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Posted to commits@datalab.apache.org by lf...@apache.org on 2020/12/15 11:22:41 UTC
[incubator-datalab] branch DATALAB-2189 created (now ee5c9f0)
This is an automated email from the ASF dual-hosted git repository.
lfrolov pushed a change to branch DATALAB-2189
in repository https://gitbox.apache.org/repos/asf/incubator-datalab.git.
at ee5c9f0 [DATALAB-2190]: specified caTools version for R 3.4.4
This branch includes the following new commits:
new a87a5de [DATALAB-2190]: changed how r_libs are installed in ensure_r
new ee5c9f0 [DATALAB-2190]: specified caTools version for R 3.4.4
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
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[incubator-datalab] 01/02: [DATALAB-2190]: changed how r_libs are
installed in ensure_r
Posted by lf...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
lfrolov pushed a commit to branch DATALAB-2189
in repository https://gitbox.apache.org/repos/asf/incubator-datalab.git
commit a87a5deba61c92ef1c11e80a37e0ebde327657bd
Author: leonidfrolov <fr...@gmail.com>
AuthorDate: Tue Dec 15 13:21:58 2020 +0200
[DATALAB-2190]: changed how r_libs are installed in ensure_r
---
.../src/general/lib/os/debian/notebook_lib.py | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
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 3a1d21a..8375cb3 100644
--- a/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py
+++ b/infrastructure-provisioning/src/general/lib/os/debian/notebook_lib.py
@@ -95,8 +95,16 @@ def ensure_r(os_user, r_libs, region, r_mirror):
manage_pkg('-y install', 'remote', 'r-base r-base-dev')
sudo('R CMD javareconf')
sudo('cd /root; git clone https://github.com/zeromq/zeromq4-x.git; cd zeromq4-x/; mkdir build; cd build; cmake ..; make install; ldconfig')
+ sudo('R -e "install.packages(\'devtools\',repos=\'{}\')"'.format(r_repository))
for i in r_libs:
- sudo('R -e "install.packages(\'{}\',repos=\'{}\')"'.format(i, r_repository))
+ if '=' in i:
+ name = i.split('=')[0]
+ vers = '"{}"'.format(i.split('=')[1])
+ else:
+ name = i
+ vers = ''
+ sudo('R -e \'devtools::install_version("{}", version = {}, repos ="{}", dependencies = NA)\''.format(name, vers, r_repository))
+ #sudo('R -e "install.packages(\'{}\',repos=\'{}\')"'.format(i, r_repository))
sudo('R -e "library(\'devtools\');install.packages(repos=\'{}\',c(\'rzmq\',\'repr\',\'digest\',\'stringr\',\'RJSONIO\',\'functional\',\'plyr\'))"'.format(r_repository))
try:
sudo('R -e "library(\'devtools\');install_github(\'IRkernel/repr\');install_github(\'IRkernel/IRdisplay\');install_github(\'IRkernel/IRkernel\');"')
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[incubator-datalab] 02/02: [DATALAB-2190]: specified caTools
version for R 3.4.4
Posted by lf...@apache.org.
This is an automated email from the ASF dual-hosted git repository.
lfrolov pushed a commit to branch DATALAB-2189
in repository https://gitbox.apache.org/repos/asf/incubator-datalab.git
commit ee5c9f0cfc7bb38e942336c7a1295512e97902de
Author: leonidfrolov <fr...@gmail.com>
AuthorDate: Tue Dec 15 13:22:26 2020 +0200
[DATALAB-2190]: specified caTools version for R 3.4.4
---
.../src/dataengine/scripts/configure_dataengine.py | 2 +-
infrastructure-provisioning/src/general/conf/datalab.ini | 2 ++
.../src/jupyter/scripts/configure_jupyter_node.py | 2 +-
.../src/jupyterlab/scripts/configure_jupyterlab_node.py | 2 +-
.../src/rstudio/scripts/configure_rstudio_node.py | 2 +-
.../src/tensor-rstudio/scripts/configure_tensor-rstudio_node.py | 2 +-
.../src/zeppelin/scripts/configure_zeppelin_node.py | 2 +-
7 files changed, 8 insertions(+), 6 deletions(-)
diff --git a/infrastructure-provisioning/src/dataengine/scripts/configure_dataengine.py b/infrastructure-provisioning/src/dataengine/scripts/configure_dataengine.py
index 50d9483..7b094c0 100644
--- a/infrastructure-provisioning/src/dataengine/scripts/configure_dataengine.py
+++ b/infrastructure-provisioning/src/dataengine/scripts/configure_dataengine.py
@@ -71,7 +71,7 @@ templates_dir = '/root/templates/'
files_dir = '/root/files/'
local_spark_path = '/opt/spark/'
jars_dir = '/opt/jars/'
-r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2']
+r_libs = ['R6', 'pbdZMQ', 'RCurl', 'reshape2', 'caTools={}'.format(os.environ['notebook_caTools_version']), 'rJava', 'ggplot2']
if os.environ['application'] == 'deeplearning':
tensorflow_version = '1.4.0'
cuda_version = '8.0'
diff --git a/infrastructure-provisioning/src/general/conf/datalab.ini b/infrastructure-provisioning/src/general/conf/datalab.ini
index ae93aa6..dd9b9d1 100644
--- a/infrastructure-provisioning/src/general/conf/datalab.ini
+++ b/infrastructure-provisioning/src/general/conf/datalab.ini
@@ -294,6 +294,8 @@ ungit_version = 1.4.36
numpy_version = 1.18.3
### Numpy version for python 2
numpy2_version = 1.16.6
+### caTools version for R 3.4.4
+caTools_version = 1.17.1.4
### Apache Ivy version
ivy_version = 2.4.0
### Matplotlib version
diff --git a/infrastructure-provisioning/src/jupyter/scripts/configure_jupyter_node.py b/infrastructure-provisioning/src/jupyter/scripts/configure_jupyter_node.py
index 83cb899..3667e5a 100644
--- a/infrastructure-provisioning/src/jupyter/scripts/configure_jupyter_node.py
+++ b/infrastructure-provisioning/src/jupyter/scripts/configure_jupyter_node.py
@@ -63,7 +63,7 @@ templates_dir = '/root/templates/'
files_dir = '/root/files/'
local_spark_path = '/opt/spark/'
toree_link = 'http://archive.apache.org/dist/incubator/toree/0.3.0-incubating/toree-pip/toree-0.3.0.tar.gz'
-r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2']
+r_libs = ['R6', 'pbdZMQ', 'RCurl', 'reshape2', 'caTools=1.17.1.4', 'rJava', 'ggplot2']
gitlab_certfile = os.environ['conf_gitlab_certfile']
diff --git a/infrastructure-provisioning/src/jupyterlab/scripts/configure_jupyterlab_node.py b/infrastructure-provisioning/src/jupyterlab/scripts/configure_jupyterlab_node.py
index 4d0fcb1..6ac62ed 100644
--- a/infrastructure-provisioning/src/jupyterlab/scripts/configure_jupyterlab_node.py
+++ b/infrastructure-provisioning/src/jupyterlab/scripts/configure_jupyterlab_node.py
@@ -71,7 +71,7 @@ templates_dir = '/root/templates/'
files_dir = '/root/files/'
local_spark_path = '/opt/spark/'
toree_link = 'http://archive.apache.org/dist/incubator/toree/0.3.0-incubating/toree-pip/toree-0.3.0.tar.gz'
-r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2']
+r_libs = ['R6', 'pbdZMQ', 'RCurl', 'reshape2', 'caTools={}'.format(os.environ['notebook_caTools_version']), 'rJava', 'ggplot2']
gitlab_certfile = os.environ['conf_gitlab_certfile']
diff --git a/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py b/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py
index 8b52858..7367101 100644
--- a/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py
+++ b/infrastructure-provisioning/src/rstudio/scripts/configure_rstudio_node.py
@@ -56,7 +56,7 @@ local_spark_path = '/opt/spark/'
jars_dir = '/opt/jars/'
templates_dir = '/root/templates/'
files_dir = '/root/files/'
-r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2', 'evaluate', 'formatR', 'yaml',
+r_libs = ['R6', 'pbdZMQ', 'RCurl', 'reshape2', 'caTools={}'.format(os.environ['notebook_caTools_version']), 'rJava', 'ggplot2', 'evaluate', 'formatR', 'yaml',
'Rcpp', 'rmarkdown', 'base64enc', 'tibble', 'sparklyr']
gitlab_certfile = os.environ['conf_gitlab_certfile']
diff --git a/infrastructure-provisioning/src/tensor-rstudio/scripts/configure_tensor-rstudio_node.py b/infrastructure-provisioning/src/tensor-rstudio/scripts/configure_tensor-rstudio_node.py
index 98452dd..1b97f67 100644
--- a/infrastructure-provisioning/src/tensor-rstudio/scripts/configure_tensor-rstudio_node.py
+++ b/infrastructure-provisioning/src/tensor-rstudio/scripts/configure_tensor-rstudio_node.py
@@ -65,7 +65,7 @@ jars_dir = '/opt/jars/'
templates_dir = '/root/templates/'
files_dir = '/root/files/'
gitlab_certfile = os.environ['conf_gitlab_certfile']
-r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2', 'evaluate', 'formatR', 'yaml',
+r_libs = ['R6', 'pbdZMQ', 'RCurl', 'reshape2', 'caTools={}'.format(os.environ['notebook_caTools_version']), 'rJava', 'ggplot2', 'evaluate', 'formatR', 'yaml',
'Rcpp', 'rmarkdown', 'base64enc', 'tibble', 'tensorflow']
diff --git a/infrastructure-provisioning/src/zeppelin/scripts/configure_zeppelin_node.py b/infrastructure-provisioning/src/zeppelin/scripts/configure_zeppelin_node.py
index 3c3051a..cc4ecca 100644
--- a/infrastructure-provisioning/src/zeppelin/scripts/configure_zeppelin_node.py
+++ b/infrastructure-provisioning/src/zeppelin/scripts/configure_zeppelin_node.py
@@ -71,7 +71,7 @@ local_spark_path = '/opt/spark/'
templates_dir = '/root/templates/'
files_dir = '/root/files/'
jars_dir = '/opt/jars/'
-r_libs = ['R6', 'pbdZMQ', 'RCurl', 'devtools', 'reshape2', 'caTools', 'rJava', 'ggplot2']
+r_libs = ['R6', 'pbdZMQ', 'RCurl', 'reshape2', 'caTools={}'.format(os.environ['notebook_caTools_version']), 'rJava', 'ggplot2']
r_enabled = os.environ['notebook_r_enabled']
gitlab_certfile = os.environ['conf_gitlab_certfile']
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