Merge pull request #311 from DEploid-dev/issue309

resolve #309

.travis.yml

@@ -39,6 +39,17 @@ script:
   - ./tests/test-against-previous-version.sh
   - ./tests/test_binaryReproducible.sh
   - if [ $TRAVIS_OS_NAME == linux ]; then cd docs/doxygen; doxygen Doxyfile; cd ../..; fi
-
+  - rm -r *
+  - wget --no-check-certificate https://github.com/DEploid-dev/DEploid/archive/issue309.tar.gz -o /dev/null
+  - tar -xf issue309.tar.gz
+  - cd DEploid-issue309
+  - ./bootstrap
+  - make; make check
+  - cd ..; rm -r *
+  - wget --no-check-certificate https://github.com/DEploid-dev/DEploid/archive/issue309.tar.gz -o /dev/null
+  - tar -xf issue309.tar.gz
+  - mv DEploid-issue309/* .
+  - ./bootstrap
+  - make; make check
 after_success:
   - coveralls --exclude lib --exclude tests --exclude src/random --exclude src/codeCogs/ --exclude src/export/ --exclude src/gzstream/ --gcov-options '\-lp'

bootstrap

@@ -2,9 +2,26 @@
 
 rm -r Makefile Makefile.in autom4te.cache config.* depcomp install-sh missing configure aclocal.m4 .deps INSTALL compile test-driver docs/doxygen/Makefile docs/doxygen/Makefile.in
 
+root_dir=$PWD
+if [ ! -d "${root_dir}/src" ]; then
+  "Error: please execute this script from DEploid root directory"
+  exit 1
+fi
+
+echo -n "Preparing ..."
+echo ""
+echo $root_dir/.git
+# First check if this is downloaded from zip or a git clone
+if [ -d ${root_dir}/.git ]; then
+	# use git submodule to down load files
+	git submodule update --init --recursive
+else
+	./checkfiles.sh
+fi # [-f ${root_dir}/.git]
+echo " done."
+
 
 aclocal
 autoconf
 automake -a
 ./configure
-

checkfiles.sh

@@ -0,0 +1,70 @@
+#!/bin/bash
+
+#if [ ! -z "$src_dir+x" ]; then
+src_dir=$PWD/src
+#fi
+
+if [ ! -f "${src_dir}/dEploid.cpp" ]; then
+ "Error: please execute \".checkfiles.sh\" from DEploid root directory"
+ exit 1
+fi
+
+
+OS=`uname -s`
+#echo "operating system is ${OS}"
+# VERSION=$(cat VERSION | tr -d '\n')
+VERSION=0.1-release
+echo -n "." # echo "ok not git clone, now check plot and figure"
+
+#rm master.tar.gz  # just making sure download the one we actually want to
+
+extract_submodule_from(){
+ account=$1
+ submodule=$2
+ placeto=$3
+ echo "Extract submodule $submodule from account $account, place at $3"
+ if [ ! -d ${submodule}_dir ]; then mkdir ${submodule}_dir; fi
+ echo -n "." # echo "ok, do something" #
+
+ if [[ "${OS}" == "Linux" ]]; then
+   wget --no-check-certificate https://github.com/${account}/${submodule}/archive/v${VERSION}.tar.gz -o /dev/null
+ elif [[ "${OS}" == "Darwin"* ]]; then
+   curl -LOk https://github.com/${account}/${submodule}/archive/v${VERSION}.tar.gz
+ else
+   echo "Unknown OS, fail to download package from https://github.com/${account}/${submodule}/archive/v${VERSION}.tar.gz"
+   echo "Please contact Joe at [email protected] if assistance is needed"
+   exit 1
+ fi
+ls *gz
+
+ if [ ! -f v${VERSION}.tar.gz ]; then
+   echo "Error: Download package from https://github.com/${account}/${submodule}/archive/v${VERSION}.tar.gz failed"
+   echo "Please contact Joe at [email protected] if assistance is needed"
+   exit 1
+ fi
+ tar -xf v${VERSION}.tar.gz -C ${submodule}_dir
+ if [ ! -d ${placeto} ]; then mkdir ${placeto}; fi
+ cp -r ${submodule}_dir/${submodule}-${VERSION}/* ${placeto}/
+ rm -r ${submodule}_dir v${VERSION}.tar.gz
+}
+
+
+ACCOUNT=DEploid-dev
+SUBMODLUE=DEploid-Utilities
+PLACETO=utilities
+tmp_dir=$PWD/utilities
+if [ -f ${tmp_dir}/DEploidR.R  -a -f ${tmp_dir}/dEploidTools.r ];then
+ echo -n "." # echo "ok, do nothing"
+else
+ extract_submodule_from $ACCOUNT $SUBMODLUE $PLACETO
+fi
+
+ACCOUNT=shajoezhu
+SUBMODLUE=DEploid-Lasso-lib
+PLACETO=$PWD/src/lasso
+tmp_dir=$PWD/src/lasso
+if [ -f ${tmp_dir}/main.cpp  -a -f ${tmp_dir}/README.md ];then
+ echo -n "." # echo "ok, do nothing"
+else
+ extract_submodule_from $ACCOUNT $SUBMODLUE $PLACETO
+fi