Merge branch 'master' into fix-503

ucbds-infra · Sep 20, 2022 · 8dc860f · 8dc860f
2 parents 3868de0 + 471d8a2
commit 8dc860f
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Showing 16 changed files with 42 additions and 20 deletions.
diff --git a/.gitignore b/.gitignore
@@ -22,3 +22,4 @@ docs/_static/notebooks/html
 arm-Dockerfile
 htmlcov/
 .pytest_cache/
+/sync.sh
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 * Close temporary file handle before removal when checking tests in `otter.Notebook.export`
 * Fixed bug caused by unspecified encoding in Windows JSON loads per [#524](https://github.com/ucbds-infra/otter-grader/issues/524)
+* Updated autograder zip `setup.sh` file and `r-base` version per [#514](https://github.com/ucbds-infra/otter-grader/issues/514)
 * Fix point value filtering for student tests in Otter Assign per [#503](https://github.com/ucbds-infra/otter-grader/issues/503)
 
 **v4.0.1:**

diff --git a/environment.yml b/environment.yml
@@ -4,7 +4,7 @@ channels:
     - defaults
 dependencies:
     - python>=3.6
-    - r-base
+    - r-base>=4.0.0
     - r-essentials
     - r-devtools
     - pip

diff --git a/otter/generate/templates/python/setup.sh b/otter/generate/templates/python/setup.sh
@@ -3,9 +3,11 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/otter/generate/templates/r/environment.yml b/otter/generate/templates/r/environment.yml
@@ -6,8 +6,8 @@ dependencies:
     - python=3.7
     - pip
     - nb_conda_kernels
-    - r-base 
-    - r-essentials 
+    - r-base>=4.0.0
+    - r-essentials
     - r-devtools
     - libgit2
     - libgomp

diff --git a/otter/generate/templates/r/setup.sh b/otter/generate/templates/r/setup.sh
@@ -3,10 +3,12 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
-    apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test-assign/example-autograder-correct/setup.sh b/test/test-assign/example-autograder-correct/setup.sh
@@ -3,9 +3,11 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test-assign/gs-autograder-correct/setup.sh b/test/test-assign/gs-autograder-correct/setup.sh
@@ -3,9 +3,11 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test-assign/rmd-autograder-correct/environment.yml b/test/test-assign/rmd-autograder-correct/environment.yml
@@ -6,8 +6,8 @@ dependencies:
     - python=3.7
     - pip
     - nb_conda_kernels
-    - r-base 
-    - r-essentials 
+    - r-base>=4.0.0
+    - r-essentials
     - r-devtools
     - libgit2
     - libgomp

diff --git a/test/test-assign/rmd-autograder-correct/setup.sh b/test/test-assign/rmd-autograder-correct/setup.sh
@@ -3,10 +3,12 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
-    apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test-run/autograder/source/setup.sh b/test/test-run/autograder/source/setup.sh
@@ -7,9 +7,11 @@
 apt-get clean
 apt-get update
 apt-get install -y pandoc
-apt-get install -y texlive-xetex texlive-fonts-recommended texlive-generic-recommended
+apt-get install -y texlive-xetex texlive-fonts-recommended texlive-plain-generic
 
 # install wkhtmltopdf
+wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+apt-get install -y /tmp/libssl1.1.deb
 wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
 apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test_generate/test-autograder/autograder-correct/setup.sh b/test/test_generate/test-autograder/autograder-correct/setup.sh
@@ -3,9 +3,11 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test_generate/test-autograder/autograder-custom-env/setup.sh b/test/test_generate/test-autograder/autograder-custom-env/setup.sh
@@ -3,9 +3,11 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test_generate/test-autograder/autograder-r-correct/environment.yml b/test/test_generate/test-autograder/autograder-r-correct/environment.yml
@@ -6,8 +6,8 @@ dependencies:
     - python=3.7
     - pip
     - nb_conda_kernels
-    - r-base 
-    - r-essentials 
+    - r-base>=4.0.0
+    - r-essentials
     - r-devtools
     - libgit2
     - libgomp

diff --git a/test/test_generate/test-autograder/autograder-r-correct/setup.sh b/test/test_generate/test-autograder/autograder-r-correct/setup.sh
@@ -3,10 +3,12 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
-    apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y libnlopt-dev cmake libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev apt-utils libpoppler-cpp-dev libavfilter-dev  libharfbuzz-dev libfribidi-dev imagemagick libmagick++-dev pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese libxft-dev
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb
 

diff --git a/test/test_generate/test-autograder/autograder-token-correct/setup.sh b/test/test_generate/test-autograder/autograder-token-correct/setup.sh
@@ -3,9 +3,11 @@
 if [ "${BASE_IMAGE}" != "ucbdsinfra/otter-grader" ]; then
     apt-get clean
     apt-get update
-    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-generic-recommended build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
+    apt-get install -y pandoc texlive-xetex texlive-fonts-recommended texlive-plain-generic build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev texlive-lang-chinese
 
     # install wkhtmltopdf
+    wget --quiet -O /tmp/libssl1.1.deb http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.1_1.1.1-1ubuntu2.1~18.04.20_amd64.deb
+    apt-get install -y /tmp/libssl1.1.deb
     wget --quiet -O /tmp/wkhtmltopdf.deb https://github.com/wkhtmltopdf/packaging/releases/download/0.12.6-1/wkhtmltox_0.12.6-1.bionic_amd64.deb
     apt-get install -y /tmp/wkhtmltopdf.deb