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RBigData · Aug 4, 2018 · 5ee86a4 · 5ee86a4
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commit 5ee86a4
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diff --git a/ChangeLog b/ChangeLog
@@ -1,6 +1,9 @@
+2018-08-03: Ver. 0.3-8
+  * Fedora28 use "module load mpi/openmpi-x86_64" to obtain mpiexec.
+
 2018-07-29: Ver. 0.3-7
   * Add "pkg-config" to "configure.ac".
-  * Check "OpenMPI" and "MPICH2" with "pkg-config"
+  * Check "OpenMPI" and "MPICH2" with "pkg-config".
 
 2018-05-18: Ver. 0.3-6
   * Move "rlecuyer" to Imports.

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pbdMPI
-Version: 0.3-7
-Date: 2018-07-29
+Version: 0.3-8
+Date: 2018-08-03
 Title: Programming with Big Data -- Interface to MPI
 Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
         "[email protected]"),
@@ -33,3 +33,14 @@ MailingList: Please send questions and comments regarding pbdR to
         [email protected]
 NeedsCompilation: yes
 Maintainer: Wei-Chen Chen <[email protected]>
+Packaged: 2018-07-30 01:19:36 UTC; snoweye
+Author: Wei-Chen Chen [aut, cre],
+  George Ostrouchov [aut],
+  Drew Schmidt [aut],
+  Pragneshkumar Patel [aut],
+  Hao Yu [aut],
+  Christian Heckendorf [ctb] (FreeBSD),
+  Brian Ripley [ctb] (Windows HPC Pack 2012),
+  R Core team [ctb] (some functions are modified from the base packages)
+Repository: CRAN
+Date/Publication: 2018-08-01 15:20:14 UTC
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # pbdMPI
 
+* **Version:** 0.3-4
 * **License:** [![License](http://img.shields.io/badge/license-MPL%202-orange.svg?style=flat)](https://www.mozilla.org/MPL/2.0/)
 * **Download:** [![Download](http://cranlogs.r-pkg.org/badges/pbdMPI)](https://cran.r-project.org/package=pbdMPI)
 * **Status:** [![Build Status](https://travis-ci.org/snoweye/pbdMPI.png)](https://travis-ci.org/snoweye/pbdMPI) [![Appveyor Build status](https://ci.appveyor.com/api/projects/status/32r7s2skrgm9ubva?svg=true)](https://ci.appveyor.com/project/snoweye/pbdMPI)

diff --git a/configure b/configure
@@ -673,7 +673,6 @@ infodir
 docdir
 oldincludedir
 includedir
-runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -751,7 +750,6 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
-runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE}'
@@ -1004,15 +1002,6 @@ do
   | -silent | --silent | --silen | --sile | --sil)
     silent=yes ;;
 
-  -runstatedir | --runstatedir | --runstatedi | --runstated \
-  | --runstate | --runstat | --runsta | --runst | --runs \
-  | --run | --ru | --r)
-    ac_prev=runstatedir ;;
-  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
-  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
-  | --run=* | --ru=* | --r=*)
-    runstatedir=$ac_optarg ;;
-
   -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
     ac_prev=sbindir ;;
   -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1150,7 +1139,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir runstatedir
+		libdir localedir mandir
 do
   eval ac_val=\$$ac_var
   # Remove trailing slashes.
@@ -1303,7 +1292,6 @@ Fine tuning of the installation directories:
   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
-  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
   --libdir=DIR            object code libraries [EPREFIX/lib]
   --includedir=DIR        C header files [PREFIX/include]
   --oldincludedir=DIR     C header files for non-gcc [/usr/include]
@@ -2377,53 +2365,17 @@ if test -z "${MPI_INCLUDE_PATH}" ; then
     TMP_INC="F"
     TMP_LIB="F"
 
-    if test -n "${PKG_CONFIG}" ; then
-      echo "found pkg-config ..."
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking if pkg-config knows about OpenMPI" >&5
-$as_echo_n "checking if pkg-config knows about OpenMPI... " >&6; }
-
-      if "${PKG_CONFIG}" --exists ompi; then
-        { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-
-        TMP_INC_DIRS=`"${PKG_CONFIG}" --cflags ompi`
-        echo ">> TMP_INC_DIRS = ${TMP_INC_DIRS}"
-
-        TMP_LIB_DIRS=`"${PKG_CONFIG}" --libs ompi`
-        echo ">> TMP_LIB_DIRS = ${TMP_LIB_DIRS}"
-
-        if test "${TMP_INC_DIRS}" != "" -a "${TMP_LIB_DIRS}" != "" ; then
-          TMP_INC=${TMP_INC_DIRS}
-          TMP_LIB=${TMP_LIB_DIRS}
-        fi
-
-        if test "${TMP_INC}" != "F" -a "${TMP_LIB}" != "F" ; then
-          echo "found mpi.h and libmpi.so ..."
-          echo ">> TMP_INC = ${TMP_INC}"
-          echo ">> TMP_LIB = ${TMP_LIB}"
-          MPITYPE="OPENMPI"
-          MPI_INCLUDE_PATH="${TMP_INC}"
-          MPI_LIBPATH="${TMP_LIB}"
-          MPI_LIBNAME=""
-          MPI_ROOT="NONEED"
-        fi
-      else
-        { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-      fi
-    fi
-
-    if test "$SED" != "F" -a "$MPICC" != "F" -a "$OMPI_INFO" != "F" -a "$TMP_INC" = "F" -a "$TMP_LIB" = "F" ; then
-      echo "found sed, mpicc, and ompi_info ..."
+    if test "$SED" != "F" -a "$MPICC" != "F" -a "$OMPI_INFO" != "F" ; then
+      echo "Try sed, mpicc, and ompi_info ..."
 
       TMP_INC_DIRS=`mpicc --showme:incdirs`
       echo ">> TMP_INC_DIRS = ${TMP_INC_DIRS}"
 
       TMP_IFS="${IFS}"; IFS=" "
       for dir in ${TMP_INC_DIRS}; do
-        echo "checking ${dir} ..."
+        echo "Checking ${dir} ..."
         if test -f "${dir}/mpi.h" ; then
-          echo "found ${dir}/mpi.h ..."
+          echo "Found ${dir}/mpi.h ..."
           TMP_INC=${dir}
           break
         fi
@@ -2435,15 +2387,15 @@ $as_echo "no" >&6; }
 
       TMP_IFS="${IFS}"; IFS=" "
       for dir in ${TMP_LIB_DIRS}; do
-        echo "checking ${dir} ..."
+        echo "Checking ${dir} ..."
         if test -f "${dir}/libmpi.so" ; then
-          echo "found ${dir}/libmpi.so ..."
+          echo "Found ${dir}/libmpi.so ..."
           TMP_LIB=${dir}
           TMP_LIBNAME="libmpi.so"
           break
         fi
                 if test -f "${dir}/libmpi.dylib" ; then
-          echo "found ${dir}/libmpi.dylib ..."
+          echo "Found ${dir}/libmpi.dylib ..."
           TMP_LIB=${dir}
           TMP_LIBNAME="libmpi.dylib"
           break
@@ -2452,15 +2404,58 @@ $as_echo "no" >&6; }
       IFS="${TMP_IFS}"
 
       if test "${TMP_INC}" != "F" -a "${TMP_LIB}" != "F" ; then
-        echo "found mpi.h and libmpi.so ..."
+        echo "Found mpi.h and libmpi.so ... via mpicc --showme"
         echo ">> TMP_INC = ${TMP_INC}"
         echo ">> TMP_LIB = ${TMP_LIB}"
         MPITYPE="OPENMPI"
         MPI_INCLUDE_PATH="${TMP_INC}"
         MPI_LIBPATH="${TMP_LIB}"
         MPI_LIBNAME="${TMP_LIBNAME}"
+      else
+        echo "Found no mpi.h or libmpi.so ... via mpicc --showme"
       fi
     fi
+
+    if test "$TMP_INC" = "F" -o "$TMP_LIB" = "F" ; then
+            if test -n "${PKG_CONFIG}" ; then
+        echo "Try pkg-config ..."
+        { $as_echo "$as_me:${as_lineno-$LINENO}: checking if pkg-config knows about OpenMPI" >&5
+$as_echo_n "checking if pkg-config knows about OpenMPI... " >&6; }
+
+        if "${PKG_CONFIG}" --exists ompi; then
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+
+          TMP_INC_DIRS=`"${PKG_CONFIG}" --cflags ompi`
+          echo ">> TMP_INC_DIRS = ${TMP_INC_DIRS}"
+
+          TMP_LIB_DIRS=`"${PKG_CONFIG}" --libs ompi`
+          echo ">> TMP_LIB_DIRS = ${TMP_LIB_DIRS}"
+
+          if test "${TMP_INC_DIRS}" != "" -a "${TMP_LIB_DIRS}" != "" ; then
+            TMP_INC=${TMP_INC_DIRS}
+            TMP_LIB=${TMP_LIB_DIRS}
+          fi
+
+          if test "${TMP_INC}" != "F" -a "${TMP_LIB}" != "F" ; then
+            echo "Found mpi.h and libmpi.so ... via pkg-config"
+            echo ">> TMP_INC = ${TMP_INC}"
+            echo ">> TMP_LIB = ${TMP_LIB}"
+            MPITYPE="OPENMPI"
+            MPI_INCLUDE_PATH="${TMP_INC}"
+            MPI_LIBPATH="${TMP_LIB}"
+            MPI_LIBNAME=""
+            MPI_ROOT="NONEED"
+          else
+            echo "Found no mpi.h or libmpi.so ... via pkg-config"
+          fi
+        else
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+        fi
+      fi
+    fi
+
   fi
 fi
 
@@ -2471,47 +2466,8 @@ if test -z "${MPI_INCLUDE_PATH}" ; then
     TMP_INC="F"
     TMP_LIB="F"
 
-    if test -n "${PKG_CONFIG}" ; then
-      echo "found pkg-config ..."
-      { $as_echo "$as_me:${as_lineno-$LINENO}: checking if pkg-config knows about MPICH" >&5
-$as_echo_n "checking if pkg-config knows about MPICH... " >&6; }
-
-            if "${PKG_CONFIG}" --exists mpich; then
-        { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-
-        TMP_INC_DIRS=`"${PKG_CONFIG}" --cflags mpich`
-        echo ">> TMP_INC_DIRS = ${TMP_INC_DIRS}"
-
-        TMP_LIB_DIRS=`"${PKG_CONFIG}" --libs mpich`
-        echo ">> TMP_LIB_DIRS = ${TMP_LIB_DIRS}"
-
-        TMP_LIB_PATH=`"${PKG_CONFIG}" --variable=libdir mpich`
-        echo ">> TMP_LIB_PATH = ${TMP_LIB_PATH}"
-
-        if test "$TMP_INC_DIRS" != "" -a "$TMP_LIB_DIRS" != "" ; then
-          TMP_INC=${TMP_INC_DIRS}
-          TMP_LIB="-L${TMP_LIB_PATH} ${TMP_LIB_DIRS}"
-        fi
-
-        if test "$TMP_INC" != "" -a "$TMP_LIB" != "" ; then
-          echo "found mpi.h and libmpich.so ..."
-          echo ">> TMP_INC = ${TMP_INC}"
-          echo ">> TMP_LIB = ${TMP_LIB}"
-          MPITYPE="MPICH2"
-          MPI_INCLUDE_PATH="${TMP_INC}"
-          MPI_LIBPATH="${TMP_LIB}"
-          MPI_LIBNAME=""
-          MPI_ROOT="NONEED"
-        fi
-      else
-        { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-      fi
-    fi
-
-    if test "$SED" != "F" -a "$MPICC" != "F" -a "$TMP_INC" = "F" -a "$TMP_LIB" = "F" ; then
-      echo "found sed and mpicc ..."
+    if test "$SED" != "F" -a "$MPICC" != "F" ; then
+      echo "Try sed and mpicc ..."
 
       TMP_CMD=`mpicc -show`
       echo ">> TMP_CMD = ${TMP_CMD}"
@@ -2524,9 +2480,9 @@ $as_echo "no" >&6; }
           dir_inc=`echo ${dir} | sed -e "s/-I\(.*\)/\1/"`
         fi
 
-        echo "checking ${dir_inc} ..."
+        echo "Checking ${dir_inc} ..."
         if test -f "${dir_inc}/mpi.h" ; then
-          echo "found ${dir_inc}/mpi.h ..."
+          echo "Found ${dir_inc}/mpi.h ..."
           TMP_INC=${dir_inc}
           break
         fi
@@ -2541,15 +2497,15 @@ $as_echo "no" >&6; }
           dir_lib=`echo ${dir} | sed -e "s/-L\(.*\)/\1/"`
         fi
 
-        echo "checking ${dir_lib} ..."
+        echo "Checking ${dir_lib} ..."
         if test -f "${dir_lib}/libmpich.so" ; then
-          echo "found ${dir_lib}/libmpich.so ..."
+          echo "Found ${dir_lib}/libmpich.so ... via mpicc --show & sed"
           TMP_LIB=${dir_lib}
           TMP_LIBNAME="libmpich.so"
           break
         fi
                 if test -f "${dir_lib}/libmpich.dylib" ; then
-          echo "found ${dir_lib}/libmpich.dylib ..."
+          echo "Found ${dir_lib}/libmpich.dylib ... via mpicc --show & sed"
           TMP_LIB=${dir_lib}
           TMP_LIBNAME="libmpich.dylib"
           break
@@ -2558,15 +2514,61 @@ $as_echo "no" >&6; }
       IFS="${TMP_IFS}"
 
       if test "${TMP_INC}" != "F" -a "${TMP_LIB}" != "F" ; then
-        echo "found mpi.h and libmpich.so ..."
+        echo "Found mpi.h and libmpich.so ... via mpicc --show & sed"
         echo ">> TMP_INC = ${TMP_INC}"
         echo ">> TMP_LIB = ${TMP_LIB}"
         MPITYPE="${MPITYPE}"
         MPI_INCLUDE_PATH="${TMP_INC}"
         MPI_LIBPATH="${TMP_LIB}"
         MPI_LIBNAME="${TMP_LIBNAME}"
+      else
+        echo "Found no mpi.h or libmpi.so ... via mpicc --show & sed"
       fi
     fi
+
+    if test "$TMP_INC" = "F" -o "$TMP_LIB" = "F" ; then
+            if test -n "${PKG_CONFIG}" ; then
+        echo "Try pkg-config ..."
+        { $as_echo "$as_me:${as_lineno-$LINENO}: checking if pkg-config knows about MPICH" >&5
+$as_echo_n "checking if pkg-config knows about MPICH... " >&6; }
+
+                if "${PKG_CONFIG}" --exists mpich; then
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+
+          TMP_INC_DIRS=`"${PKG_CONFIG}" --cflags mpich`
+          echo ">> TMP_INC_DIRS = ${TMP_INC_DIRS}"
+
+          TMP_LIB_DIRS=`"${PKG_CONFIG}" --libs mpich`
+          echo ">> TMP_LIB_DIRS = ${TMP_LIB_DIRS}"
+
+          TMP_LIB_PATH=`"${PKG_CONFIG}" --variable=libdir mpich`
+          echo ">> TMP_LIB_PATH = ${TMP_LIB_PATH}"
+
+          if test "$TMP_INC_DIRS" != "" -a "$TMP_LIB_DIRS" != "" ; then
+            TMP_INC=${TMP_INC_DIRS}
+            TMP_LIB="-L${TMP_LIB_PATH} ${TMP_LIB_DIRS}"
+          fi
+
+          if test "$TMP_INC" != "" -a "$TMP_LIB" != "" ; then
+            echo "Found mpi.h and libmpich.so ... via pkg-config"
+            echo ">> TMP_INC = ${TMP_INC}"
+            echo ">> TMP_LIB = ${TMP_LIB}"
+            MPITYPE="MPICH2"
+            MPI_INCLUDE_PATH="${TMP_INC}"
+            MPI_LIBPATH="${TMP_LIB}"
+            MPI_LIBNAME=""
+            MPI_ROOT="NONEED"
+          else
+            echo "Found no mpi.h or libmpi.so ... via pkg-config"
+          fi
+        else
+          { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+        fi
+      fi
+    fi
+
   fi
 fi