From 70fe81985fa5de32d63aaa25e5edb910fc0e7624 Mon Sep 17 00:00:00 2001 From: Jonathan Curran Date: Mon, 4 May 2020 11:01:53 -0600 Subject: [PATCH 1/3] Including libopenblas fails to build --- builder/Dockerfile.ubuntu-2004 | 2 +- builder/package.ubuntu-2004 | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/builder/Dockerfile.ubuntu-2004 b/builder/Dockerfile.ubuntu-2004 index 8181332..c986484 100644 --- a/builder/Dockerfile.ubuntu-2004 +++ b/builder/Dockerfile.ubuntu-2004 @@ -6,7 +6,7 @@ RUN set -x \ && sed -i "s|# deb-src|deb-src|g" /etc/apt/sources.list \ && export DEBIAN_FRONTEND=noninteractive \ && apt-get update \ - && apt-get install -y libcurl4-openssl-dev libicu-dev libopenblas-base libpcre2-dev wget python3-pip ruby ruby-dev \ + && apt-get install -y libcurl4-openssl-dev libicu-dev libpcre2-dev wget python3-pip ruby ruby-dev \ && apt-get build-dep -y r-base RUN pip3 install awscli diff --git a/builder/package.ubuntu-2004 b/builder/package.ubuntu-2004 index 18a60f0..e5510ce 100644 --- a/builder/package.ubuntu-2004 +++ b/builder/package.ubuntu-2004 @@ -21,6 +21,7 @@ fpm \ -d gcc \ -d gfortran \ -d libbz2-1.0 \ + -d libblas3 \ -d libc6 \ -d libcairo2 \ -d libcurl4 \ @@ -29,7 +30,6 @@ fpm \ -d libicu66 \ -d libjpeg8 \ -d liblzma5 \ - -d libopenblas-dev \ -d libpango-1.0-0 \ -d libpangocairo-1.0-0 \ -d libpaper-utils \ @@ -51,4 +51,3 @@ fpm \ shopt -s extglob export PKG_FILE=$(ls /tmp/output/ubuntu-2004/[rR]-${R_VERSION}*.@(deb|rpm) | head -1) - From 034b3712d72cfef28cbfa924169130f2943d73cd Mon Sep 17 00:00:00 2001 From: Greg Lin Date: Mon, 4 May 2020 11:28:27 -0500 Subject: [PATCH 2/3] Add timeout to Batch jobs R builds can hang forever; for example, the Ubuntu 20.04 builds with OpenBLAS present. --- serverless-resources.yml | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/serverless-resources.yml b/serverless-resources.yml index dcca0fa..7137d83 100644 --- a/serverless-resources.yml +++ b/serverless-resources.yml @@ -143,6 +143,8 @@ rBuildsBatchJobDefinitionUbuntu1604: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:ubuntu-1604" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionUbuntu1804: Type: AWS::Batch::JobDefinition Properties: @@ -155,6 +157,8 @@ rBuildsBatchJobDefinitionUbuntu1804: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:ubuntu-1804" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionUbuntu2004: Type: AWS::Batch::JobDefinition Properties: @@ -167,6 +171,8 @@ rBuildsBatchJobDefinitionUbuntu2004: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:ubuntu-2004" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionDebian9: Type: AWS::Batch::JobDefinition Properties: @@ -179,6 +185,8 @@ rBuildsBatchJobDefinitionDebian9: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:debian-9" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionCentos6: Type: AWS::Batch::JobDefinition Properties: @@ -191,6 +199,8 @@ rBuildsBatchJobDefinitionCentos6: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:centos-6" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionCentos7: Type: AWS::Batch::JobDefinition Properties: @@ -203,6 +213,8 @@ rBuildsBatchJobDefinitionCentos7: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:centos-7" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionCentos8: Type: AWS::Batch::JobDefinition Properties: @@ -215,6 +227,8 @@ rBuildsBatchJobDefinitionCentos8: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:centos-8" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionOpensuse42: Type: AWS::Batch::JobDefinition Properties: @@ -227,6 +241,8 @@ rBuildsBatchJobDefinitionOpensuse42: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:opensuse-42" + Timeout: + AttemptDurationSeconds: 7200 rBuildsBatchJobDefinitionOpensuse15: Type: AWS::Batch::JobDefinition Properties: @@ -239,6 +255,8 @@ rBuildsBatchJobDefinitionOpensuse15: JobRoleArn: "Fn::GetAtt": [ rBuildsEcsTaskIamRole, Arn ] Image: "#{AWS::AccountId}.dkr.ecr.#{AWS::Region}.amazonaws.com/r-builds:opensuse-15" + Timeout: + AttemptDurationSeconds: 7200 # step function cloudwatch event trigger resources rBuildsEventRuleIamRole: From eb9eb9d056f91ec4b115c55163a542cf68f100f2 Mon Sep 17 00:00:00 2001 From: Jonathan Curran Date: Mon, 4 May 2020 13:54:10 -0600 Subject: [PATCH 3/3] Use dev dependencies --- builder/Dockerfile.ubuntu-2004 | 2 +- builder/package.ubuntu-2004 | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/builder/Dockerfile.ubuntu-2004 b/builder/Dockerfile.ubuntu-2004 index c986484..774222a 100644 --- a/builder/Dockerfile.ubuntu-2004 +++ b/builder/Dockerfile.ubuntu-2004 @@ -6,7 +6,7 @@ RUN set -x \ && sed -i "s|# deb-src|deb-src|g" /etc/apt/sources.list \ && export DEBIAN_FRONTEND=noninteractive \ && apt-get update \ - && apt-get install -y libcurl4-openssl-dev libicu-dev libpcre2-dev wget python3-pip ruby ruby-dev \ + && apt-get install -y libblas-dev libcurl4-openssl-dev libicu-dev liblapack-dev libpcre2-dev wget python3-pip ruby ruby-dev \ && apt-get build-dep -y r-base RUN pip3 install awscli diff --git a/builder/package.ubuntu-2004 b/builder/package.ubuntu-2004 index e5510ce..60f8f28 100644 --- a/builder/package.ubuntu-2004 +++ b/builder/package.ubuntu-2004 @@ -21,7 +21,7 @@ fpm \ -d gcc \ -d gfortran \ -d libbz2-1.0 \ - -d libblas3 \ + -d libblas-dev \ -d libc6 \ -d libcairo2 \ -d libcurl4 \ @@ -29,6 +29,7 @@ fpm \ -d libgomp1 \ -d libicu66 \ -d libjpeg8 \ + -d liblapack-dev \ -d liblzma5 \ -d libpango-1.0-0 \ -d libpangocairo-1.0-0 \