Merge pull request #46 from lavakin/master

CRAN submission

DESCRIPTION

@@ -1,8 +1,10 @@
 Package: myTAI
 Type: Package
 Title: Evolutionary Transcriptomics
-Version: 1.0.2.9000
-Date: 2023-07-08
+Version: 2.0.0.0
+Date: 2024-09-30
+Maintainer: Jane Doe <[email protected]>
+Author: Jane Doe [aut], John Smith [aut]
 Authors@R: c(person("Hajk-Georg", "Drost",
                 role = c("aut", "cre"),
                 email = "[email protected]",

cleanup

@@ -0,0 +1,2 @@
+#!/bin/sh
+rm -f src/Makevars

configure

@@ -0,0 +1,190 @@
+#!/usr/bin/env sh
+
+# Find R compilers
+CC=`${R_HOME}/bin/R CMD config CC`
+CFLAGS=`${R_HOME}/bin/R CMD config CFLAGS`
+# compiler and flags to 'cc' file
+echo "CC=${CC}" > inst/cc
+echo "CFLAGS=${CFLAGS}" >> inst/cc
+
+# gcc compiler info to output #3291
+case $CC in gcc*)
+  GCCV=`${CC} -dumpfullversion -dumpversion`
+  echo "$CC $GCCV"
+esac
+
+# Let's keep this simple. If pkg-config is available, use it. Otherwise print
+# the helpful message to aid user if compilation does fail. Note 25 of R-exts:
+# "[pkg-config] is available on the machines used to produce the CRAN binary packages"
+# This script should pass `checkbashisms` for portability; e.g. CRAN's Solaris 10,
+# and R-exts note 24 now suggests 'checkbashisms' as we proposed.
+
+msg=0
+NOZLIB=1 # if pkg-config is not available then zlib will be disabled for higher chance of compilation success
+pkg-config --version > config.log 2>&1
+if [ $? -ne 0 ]; then
+  echo "*** pkg-config is not installed."
+  msg=1
+else
+  pkg-config --exists zlib
+  if [ $? -ne 0 ]; then
+    echo "*** pkg-config is installed but 'pkg-config --exists zlib' did not return 0."
+    msg=1
+  else
+    NOZLIB=0
+    lib=`pkg-config --libs zlib`
+    cflag=`pkg-config --cflags zlib`
+    expr -- "$lib" : ".*-lz$" >> config.log  # -- for FreeBSD, #4652
+    if [ $? -ne 0 ]; then
+      expr -- "$lib" : ".*-lz " >> config.log
+      # would use \b in one expr but MacOS does not support \b
+      if [ $? -ne 0 ]; then
+        echo "*** pkg-config is installed and 'pkg-config --exists zlib' succeeds but"
+        echo "*** 'pkg-config --libs zlib' returns '${lib}' which does not include the standard -lz."
+        msg=1
+      fi
+    fi
+  fi
+fi
+
+if [ $msg -ne 0 ]; then
+  echo "*** Compilation will now be attempted and if it works you can ignore this message. In"
+  echo "*** particular, this should be the case on Mac where zlib is built in or pkg-config"
+  echo "*** is not installed. However, if compilation fails, try 'locate zlib.h zconf.h' and"
+  echo "*** ensure the zlib development library is installed :"
+  echo "***   deb: zlib1g-dev (Debian, Ubuntu, ...)"
+  echo "***   rpm: zlib-devel (Fedora, EPEL, ...)"
+  echo "***   There is a zlib in brew for OSX but the built in zlib should work."
+  echo "*** Note that zlib is required to compile R itself so you may find the advice in the R-admin"
+  echo "*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as"
+  echo "*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore"
+  echo "*** 'sudo apt-get build-dep r-base' should be sufficient too."
+  echo "*** To silence this message, please ensure that :"
+  echo "***   1) 'pkg-config --exists zlib' succeeds (i.e. \$? -eq 0)"
+  echo "***   2) 'pkg-config --libs zlib' contains -lz"
+  echo "*** Compilation will now be attempted ..."
+else
+  version=`pkg-config --modversion zlib`
+  echo "zlib ${version} is available ok"
+fi
+
+# Test if we have a OPENMP compatible compiler
+# Aside: ${SHLIB_OPENMP_CFLAGS} does not appear to be defined at this point according to Matt's testing on
+# Linux, and R CMD config SHLIB_OPENMP_CFLAGS also returns 'no information for variable'. That's not
+# inconsistent with R-exts$1.2.1.1, though, which states it's 'available for use in Makevars' (so not
+# necessarily here in configure). Hence use -fopenmp directly for this detection step.
+# printf not echo to pass checkbashisms w.r.t. to the \n
+
+cat <<EOF > test-omp.c
+#include <omp.h>
+int main() {
+  return omp_get_num_threads();
+}
+EOF
+
+detect_openmp () {
+  export PKG_CXXFLAGS=""
+  if [ "$(uname)" = "Linux" ]; then
+
+    printf "%s" "* checking if R installation supports OpenMP without any extra hints... "
+    if "${R_HOME}/bin/R" CMD SHLIB test-omp.c >> config.log 2>&1; then
+      echo "yes"
+      export R_OPENMP_ENABLED=1
+      return
+    else
+      echo "no"
+    fi
+
+
+    printf "%s" "* checking if R installation supports openmp with \"-fopenmp\" flag... "
+    if ${CC} ${CFLAGS} -fopenmp test-omp.c >> config.log 2>&1; then
+      echo "yes"
+      export PKG_CFLAGS="${PKG_CFLAGS} -fopenmp"
+      export R_OPENMP_ENABLED=1
+      return
+    else
+      echo "no"
+    fi
+  fi # uname=Linux
+
+  if [ "$(uname)" = "Darwin" ]; then
+    export openmapp="-fopenmp"
+
+    # https://mac.r-project.org/openmp
+    printf "%s" "* checking if R installation supports OpenMP with \"-Xclang -fopenmp\" ... "
+
+      echo "yes"
+      export PKG_CFLAGS="${PKG_CFLAGS} -Xclang -fopenmp"
+      export PKG_LIBS="${PKG_LIBS} -lomp"
+      export R_OPENMP_ENABLED=1
+      export PKG_CXXFLAGS="-Xpreprocessor -fopenmp"
+      return
+
+    printf "%s" "* checking if R installation supports OpenMP with \"-fopenmp\" ... "
+
+      echo "yes"
+      export PKG_CFLAGS="${PKG_CFLAGS} -fopenmp"
+      export R_OPENMP_ENABLED=1
+      export PKG_CXXFLAGS="-Xpreprocessor -fopenmp"
+      return
+
+    if [ "$(uname -m)" = "arm64" ]; then
+      HOMEBREW_PREFIX=/usr/local
+    else
+      HOMEBREW_PREFIX=/usr/local
+    fi
+
+    if [ -e "${HOMEBREW_PREFIX}/opt/libomp" ]; then
+      printf "%s" "* checking if libomp installation at ${HOMEBREW_PREFIX}/opt/libomp can be used... 
+"
+      LIBOMP_INCLUDE="-I${HOMEBREW_PREFIX}/opt/libomp/include -Xclang -fopenmp"
+      LIBOMP_LINK="-L${HOMEBREW_PREFIX}/opt/libomp/lib -lomp"
+      if ${CC} ${CFLAGS} ${LIBOMP_INCLUDE} ${LIBOMP_LINK} test-omp.c >> config.log 2>&1; then
+        echo "yes"
+        export PKG_CFLAGS="${PKG_CFLAGS} ${LIBOMP_INCLUDE}"
+        export PKG_LIBS="${PKG_LIBS} ${LIBOMP_LINK}"
+        export R_OPENMP_ENABLED=1
+        return
+      else
+        echo "no"
+      fi
+    fi
+
+  fi # uname=Darwin
+
+  # No support for OpenMP available
+  export R_OPENMP_ENABLED=0
+}
+
+detect_openmp
+
+# Clean up.
+rm -f test-omp.* a.out
+
+if [ "${R_OPENMP_ENABLED}" = "0" ]; then
+  echo "***"
+  echo "*** OpenMP not supported!"
+  echo "***   parallelize operations like sorting, grouping, file reading, etc."
+  echo "*** Continuing installation without OpenMP support..."
+  echo "***"
+  sed -e "s|@openmp_cflags@||" src/Makevars.in > src/Makevars
+else
+  sed -e "s|@openmp_cflags@|\$(SHLIB_OPENMP_CFLAGS)|" src/Makevars.in > src/Makevars
+fi
+
+# retain user supplied PKG_ env variables, #4664. See comments in Makevars.in too.
+sed -e "s|@PKG_CFLAGS@|$PKG_CFLAGS|" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+sed -e "s|@PKG_CXXFLAGS@|$PKG_CXXFLAGS|" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+sed -e "s|@PKG_LIBS@|$PKG_LIBS|" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+
+# optional dependency on zlib
+if [ "$NOZLIB" = "1" ]; then
+  echo "*** Compilation without compression support in fwrite"
+  sed -e "s|@zlib_cflags@|-DNOZLIB|" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+  sed -e "s|@zlib_libs@||" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+else
+  sed -e "s|@zlib_cflags@|${cflag}|" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+  sed -e "s|@zlib_libs@|${lib}|" src/Makevars > src/Makevars.tmp && mv src/Makevars.tmp src/Makevars
+fi
+
+exit 0

src/Makevars.in

@@ -0,0 +1,10 @@
+PKG_CPPFLAGS =  -I/usr/local/opt/libomp/include
+PKG_CXXFLAGS =  @PKG_CXXFLAGS@
+#PKG_CFLAGS = @PKG_CFLAGS@ @openmp_cflags@ @zlib_cflags@
+PKG_LIBS = @PKG_LIBS@ @openmp_cflags@ @zlib_libs@
+all: $(SHLIB)
+#	@echo PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS) 
+#	@echo PKG_LIBS = $(PKG_LIBS)
+	if [ "$(SHLIB)" != "myTAI$(SHLIB_EXT)" ]; then mv $(SHLIB) myTAI$(SHLIB_EXT); fi
+	if [ "$(OS)" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id myTAI$(SHLIB_EXT) myTAI$(SHLIB_EXT); fi
+

src/Makevars.win

@@ -0,0 +1,6 @@
+#PKG_CFLAGS = $(SHLIB_OPENMP_CFLAGS)
+#PKG_LIBS = $(SHLIB_OPENMP_CFLAGS) -lz
+
+
+#all: $(SHLIB)
+#	mv $(SHLIB) myTAI$(SHLIB_EXT)