h2o.ai/opsh2oai/h2o-3/dev-r-4.4.0 \
+		--build-arg INSTALL_JAVA_VERSION=$* \
+		--build-arg H2O_BRANCH=$(H2O_BRANCH) \
+		.
+ifeq ($(shell echo $(PUSH) | tr [:upper:] [:lower:] ),true)
+	docker push harbor.h2o.ai/opsh2oai/h2o-3/dev-r-4.4.0-jdk-$*:$(VERSION)
+endif
+
 ifneq ($(CI), 1)
 dev-r-%: dev-r-base
 endif

docker/jenkins-images/Dockerfile-r

@@ -9,7 +9,8 @@ ENV R_VERSION=${R_VERSION}
 # In C, global variables with multiple tentative definitions now result in linker errors. With -fcommon such definitions
 # are silently merged during linking.). I tried using -fcommon but without much luck so due to the time constrain I
 # decided to use gcc-9 instead.
-RUN apt-get update && apt-get install -y gcc-9 gfortran-9 g++-9 tcl-dev tk-dev && apt-get clean && apt-get autoremove -y && \
+RUN apt-get update && apt-get install -y gcc-9 gfortran-9 g++-9 tcl-dev tk-dev tidy && \
+    apt-get clean && apt-get autoremove -y && \
     rm -rf /var/cache/apt/*  &&\
     update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-9 99 --slave /usr/bin/g++ g++ /usr/bin/g++-9 \
     --slave /usr/bin/gcov gcov /usr/bin/gcov-9 && update-alternatives --install /usr/bin/gfortran f95 /usr/bin/gfortran-9 99