version 0.1-9

ChangeLog

@@ -1,6 +1,10 @@
+2020-02-26
+    * By default the new fedora only knows the command python3 but not python,
+      changed the configure script to cover this change in fedora.
+
 2018-07-27
 
-	* activated debug printing of Makevars again
+    * activated debug printing of Makevars again
 
 2018-01-16
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PythonInR
 Title: Use 'Python' from Within 'R'
-Version: 0.1-7
+Version: 0.1-9
 Authors@R: c( person("Florian", "Schwendinger", role = c("aut", "cre"), 
                      email = "FlorianSchwendinger@gmx.at"),
               person("Kimyen", "Truong", role = "ctb") )
@@ -15,10 +15,10 @@ URL: https://bitbucket.org/Floooo/pythoninr/
 BugReports: https://bitbucket.org/Floooo/pythoninr/issues
 License: GPL-3
 NeedsCompilation: yes
-RoxygenNote: 6.0.0
-Packaged: 2019-04-22 12:53:26 UTC; florian
+RoxygenNote: 6.1.1
+Packaged: 2020-03-09 18:53:39 UTC; florian
 Author: Florian Schwendinger [aut, cre],
   Kimyen Truong [ctb]
 Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
 Repository: CRAN
-Date/Publication: 2019-04-23 07:10:03 UTC
+Date/Publication: 2020-03-10 06:50:21 UTC

MD5

@@ -1,8 +1,8 @@
-541395f2d3aea6393956bb23bcad5fb3 *ChangeLog
-16c639b795b3c162fa60016c938e6a97 *DESCRIPTION
+0c9df7953c463761b277567bb139853f *ChangeLog
+f120060a5c39e26e24969f5b8393f847 *DESCRIPTION
 fdf8803f84f1d032720c76c1dabdba0e *NAMESPACE
 8f23ca90a540abd478e8eae1d9f7ca1a *R/AutodetectPython.R
-82ef4cf949d70774f311c906df0896be *R/Basics.R
+37aab45a28757b4fd42d86ca69f2a817 *R/Basics.R
 2cb549a7b1bbeafde04d7a5329bf2a65 *R/PyAttach.R
 6bb89d261699323e50d521d81dbca6ac *R/PyCall.R
 74b5c060c224d2b9a4b7b9c8e5f80f06 *R/PyClasses.R
@@ -15,14 +15,14 @@ d9eab43f33e8f35cf562b98b8d392ea4 *R/PyObjectDict.R
 bb2be964ec8bdea823542bf7a7faab95 *R/PyObjectTuple.R
 4f06f22e66785fd8dc9d8b10fb930e0e *R/PyOptions.R
 a5e7059dbff4935aa2087bd8bc3ab523 *R/PySet.R
-8129b32851b15ca444f1a2cbd78a3e6f *R/PySource.R
+2c814c4f07f1f8a05f1ea5b2bc28845e *R/PySource.R
 2cf4d7429fcbb99d87ac5b79ec2e7b00 *R/PythonInR.R
 033dfb5f35fbbf6f109d228a0b53186d *R/TransformReturnValues.R
 e9b54a51e96a787b28ad51f94e03c898 *R/Utility.R
 b8313baf3d27ccdb477556c07b37f2b1 *R/zzz.R
 873763a1e1dc563e392f21866860a148 *README.md
 75a78cb0c1fa53ba6696b487f37ef4c2 *cleanup
-0693eaeda7d05f9cc04b54faa26d7725 *configure
+2279dda51f0fa53ccd2b57dc0370100e *configure
 70031f25497e1421e156bd2d5316fc9e *inst/testing/Basics.R
 aa867dd99ecb0cddd42f1af8d31e592c *inst/testing/NA_NaN_Inf.R
 a4f40b6366bc25896b02d8c2a13fff19 *inst/testing/PyAttach.R
@@ -37,7 +37,7 @@ d1c2230280e49bc7d07ad6cad531f32c *inst/testing/PyOptions.R
 be7608bcd269973c9aebd61531f7a63e *inst/testing/Test_cases.py
 896888f9d5d5f91e5729ae1b53830865 *inst/testing/Utf8.R
 f0ab85292080c6f33ec7c32cbe5b9594 *inst/testing/all.R
-3c2e55d7ff670b8b604b96151d1e8c0d *man/BEGIN.Python.Rd
+906a264ed7c8e046ce900d1b8e9a3b7f *man/BEGIN.Python.Rd
 314f3e26badfaaa135098da9a1d62110 *man/autodetectPython.Rd
 a10a59d6fd185cd885e2a681efb58eba *man/pyAttach.Rd
 df989a552858494ba638839d565657e4 *man/pyCall.Rd
@@ -52,7 +52,7 @@ f14bee65bfe64de165bbd9ead37d7b19 *man/pyExit.Rd
 16726509ab63030160571ce5baa88e23 *man/pyFunction.Rd
 f8e52a66f6b879e83f3f975ed461a8df *man/pyGet.Rd
 a35bdcf5644729f15993c00168d912c4 *man/pyGet0.Rd
-bcd51012f9f97acfa00c3a55cbe0af5f *man/pyHelp.Rd
+8cd064e1c651bd0030907c6f27c38f64 *man/pyHelp.Rd
 4acf3d6a674b089c083c3080911c434e *man/pyImport.Rd
 2c4cb67c7ad6ebd6efd940402735a415 *man/pyIsConnected.Rd
 58a09fb7082904b081f208e8982d2dda *man/pyList.Rd
@@ -71,6 +71,7 @@ db5c84655c1e971494d99587c9e14820 *man/pyTuple.Rd
 1f5354226008b9de135e496d48884822 *src/CastRObjects.h
 91471cf85c09b13d3ab936fba7e0e542 *src/GetPyObjects.c
 12fa0d8d4591328ddb4c1a680bad13d5 *src/GetPyObjects.h
+049dc07c7696793feecf168f968da0b1 *src/Makevars.in
 67e8d5b072c91b99b6ec67f5fa0f80d8 *src/PyCall.c
 254e9df8b96b33f9d891f1fcadd81768 *src/PyCall.h
 a4ecd1bb63a3a910f88ef47d06b15cef *src/PyRunString.c

R/Basics.R

@@ -46,7 +46,9 @@ pyDir <- function(objName=NULL){
 #' @return Prints the help to the given string.
 #' @examples
 #' \dontshow{PythonInR:::pyCranConnect()}
+#' \dontrun{
 #' pyHelp("abs")
+#' }
 #  -----------------------------------------------------------
 pyHelp <- function(topic){
     if ( pyConnectionCheck() ) return(invisible(NULL))

R/PySource.R

@@ -56,6 +56,8 @@ pySource <- function(file, local = FALSE, echo = verbose, print.eval = echo,
 #  -----------------------------------------------------------
 #  BEGIN.Python
 #  ============
+#  note This won't work with RStudio because of a known  
+#  \href{https://support.rstudio.com/hc/communities/public/questions/206744317-readLines-Bug-?page=1#answer-206647788}{RStudio issue}.
 #' @title Execute Python interactively from within R
 #'
 #' @description The function BEGIN.Python starts an Python read-eval-print loop.
@@ -64,8 +66,6 @@ pySource <- function(file, local = FALSE, echo = verbose, print.eval = echo,
 #'          from within R.
 #' @return Returns the entered code as character, code lines which throw an
 #'         exception are omitted.
-#' @note This won't work with RStudio because of a known  
-#' \href{https://support.rstudio.com/hc/communities/public/questions/206744317-readLines-Bug-?page=1#answer-206647788}{RStudio issue}.
 #' @examples
 #' \dontshow{PythonInR:::pyCranConnect()}
 #' \dontrun{

configure

@@ -5,87 +5,103 @@
 #
 # NOTES:
 # The system variable USESPECIALPYTHONVERSION can be used to link to a special
-# python version. 
+# python version.
 # export USESPECIALPYTHONVERSION="python3.4"
 # it can be very usefull especially for testing but one has to ensure  that
 # the file PYVERSION-config is present at the provided location else it will
 # fail.
-# But when using python3 also python3-dev has to be installed 
+# But when using python3 also python3-dev has to be installed
 # (apt-get install python3-dev)
-# 
+#
 # gcc:
 # there seems to be a new option which doesn't allows me to compile
 # -fstack-protector-strong so I just remove it
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 if ! [ -z "$USESPECIALPYTHONVERSION" ]; then
-    echo "use special version"
-    alias python="$USESPECIALPYTHONVERSION"
-fi 
+  echo "use special version"
+  alias python3="$USESPECIALPYTHONVERSION"
+fi
 
-PYVERSION=`python -c "import sys;import distutils.sysconfig as sc;sys.stdout.write(sc.get_config_var('VERSION'))"`
-PYINCLUDE=`python -c "import sys;import distutils.sysconfig as sc;sys.stdout.write(sc.get_config_var('INCLUDEPY'))"`
-PYBINPATH=`python -c "import sys;import os;sys.stdout.write(os.path.dirname(sys.executable))"`
+PYVERSION=`python3 -c "import sys;import distutils.sysconfig as sc;sys.stdout.write(sc.get_config_var('VERSION'))"`
+PYINCLUDE=`python3 -c "import sys;import distutils.sysconfig as sc;sys.stdout.write(sc.get_config_var('INCLUDEPY'))"`
+PYBINPATH=`python3 -c "import sys;import os;sys.stdout.write(os.path.dirname(sys.executable))"`
 # sys.version_info.major would be a alternative to hexversion
-PY3FLAG=`python -c 'import sys; print("%i" % (sys.hexversion<0x03000000))'`
+PY3FLAG=`python3 -c 'import sys; print("%i" % (sys.hexversion<0x03000000))'`
+PYABOVE38FLAG=`python3 -c 'import sys; print("%i" % (sys.hexversion>0x03080000))'`
 PICFLAGS=`"${R_HOME}/bin/R" CMD config CXX11PICFLAGS`
 
+if [ $PYABOVE38FLAG -eq 1 ]; then
+  echo "detected python3.8 or newer"
+  PYEMBEDPKGCONF="-embed"
+  PYEMBEDPYCONF="--embed"
+fi
+
+#python-3.8-embed
+
 ## echo $PYVERSION
 ## echo $PYBINPATH
 ## echo $PY3FLAG
 ## echo $PICFLAGS
 ## echo ""
 
-## TODO: 
-## Change the generation of PKG_LIBS so it works with coda.
+## TODO:
+## Change the generation of PKG_LIBS so it works with conda.
 ## PYLIBS="PKG_LIBS="`python -c 'import sysconfig; print(" ".join(sysconfig.get_config_var("LDSHARED").split()[1:]))'`
 if [ $PY3FLAG -eq 0 ]; then
-    echo "python version is > 3"
-    PYXY="PYTHONLIBXY=libpython"$PYVERSION"m.so"    
-else 
-    echo "python version is < 3"
-    PYXY="PYTHONLIBXY=libpython"$PYVERSION".so"
+  echo "python version is > 3"
+  PYXY="PYTHONLIBXY=libpython"$PYVERSION"m.so"
+else
+  echo "python version is < 3"
+  PYXY="PYTHONLIBXY=libpython"$PYVERSION".so"
 fi
 
-PYLIBS="PKG_LIBS="`$PYBINPATH/python$PYVERSION-config --ldflags`
-PYCFLAGS="PKG_CFLAGS="`$PYBINPATH/python$PYVERSION-config --cflags`" -D $PYXY -D PYTHON_IN_R_NO_EXPLICIT_LINKING"
+PKG_LIBS=`$PYBINPATH/python$PYVERSION-config --ldflags $PYEMBEDPYCONF`
 
-## echo ""
-## echo "Makevars:"
-## echo $PYLIBS
-## echo $PYCFLAGS | sed 's/Wstrict-prototypes/pedantic/' | sed 's/ -fstack-protector-strong//'
-## echo ""
+##
+## PKG_CFLAGS
+##
+if [ -z "$(pkg-config --version 2>&1 | grep 'pkg-config')" ]; then
+  if (pkg-config --exists python-$PYVERSION$PYEMBEDPKGCONF); then
+    echo "pkg-config"
+    PKG_CFLAGS=`pkg-config --cflags python-$PYVERSION$PYEMBEDPKGCONF`
+  else
+    #echo "python-config"
+    #PKG_CFLAGS=`$PYBINPATH/python$PYVERSION-config --cflags $PYEMBEDPYCONF`
+    PKG_CFLAGS="-I$PYINCLUDE"
+  fi
+else
+  #echo "python-config"
+  #PKG_CFLAGS=`$PYBINPATH/python$PYVERSION-config --cflags $PYEMBEDPYCONF`
+  PKG_CFLAGS="-I$PYINCLUDE"
+fi
 
-# replacing Wstric-prototypes removes some unnecessary warnings
 
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -Wstrict-prototypes//')
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -fstack-protector-strong//')
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -Wdate-time//')
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -Werror=format-security//')
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -Wformat//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -Wstrict-prototypes//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -fstack-protector-strong//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -Wdate-time//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -Werror=format-security//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -Wformat//')
 
 ## added 27.07.2018
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -fstack-clash-protection//')
-PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -fcf-protection//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -fstack-clash-protection//')
+PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -fcf-protection//')
 
 if ! [ -z "$PICFLAGS" ]; then
-  PYCFLAGS=$(echo $PYCFLAGS | sed 's/ -fpic//')
-fi 
+  PKG_CFLAGS=$(echo $PKG_CFLAGS | sed 's/ -fpic//')
+fi
 
-# if [ -z "$PICFLAGS" ]; then
-#   echo $PYCFLAGS | sed 's/Wstrict-prototypes/pedantic/' | sed 's/ -fstack-protector-strong//' | sed 's/ -Wdate-time//' | sed 's/ -Werror=format-security//' | sed 's/ -Wformat//' >> src/Makevars 
-# else 
-#   echo $PYCFLAGS | sed 's/Wstrict-prototypes/pedantic/' | sed 's/ -fstack-protector-strong//' | sed 's/ -Wdate-time//' | sed 's/ -Werror=format-security//' | sed 's/ -Wformat//' | sed 's/ -fpic//' >> src/Makevars  
-# fi
+
+
+sed -e "s|@PKG_CFLAGS@|$PKG_CFLAGS|" -e "s|@PKG_LIBS@|$PKG_LIBS|" -e "s|@PYXY@|$PYXY|" src/Makevars.in > src/Makevars
 
 echo ""
+echo "-----------------------------------"
 echo "  Makevars:"
 echo ""
-echo "    "$PYLIBS
-echo ""
-echo "    "$PYCFLAGS
+cat src/Makevars
 echo ""
+echo "-----------------------------------"
 echo ""
 
-echo ${PYLIBS} > src/Makevars
-echo ${PYCFLAGS} >> src/Makevars
+exit 0

src/Makevars.in

@@ -0,0 +1,25 @@
+# Compilation used the following non-portable flag(s):
+#   ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’
+
+PKG_LIBS=@PKG_LIBS@
+PKG_CFLAGS=@PKG_CFLAGS@ -D @PYXY@ -D PYTHON_IN_R_NO_EXPLICIT_LINKING
+
+OBJECTS = CToR.o PythonInR.o CastPyObjects.o CastRObjects.o GetPyObjects.o init.o PyCall.o PyRunString.o Python_Explicit_Linking.o SetPyObjects.o
+
+all: $(SHLIB)
+
+$(SHLIB): $(OBJECTS)
+
+#ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
+#ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
+
+ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) 
+ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS)
+
+
+%.o: %.c
+	$(CC) $(R_XTRA_CPPFLAGS) $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) -c $< -o $@
+
+# original from /etc/R/Makeconf
+# %.o: %.c
+# $(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@