Merge branch 'master' into windows-standalone

.github/workflows/ci.yaml

@@ -15,7 +15,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Compile standalone programs
-      run: cd standalone && make
+      run: cd standalone && make -f nii_info.make
 
     - name: Test standalone programs
       run: |

cleanup

@@ -1,3 +1,4 @@
 #!/bin/sh
 
-rm -f src/Makevars src/*.o src/niftilib/*.o src/zlib/*.o src/znzlib/*.o
+rm -f src/Makevars src/*.o src/niftilib/*.o src/znzlib/*.o inst/include/zlib.h inst/include/zconf.h
+rm -f src/zlib/*.o src/zlib/libz.*

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for RNifti 1.4.0.
+# Generated by GNU Autoconf 2.71 for RNifti 1.6.0.
 #
 # Report bugs to <code@clayden.org>.
 #
@@ -610,15 +610,15 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='RNifti'
 PACKAGE_TARNAME='rnifti'
-PACKAGE_VERSION='1.4.0'
-PACKAGE_STRING='RNifti 1.4.0'
+PACKAGE_VERSION='1.6.0'
+PACKAGE_STRING='RNifti 1.6.0'
 PACKAGE_BUGREPORT='code@clayden.org'
 PACKAGE_URL=''
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
-ZLIB_OBJECTS
-ZLIB_FLAGS
+ZLIB_LIBPATH
+ZLIB_OBJECT
 OBJEXT
 EXEEXT
 ac_ct_CC
@@ -1225,7 +1225,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures RNifti 1.4.0 to adapt to many kinds of systems.
+\`configure' configures RNifti 1.6.0 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1287,7 +1287,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of RNifti 1.4.0:";;
+     short | recursive ) echo "Configuration of RNifti 1.6.0:";;
    esac
   cat <<\_ACEOF
 
@@ -1367,7 +1367,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-RNifti configure 1.4.0
+RNifti configure 1.6.0
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1490,7 +1490,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by RNifti $as_me 1.4.0, which was
+It was created by RNifti $as_me 1.6.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -2153,8 +2153,6 @@ CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
 # Checks for libraries.
-ZLIB_FLAGS="-Izlib"
-ZLIB_OBJECTS=`ls -1 src/zlib/*.c | sed 's/^src\///' | sed 's/\\.c$/\\.o/' | tr '\n' ' '`
 
 
 
@@ -3208,8 +3206,12 @@ if test "$ac_res" != no
 then :
   test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
 
-    ZLIB_FLAGS=""
-    ZLIB_OBJECTS=""
+else $as_nop
+
+    ac_config_commands="$ac_config_commands zlib"
+
+    ZLIB_OBJECT="zlib/libz.a"
+    ZLIB_LIBPATH="-Lzlib"
 
 fi
 
@@ -3754,7 +3756,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by RNifti $as_me 1.4.0, which was
+This file was extended by RNifti $as_me 1.6.0, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -3777,6 +3779,7 @@ esac
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 # Files that config.status was made for.
 config_files="$ac_config_files"
+config_commands="$ac_config_commands"
 
 _ACEOF
 
@@ -3801,6 +3804,9 @@ Usage: $0 [OPTION]... [TAG]...
 Configuration files:
 $config_files
 
+Configuration commands:
+$config_commands
+
 Report bugs to <code@clayden.org>."
 
 _ACEOF
@@ -3809,7 +3815,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-RNifti config.status 1.4.0
+RNifti config.status 1.6.0
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 
@@ -3919,6 +3925,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 for ac_config_target in $ac_config_targets
 do
   case $ac_config_target in
+    "zlib") CONFIG_COMMANDS="$CONFIG_COMMANDS zlib" ;;
     "src/Makevars") CONFIG_FILES="$CONFIG_FILES src/Makevars" ;;
 
   *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
@@ -3932,6 +3939,7 @@ done
 # bizarre bug on SunOS 4.1.3.
 if $ac_need_defaults; then
   test ${CONFIG_FILES+y} || CONFIG_FILES=$config_files
+  test ${CONFIG_COMMANDS+y} || CONFIG_COMMANDS=$config_commands
 fi
 
 # Have a temporary directory for convenience.  Make it in the build tree
@@ -4120,7 +4128,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 fi # test -n "$CONFIG_FILES"
 
 
-eval set X "  :F $CONFIG_FILES      "
+eval set X "  :F $CONFIG_FILES      :C $CONFIG_COMMANDS"
 shift
 for ac_tag
 do
@@ -4330,9 +4338,16 @@ which seems to be undefined.  Please make sure it is defined" >&2;}
  ;;
 
 
-
+  :C)  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5
+printf "%s\n" "$as_me: executing $ac_file commands" >&6;}
+ ;;
   esac
 
+
+  case $ac_file$ac_mode in
+    "zlib":C) cd src/zlib && ./configure --static ;;
+
+  esac
 done # for ac_tag
 
 

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.71])
-AC_INIT([RNifti], [1.4.0], [code@clayden.org])
+AC_INIT([RNifti], [1.6.0], [code@clayden.org])
 
 # Get compiler flags from R
 : ${R_HOME=`R RHOME`}
@@ -18,15 +18,14 @@ CPPFLAGS=`"${R_HOME}/bin/R" CMD config CPPFLAGS`
 LDFLAGS=`"${R_HOME}/bin/R" CMD config LDFLAGS`
 
 # Checks for libraries.
-ZLIB_FLAGS="-Izlib"
-ZLIB_OBJECTS=`ls -1 src/zlib/*.c | sed 's/^src\///' | sed 's/\\.c$/\\.o/' | tr '\n' ' '`
-AC_SEARCH_LIBS([inflate], [z], [
-    ZLIB_FLAGS=""
-    ZLIB_OBJECTS=""
+AC_SEARCH_LIBS([inflate], [z], [], [
+    AC_CONFIG_COMMANDS([zlib], [cd src/zlib && ./configure --static])
+    ZLIB_OBJECT="zlib/libz.a"
+    ZLIB_LIBPATH="-Lzlib"
 ])
 
-AC_SUBST(ZLIB_FLAGS)
-AC_SUBST(ZLIB_OBJECTS)
+AC_SUBST(ZLIB_OBJECT)
+AC_SUBST(ZLIB_LIBPATH)
 
 AC_CONFIG_FILES([src/Makevars])
 AC_OUTPUT

inst/include/.gitignore

@@ -0,0 +1,2 @@
+/zconf.h
+/zlib.h

inst/include/znzlib/znzlib.h

@@ -72,7 +72,7 @@ extern "C" {
 #if defined(ITKZLIB) && !defined(ITK_USE_SYSTEM_ZLIB)
 #include "itk_zlib.h"
 #else
-#include "zlib/zlib.h"
+#include "zlib.h"
 #endif
 #endif
 

src/Makevars.in

@@ -1,5 +1,11 @@
-PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include @ZLIB_FLAGS@
-PKG_LIBS = @LIBS@
+PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include
+PKG_LIBS = @LIBS@ @ZLIB_LIBPATH@
 
 NIFTI_OBJECTS = znzlib/znzlib.o niftilib/nifti1_io.o niftilib/nifti2_io.o
-OBJECTS = main.o zzz.o @ZLIB_OBJECTS@ $(NIFTI_OBJECTS)
+OBJECTS = @ZLIB_OBJECT@ main.o zzz.o $(NIFTI_OBJECTS)
+
+$(SHLIB): $(OBJECTS)
+
+zlib/libz.a:
+	cd zlib && $(MAKE) libz.a CC="$(CC)" CFLAGS="$(CFLAGS) $(CPICFLAGS)"
+	cp zlib/zlib.h zlib/zconf.h ../inst/include/

src/Makevars.win

@@ -1,4 +1,5 @@
 PKG_CPPFLAGS = -DNDEBUG -DHAVE_ZLIB -DUSING_R -DRNIFTI_NIFTILIB_DEDUPLICATE -I../inst/include
 PKG_LIBS = -lz
 
-OBJECTS = main.o zzz.o znzlib/znzlib.o niftilib/nifti1_io.o niftilib/nifti2_io.o
+NIFTI_OBJECTS = znzlib/znzlib.o niftilib/nifti1_io.o niftilib/nifti2_io.o
+OBJECTS = main.o zzz.o $(NIFTI_OBJECTS)

src/niftilib/nifti1_io.c

@@ -4,6 +4,7 @@
 #include "niftilib/nifti1_io_version.h"
 
 #include <errno.h>
+#include <limits.h>
 
 /*****===================================================================*****/
 /*****     Sample functions to deal with NIFTI-1 and ANALYZE files       *****/

src/zlib/.gitignore

@@ -0,0 +1,12 @@
+*.a
+*.o
+*.dylib
+
+*.gcda
+*.gcno
+*.gcov
+
+/Makefile
+/zconf.h
+/zlib.pc
+/configure.log