This is an automated email from the ASF dual-hosted git repository. omartushevskyi pushed a commit to branch r-fix in repository https://gitbox.apache.org/repos/asf/incubator-dlab.git
commit 1c356285ac061a502b18728b4248d3dca7982393 Author: Oleh Martushevskyi <oleh_martushevs...@epam.com> AuthorDate: Mon Jan 27 15:48:56 2020 +0200 [DLAB-1479]: Fixed issue with R repository --- .../deploy_repository/templates/addCustomRepository.groovy | 2 +- .../src/general/lib/os/debian/notebook_lib.py | 4 ++-- infrastructure-provisioning/src/general/lib/os/fab.py | 14 +++++++------- .../src/general/lib/os/redhat/notebook_lib.py | 4 ++-- 4 files changed, 12 insertions(+), 12 deletions(-) diff --git a/infrastructure-provisioning/scripts/deploy_repository/templates/addCustomRepository.groovy b/infrastructure-provisioning/scripts/deploy_repository/templates/addCustomRepository.groovy index 37d2dd3..204c0eb 100644 --- a/infrastructure-provisioning/scripts/deploy_repository/templates/addCustomRepository.groovy +++ b/infrastructure-provisioning/scripts/deploy_repository/templates/addCustomRepository.groovy @@ -194,7 +194,7 @@ RProxyConfiguration = new Configuration( ] as Map ] as Map, proxy: [ - remoteUrl: 'http://cran.us.r-project.org', + remoteUrl: 'https://cloud.r-project.org', contentMaxAge: 0, metaDataMaxAge: 0 ] as Map, diff --git a/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py b/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py index 87f3819..44bf218 100644 --- a/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py +++ b/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py @@ -64,7 +64,7 @@ def ensure_r_local_kernel(spark_version, os_user, templates_dir, kernels_dir): sudo('\cp -f /tmp/r_template.json {}/ir/kernel.json'.format(kernels_dir)) sudo('ln -s /opt/spark/ /usr/local/spark') try: - sudo('cd /usr/local/spark/R/lib/SparkR; R -e "install.packages(\'roxygen2\',repos=\'http://cran.us.r-project.org\')" R -e "devtools::check(\'.\')"') + sudo('cd /usr/local/spark/R/lib/SparkR; R -e "install.packages(\'roxygen2\',repos=\'https://cloud.r-project.org\')" R -e "devtools::check(\'.\')"') except: pass sudo('cd /usr/local/spark/R/lib/SparkR; R -e "devtools::install(\'.\')"') @@ -86,7 +86,7 @@ def ensure_r(os_user, r_libs, region, r_mirror): if region == 'cn-north-1': r_repository = r_mirror else: - r_repository = 'http://cran.us.r-project.org' + r_repository = 'https://cloud.r-project.org' add_marruter_key() sudo('apt update') sudo('apt-get install -y libcurl4-openssl-dev libssl-dev libreadline-dev') diff --git a/infrastructure-provisioning/src/general/lib/os/fab.py b/infrastructure-provisioning/src/general/lib/os/fab.py index 884884e..f3aa2c6 100644 --- a/infrastructure-provisioning/src/general/lib/os/fab.py +++ b/infrastructure-provisioning/src/general/lib/os/fab.py @@ -387,8 +387,8 @@ def install_r_pkg(requisites): try: for r_pkg in requisites: if r_pkg == 'sparklyr': - run('sudo -i R -e \'install.packages("{0}", repos="http://cran.us.r-project.org", dep=TRUE)\' 2>&1 | tee /tmp/tee.tmp; if ! grep -w -E "({1})" /tmp/tee.tmp > /tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(r_pkg, error_parser)) - sudo('R -e \'install.packages("{0}", repos="http://cran.us.r-project.org", dep=TRUE)\' 2>&1 | tee /tmp/tee.tmp; if ! grep -w -E "({1})" /tmp/tee.tmp > /tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(r_pkg, error_parser)) + run('sudo -i R -e \'install.packages("{0}", repos="https://cloud.r-project.org", dep=TRUE)\' 2>&1 | tee /tmp/tee.tmp; if ! grep -w -E "({1})" /tmp/tee.tmp > /tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(r_pkg, error_parser)) + sudo('R -e \'install.packages("{0}", repos="https://cloud.r-project.org", dep=TRUE)\' 2>&1 | tee /tmp/tee.tmp; if ! grep -w -E "({1})" /tmp/tee.tmp > /tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(r_pkg, error_parser)) err = sudo('cat /tmp/install_{0}.log'.format(r_pkg)).replace('"', "'") sudo('R -e \'installed.packages()[,c(3:4)]\' | if ! grep -w {0} > /tmp/install_{0}.list; then echo "" > /tmp/install_{0}.list;fi'.format(r_pkg)) res = sudo('cat /tmp/install_{0}.list'.format(r_pkg)) @@ -470,7 +470,7 @@ def install_java_pkg(requisites): def get_available_r_pkgs(): try: r_pkgs = dict() - sudo('R -e \'write.table(available.packages(contriburl="http://cran.us.r-project.org/src/contrib"), file="/tmp/r.csv", row.names=F, col.names=F, sep=",")\'') + sudo('R -e \'write.table(available.packages(contriburl="https://cloud.r-project.org/src/contrib"), file="/tmp/r.csv", row.names=F, col.names=F, sep=",")\'') get("/tmp/r.csv", "r.csv") with open('r.csv', 'rb') as csvfile: reader = csv.reader(csvfile, delimiter=',') @@ -590,11 +590,11 @@ def set_mongo_parameters(client, mongo_parameters): def install_r_packages(os_user): if not exists('/home/' + os_user + '/.ensure_dir/r_packages_ensured'): - sudo('R -e "install.packages(\'devtools\', repos = \'http://cran.us.r-project.org\')"') - sudo('R -e "install.packages(\'knitr\', repos = \'http://cran.us.r-project.org\')"') - sudo('R -e "install.packages(\'ggplot2\', repos = \'http://cran.us.r-project.org\')"') + sudo('R -e "install.packages(\'devtools\', repos = \'https://cloud.r-project.org\')"') + sudo('R -e "install.packages(\'knitr\', repos = \'https://cloud.r-project.org\')"') + sudo('R -e "install.packages(\'ggplot2\', repos = \'https://cloud.r-project.org\')"') sudo('R -e "install.packages(c(\'devtools\',\'mplot\', \'googleVis\'), ' - 'repos = \'http://cran.us.r-project.org\'); require(devtools); install_github(\'ramnathv/rCharts\')"') + 'repos = \'https://cloud.r-project.org\'); require(devtools); install_github(\'ramnathv/rCharts\')"') sudo('touch /home/' + os_user + '/.ensure_dir/r_packages_ensured') diff --git a/infrastructure-provisioning/src/general/lib/os/redhat/notebook_lib.py b/infrastructure-provisioning/src/general/lib/os/redhat/notebook_lib.py index 17ff931..78d70af 100644 --- a/infrastructure-provisioning/src/general/lib/os/redhat/notebook_lib.py +++ b/infrastructure-provisioning/src/general/lib/os/redhat/notebook_lib.py @@ -65,7 +65,7 @@ def ensure_r_local_kernel(spark_version, os_user, templates_dir, kernels_dir): run('R -e "IRkernel::installspec()"') sudo('ln -s /opt/spark/ /usr/local/spark') try: - sudo('cd /usr/local/spark/R/lib/SparkR; R -e "install.packages(\'roxygen2\',repos=\'http://cran.us.r-project.org\')" R -e "devtools::check(\'.\')"') + sudo('cd /usr/local/spark/R/lib/SparkR; R -e "install.packages(\'roxygen2\',repos=\'https://cloud.r-project.org\')" R -e "devtools::check(\'.\')"') except: pass sudo('cd /usr/local/spark/R/lib/SparkR; R -e "devtools::install(\'.\')"') @@ -87,7 +87,7 @@ def ensure_r(os_user, r_libs, region, r_mirror): if region == 'cn-north-1': r_repository = r_mirror else: - r_repository = 'http://cran.us.r-project.org' + r_repository = 'https://cloud.r-project.org' sudo('yum install -y cmake') sudo('yum -y install libcur*') sudo('echo -e "[base]\nname=CentOS-7-Base\nbaseurl=http://buildlogs.centos.org/centos/7/os/x86_64-20140704-1/\ngpgcheck=1\ngpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7\npriority=1\nexclude=php mysql" >> /etc/yum.repos.d/CentOS-base.repo') --------------------------------------------------------------------- To unsubscribe, e-mail: commits-unsubscr...@dlab.apache.org For additional commands, e-mail: commits-h...@dlab.apache.org