diff --git a/ci-scripts/install-gsl.sh b/ci-scripts/install-gsl.sh
index 288b5bc..ddb78b9 100755
--- a/ci-scripts/install-gsl.sh
+++ b/ci-scripts/install-gsl.sh
@@ -9,7 +9,10 @@ fi
 PREFIX=$1
 
 set -ex
-INITDIR=`pwd`
+INITDIR=$(pwd -P)
+cd ${PREFIX}
+PREFIX=$(pwd -P)
+cd ${INITDIR}
 cd local/build
 wget http://ftpmirror.gnu.org/gsl/${NAME}.tar.gz
 tar -xzvf ${NAME}.tar.gz
diff --git a/ci-scripts/install-hdf5.sh b/ci-scripts/install-hdf5.sh
index 98867dd..45c0954 100755
--- a/ci-scripts/install-hdf5.sh
+++ b/ci-scripts/install-hdf5.sh
@@ -9,8 +9,10 @@ fi
 PREFIX=$1
 
 set -ex
-INITDIR=`pwd`
-cd local/build
+INITDIR=$(pwd -P)
+cd ${PREFIX}
+PREFIX=$(pwd -P)
+cd ${INITDIR}/local/build
 wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${NAME}/src/${NAME}.tar.gz
 tar -xzvf ${NAME}.tar.gz
 mkdir ${NAME}/build
diff --git a/ci-scripts/install-minuit.sh b/ci-scripts/install-minuit.sh
index eeafbda..7770168 100755
--- a/ci-scripts/install-minuit.sh
+++ b/ci-scripts/install-minuit.sh
@@ -9,8 +9,10 @@ fi
 PREFIX=$1
 
 set -ex
-INITDIR=`pwd`
-cd local/build
+INITDIR=$(pwd -P)
+cd ${PREFIX}
+PREFIX=$(pwd -P)
+cd ${INITDIR}/local/build
 wget http://www.cern.ch/mathlibs/sw/5_34_14/Minuit2/${NAME}.tar.gz
 tar -xzvf ${NAME}.tar.gz
 mkdir -p ${NAME}/build
diff --git a/ci-scripts/install-nlopt.sh b/ci-scripts/install-nlopt.sh
index 4afbeef..6f26426 100755
--- a/ci-scripts/install-nlopt.sh
+++ b/ci-scripts/install-nlopt.sh
@@ -9,17 +9,19 @@ fi
 PREFIX=$1
 
 set -ex
-INITDIR=`pwd`
-cd local/build
+INITDIR=$(pwd -P)
+cd ${PREFIX}
+PREFIX=$(pwd -P)
+cd ${INITDIR}/local/build
 wget https://github.com/stevengj/nlopt/archive/v${NAME}.tar.gz
 tar -xzvf v${NAME}.tar.gz
 NAME=nlopt-${NAME}
 mkdir -p ${NAME}/build
 cd ${NAME}/build
-cmake -DCMAKE_C_COMPILER=${CC} -DCMAKE_CXX_COMPILER=${CXX} -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+cmake -DCMAKE_C_COMPILER="${CC}" -DCMAKE_CXX_COMPILER="${CXX}" -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
 make -j4 
 make install
-cmake -DCMAKE_C_COMPILER=${CC} -DCMAKE_CXX_COMPILER=${CXX} -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
+cmake -DCMAKE_C_COMPILER="${CC}" -DCMAKE_CXX_COMPILER="${CXX}" -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} ..
 make -j4 
 make install
 cd ${INITDIR}/local
diff --git a/update_eigen.sh b/update_eigen.sh
index b140560..4ad7773 100755
--- a/update_eigen.sh
+++ b/update_eigen.sh
@@ -6,7 +6,7 @@ if (( $# != 1 )); then
 fi
 ARC=$1
 
-INITDIR=`pwd`
+INITDIR=$(pwd -P)
 rm -rf lib/Eigen
 ARCDIR=`tar -tf ${ARC} | head -n1 | sed -e 's@/.*@@'`
 tar -xf ${ARC}