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Posted to commits@dlab.apache.org by om...@apache.org on 2020/01/27 11:22:36 UTC
[incubator-dlab] 01/01: [DLAB-1479]: Fixed issue with R repository
This is an automated email from the ASF dual-hosted git repository.
omartushevskyi pushed a commit to branch DLAB-1479
in repository https://gitbox.apache.org/repos/asf/incubator-dlab.git
commit 49d2f2e8170817e3e0f1130baece586cf467d39b
Author: Oleh Martushevskyi <Ol...@epam.com>
AuthorDate: Mon Jan 27 13:22:16 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 879955a..47ef676 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')
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