ubuntu:16.04 Dockerfile -- check loadability

Author: mlin

.github/workflows/build.yml

@@ -16,6 +16,7 @@ jobs:
         fetch-depth: 0
     - name: deps
       run: |
+        sudo apt-get -qq update
         sudo apt-get install -y clang-format cppcheck python3-pip
         sudo pip3 install --system pre-commit $PIP_DEPS black flake8 pylint
     - name: pre-commit
@@ -45,6 +46,7 @@ jobs:
         fetch-depth: 0
     - name: deps
       run: |
+        sudo apt-get -qq update
         sudo apt-get install -y $APT_DEPS
         sudo pip3 install --system $PIP_DEPS
     - name: rust toolchain
@@ -65,6 +67,7 @@ jobs:
         fetch-depth: 0
     - name: build loaders
       run: |
+        sudo apt-get -qq update
         sudo apt-get install -y $APT_DEPS
         sudo pip3 install --system $PIP_DEPS
         cmake -DCMAKE_BUILD_TYPE=Release -B build . && cmake --build build -j $(nproc)

Dockerfile

@@ -2,10 +2,13 @@
 # This recipe works on 14.04 too, but there are C++ symbol differences before & after g++ 5.1:
 #   https://gcc.gnu.org/onlinedocs/gcc-5.2.0/libstdc++/manual/manual/using_dual_abi.html
 FROM ubuntu:16.04
+
 ARG CMAKE_VERSION=3.17.3
 ARG SQLITE_VERSION=3310000
 ARG ZSTD_VERSION=1.4.5
-ENV CFLAGS="-march=haswell -O3"
+ARG CPU_ARCH=haswell
+
+ENV CFLAGS="-march=${CPU_ARCH} -O3"
 ENV CXXFLAGS=${CFLAGS}
 
 # apt
@@ -20,7 +23,8 @@ RUN wget -nv https://www.sqlite.org/2020/sqlite-amalgamation-${SQLITE_VERSION}.z
         && unzip -o sqlite-amalgamation-${SQLITE_VERSION}.zip
 WORKDIR /work/sqlite-amalgamation-${SQLITE_VERSION}
 RUN gcc -shared -o libsqlite3.so.0 -fPIC -shared -Wl,-soname,libsqlite3.so.0 -g ${CFLAGS} sqlite3.c
-RUN cp libsqlite3.so.0 /usr/local/lib && cp *.h /usr/local/include
+RUN gcc -o sqlite3 -g ${CFLAGS} sqlite3.c shell.c -lpthread -ldl
+RUN cp libsqlite3.so.0 /usr/local/lib && cp *.h /usr/local/include && cp sqlite3 /usr/local/bin
 RUN ln -s /usr/local/lib/libsqlite3.so.0 /usr/local/lib/libsqlite3.so
 
 # Zstandard -- hacked with -fPIC for use with ZSTD_WHOLE_ARCHIVE
@@ -35,8 +39,11 @@ RUN wget -nv https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION
 RUN yes | sh cmake-${CMAKE_VERSION}-Linux-x86_64.sh
 RUN rsync -a cmake-${CMAKE_VERSION}-Linux-x86_64/ /usr/local/
 
+RUN ldconfig
+
 # libgenomicsqlite.so
 ADD . /work/GenomicSQLite
 WORKDIR /work/GenomicSQLite
 RUN rm -rf build && cmake -DCMAKE_BUILD_TYPE=Release -DZSTD_WHOLE_ARCHIVE=true -B build . && cmake --build build --target genomicsqlite -j $(nproc)
 RUN ldd -v -r build/libgenomicsqlite.so
+RUN sqlite3 -cmd '.load build/libgenomicsqlite.so' :memory: 'select genomicsqlite_version()'