This is an automated email from the ASF dual-hosted git repository. lfrolov pushed a commit to branch DATALAB-2448 in repository https://gitbox.apache.org/repos/asf/incubator-datalab.git
commit 5fceef5aafbe0775e51589c4b2818c8f9e1e28dd Author: leonidfrolov <[email protected]> AuthorDate: Fri Jul 2 12:39:46 2021 +0300 [DATALAB-2448]: fixed R devtools installation issues for dataproc --- infrastructure-provisioning/src/general/lib/os/fab.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/infrastructure-provisioning/src/general/lib/os/fab.py b/infrastructure-provisioning/src/general/lib/os/fab.py index 9829cc4..5682832 100644 --- a/infrastructure-provisioning/src/general/lib/os/fab.py +++ b/infrastructure-provisioning/src/general/lib/os/fab.py @@ -536,10 +536,11 @@ def install_r_pkg(requisites): if os.environ['conf_resource'] in ('dataengine-service'): if os.environ['conf_cloud_provider'] in ('aws'): manage_pkg('-y install', 'remote', 'libcurl libcurl-devel') - elif os.environ['conf_cloud_provider'] in ('gcp'): - # manage_pkg('-y build-dep', 'remote', 'libcurl4-gnutls-dev libxml2-dev') - manage_pkg('-y install', 'remote', 'libxml2-dev libcurl4-openssl-dev') - conn.sudo('R -e "install.packages(\'devtools\', repos = \'cloud.r-project.org\')"') + elif (os.environ['conf_cloud_provider'] in 'gcp') and ('-w-' in conn.sudo('hostname').stdout.replace('\n', '')): + #manage_pkg('-y build-dep', 'remote', 'libcurl4-gnutls-dev libxml2-dev') + manage_pkg('-y install', 'remote', 'libxml2-dev libcurl4-openssl-dev pkg-config') + conn.sudo('R -e ".libPaths(\'/usr/lib/R/site-library\')"') + conn.sudo('R -e "install.packages(\'devtools\', repos = \'cloud.r-project.org\'"') for r_pkg in requisites: name, vers = r_pkg version = vers @@ -552,7 +553,9 @@ def install_r_pkg(requisites): 'dependencies = NA)\' 2>&1 | tee /tmp/install_{0}.tmp; if ! grep -w -E "({2})" /tmp/install_{0}.tmp ' '> /tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(name, vers, error_parser)) else: - conn.sudo('R -e \'devtools::install_version("{0}", version = {1}, repos = "https://cloud.r-project.org";, dependencies = NA)\' 2>&1 | tee /tmp/install_{0}.tmp; if ! grep -w -E "({2})" /tmp/install_{0}.tmp > /tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(name, vers, error_parser)) + conn.sudo('R -e \'devtools::install_version("{0}", version = {1}, repos = "https://cloud.r-project.org";, ' + 'dependencies = NA)\' 2>&1 | tee /tmp/install_{0}.tmp; if ! grep -w -E "({2})" /tmp/install_{0}.tmp > ' + '/tmp/install_{0}.log; then echo "" > /tmp/install_{0}.log;fi'.format(name, vers, error_parser)) dep = conn.sudo('grep "(NA.*->". /tmp/install_' + name + '.tmp | awk \'{print $1}\'').stdout.replace('\n', ' ') dep_ver = conn.sudo('grep "(NA.*->". /tmp/install_' + name + '.tmp | awk \'{print $4}\'').stdout.replace('\n', ' ').replace(')', '').split(' ') if dep == '': @@ -565,6 +568,7 @@ def install_r_pkg(requisites): else: dep[n] = '{} v.{}'.format(dep[n], dep_ver[n]) dep = [i for i in dep if i] + conn.sudo('hostname') err = conn.sudo('cat /tmp/install_{0}.log'.format(name)).stdout.replace('"', "'").replace('\n', '') conn.sudo('R -e \'installed.packages()[,c(3:4)]\' | if ! grep -w {0} > /tmp/install_{0}.list; then echo "" > /tmp/install_{0}.list;fi'.format(name)) res = conn.sudo('cat /tmp/install_{0}.list'.format(name)).stdout.replace('\n', '') --------------------------------------------------------------------- To unsubscribe, e-mail: [email protected] For additional commands, e-mail: [email protected]
