Fix a number of OS specific bugs

1. Issue Unidata#2043
   * FreeBSD build fails because of conflicts in defining the fileno() function. So removed all extern declarations of fileno.

2. Issue Unidata#2124
   * There were a couple of problems here.
     * I was conflating msys with mingw and they need separate handling of paths. So treat mingw like windows.
     * memio.c was not always writing the full content of the memory to file. Untested fix by properly accounting for zero size writes.
     * Fix bug when skipping white space in tst_xcache.c

3. Issue Unidata#2105
   * On MINGW, bash and other POSIX utilities use a mounted root directory,
     but executables compiled for Windows do not recognise the mount point.
     Ensure that Windows paths are used in tests of Windows executables.

4. Issue Unidata#2132
   * Apparently the Intel C compiler on OSX defines isnan etc.
     So disable declaration in dutil.c under that condition.

5. Fix and re-enable test_rcmerge.sh by allowing override of where to
   look for .rc files

6. CMakeLists.txt suppresses certain ncdump directory tests because of differences in printing floats/doubles.
   * Extend the list to include those that also fail under mingw.
   * Suppress the mingw tests in ncdump/Makefile.am

RELEASE_NOTES.md

@@ -7,6 +7,7 @@ This file contains a high-level description of this package's evolution. Release
 
 ## 4.8.2 - TBD
 
+* [Bug Fix] Fix several mingw related errors. See [Github #????](https://github.com/Unidata/netcdf-c/pull/????).
 * [Enhancement] Support byte-range reading of netcdf-3 files stored in private buckets in S3. See [Github #2134](https://github.com/Unidata/netcdf-c/pull/2134)
 * [Enhancement] Support Amazon S3 access for NCZarr. Also support use of the existing Amazon SDK credentials system. See [Github #2114](https://github.com/Unidata/netcdf-c/pull/2114)
 * [Bug Fix] Fix string allocation error in H5FDhttp.c. See [Github #2127](https://github.com/Unidata/netcdf-c/pull/2127).

configure.ac

@@ -1170,14 +1170,17 @@ case "`uname`" in
   CYGWIN*) ISCYGWIN=yes;;
   Darwin*) ISOSX=yes;;
   WIN*) ISMSVC=yes;;
+  MINGW*) ISMINGW=yes;;
 esac
 AM_CONDITIONAL(ISCYGWIN, [test "x$ISCYGWIN" = xyes])
 AM_CONDITIONAL(ISMSVC, [test "x$ISMSVC" = xyes])
 AM_CONDITIONAL(ISOSX, [test "x$ISOSX" = xyes])
+AM_CONDITIONAL(ISMINGW, [test "x$ISMINGW" = xyes])
 
 AC_SUBST([ISMSVC], [${ISMSVC}])
 AC_SUBST([ISCYGWIN], [${ISCYGWIN}])
 AC_SUBST([ISOSX], [${ISOSX}])
+AC_SUBST([ISMINGW], [${ISMINGW}])
 
 ###
 # Crude hack to work around an issue

include/ncconfigure.h

@@ -60,9 +60,6 @@ extern long long int strtoll(const char*, char**, int);
 #ifndef strtoull
 extern unsigned long long int strtoull(const char*, char**, int);
 #endif
-#ifndef fileno
-extern int fileno(FILE*);
-#endif
 
 #endif /*STDC*/
 #endif /*!_WIN32*/

include/ncrc.h

@@ -19,6 +19,7 @@ and accessing rc files (e.g. .daprc).
 /* getenv() keys */
 #define NCRCENVIGNORE "NCRCENV_IGNORE"
 #define NCRCENVRC "NCRCENV_RC"
+#define NCRCENVHOME "NCRCENV_HOME"
 
 /* Known .aws profile keys */
 #define AWS_ACCESS_KEY_ID "aws_access_key_id"
@@ -38,6 +39,7 @@ typedef struct NCRCinfo {
 	int loaded; /* 1 => already loaded */
         NClist* entries; /* the rc file entry store fields*/
         char* rcfile; /* specified rcfile; overrides anything else */
+        char* rchome; /* Overrides $HOME when looking for .rc files */
 } NCRCinfo;
 
 /* Collect global state info in one place */

libdispatch/dpathmgr.c

@@ -871,10 +871,12 @@ getlocalpathkind(void)
     int kind = NCPD_UNKNOWN;
 #ifdef __CYGWIN__
 	kind = NCPD_CYGWIN;
-#elif __MSYS__
-	kind = NCPD_MSYS;
-#elif _MSC_VER /* not _WIN32 */
+#elif defined __MINGW32__
+	kind = NCPD_WIN;
+#elif defined _MSC_VER /* not _WIN32 */
 	kind = NCPD_WIN;
+#elif defined __MSYS__
+	kind = NCPD_MSYS;
 #else
 	kind = NCPD_NIX;
 #endif

libdispatch/drc.c

@@ -127,6 +127,18 @@ ncrc_initialize(void)
     }
 }
 
+static void
+ncrc_setrchome(void)
+{
+    const char* tmp = NULL;
+    if(ncrc_globalstate->rcinfo.rchome) return;
+    assert(ncrc_globalstate && ncrc_globalstate->home);
+    tmp = getenv(NCRCENVHOME);
+    if(tmp == NULL || strlen(tmp) == 0)
+	tmp = ncrc_globalstate->home;
+    ncrc_globalstate->rcinfo.rchome = strdup(tmp);
+}
+
 /* Get global state */
 NCRCglobalstate*
 ncrc_getglobalstate(void)
@@ -155,6 +167,7 @@ NC_rcclear(NCRCinfo* info)
 {
     if(info == NULL) return;
     nullfree(info->rcfile);
+    nullfree(info->rchome);
     rcfreeentries(info->entries);
 }
 
@@ -193,9 +206,9 @@ NC_rcload(void)
     /* locate the configuration files in order of use:
        1. Specified by NCRCENV_RC environment variable.
        2. If NCRCENV_RC is not set then merge the set of rc files in this order:
-	  1. $HOME/.ncrc
-  	  2. $HOME/.daprc
-	  3. $HOME/.docsrc
+	  1. $RCHOME/.ncrc
+  	  2. $RCHOME/.daprc
+	  3. $RCHOME/.docsrc
 	  4. $CWD/.ncrc
   	  5. $CWD/.daprc
 	  6. $CWD/.docsrc
@@ -208,7 +221,11 @@ NC_rcload(void)
 	const char* dirnames[3];
 	const char** dir;
 
-	dirnames[0] = globalstate->home;
+
+	/* Make sure rcinfo.rchome is defined */
+	ncrc_setrchome();
+
+	dirnames[0] = globalstate->rcinfo.rchome;
 	dirnames[1] = globalstate->cwd;
 	dirnames[2] = NULL;
 

libdispatch/dutil.c

@@ -256,6 +256,8 @@ NC_writefile(const char* filename, size_t size, void* content)
     void* p;
     size_t remain;
 
+    if(content == NULL) {content = ""; size = 0;}
+
 #ifdef _WIN32
     stream = NCfopen(filename,"wb");
 #else
@@ -343,7 +345,8 @@ NC_testmode(NCURI* uri, const char* tag)
     return found;
 }
 
-#ifdef __APPLE__
+#if ! defined __INTEL_COMPILER 
+#if defined __APPLE__ 
 int isinf(double x)
 {
     union { unsigned long long u; double f; } ieee754;
@@ -361,6 +364,8 @@ int isnan(double x)
 }
 
 #endif /*APPLE*/
+#endif /*!_INTEL_COMPILER*/
+
 
 int
 NC_split_delim(const char* arg, char delim, NClist* segments)

libsrc/memio.c

@@ -28,6 +28,8 @@
 #include "nc3internal.h"
 #include "netcdf_mem.h"
 #include "ncpathmgr.h"
+#include "ncrc.h"
+#include "ncbytes.h"
 
 #undef DEBUG
 
@@ -710,48 +712,16 @@ readfile(const char* path, NC_memio* memio)
 {
     int status = NC_NOERR;
     FILE* f = NULL;
-    size_t filesize = 0;
-    size_t count = 0;
-    char* memory = NULL;
-    char* p = NULL;
-
-    /* Open the file for reading */
-#ifdef _MSC_VER
-    f = NCfopen(path,"rb");
-#else
-    f = NCfopen(path,"r");
-#endif
-    if(f == NULL)
-	{status = errno; goto done;}
-    /* get current filesize */
-    if(fseek(f,0,SEEK_END) < 0)
-	{status = errno; goto done;}
-    filesize = (size_t)ftell(f);
-    /* allocate memory */
-    memory = malloc((size_t)filesize);
-    if(memory == NULL)
-	{status = NC_ENOMEM; goto done;}
-    /* move pointer back to beginning of file */
-    rewind(f);
-    count = filesize;
-    p = memory;
-    while(count > 0) {
-        size_t actual;
-        actual = fread(p,1,count,f);
-	if(actual == 0 || ferror(f))
-	    {status = NC_EIO; goto done;}	 
-	count -= actual;
-	p += actual;
-    }
+    NCbytes* buf = ncbytesnew();
+
+    if((status = NC_readfile(path,buf))) goto done;
     if(memio) {
-	memio->size = (size_t)filesize;
-	memio->memory = memory;
-	memory = NULL;
+	memio->size = ncbyteslength(buf);
+	memio->memory = ncbytesextract(buf);
     }
 
 done:
-    if(memory != NULL)
-	free(memory);
+    ncbytesfree(buf);
     if(f != NULL) fclose(f);
     return status;    
 }
@@ -761,30 +731,10 @@ static int
 writefile(const char* path, NCMEMIO* memio)
 {
     int status = NC_NOERR;
-    FILE* f = NULL;
-    size_t count = 0;
-    char* p = NULL;
 
-    /* Open/create the file for writing*/
-#ifdef _MSC_VER
-    f = NCfopen(path,"wb");
-#else
-    f = NCfopen(path,"w");
-#endif
-    if(f == NULL)
-        {status = errno; goto done;}
-    rewind(f);
-    count = memio->size;
-    p = memio->memory;
-    while(count > 0) {
-        size_t actual;
-        actual = fwrite(p,1,count,f);
-	if(actual == 0 || ferror(f))
-	    {status = NC_EIO; goto done;}	 
-	count -= actual;
-	p += actual;
+    if(memio) {
+        if((status = NC_writefile(path,memio->size,memio->memory))) goto done;
     }
 done:
-    if(f != NULL) fclose(f);
     return status;    
 }

ncdump/CMakeLists.txt

@@ -160,13 +160,13 @@ endif()
     SET_TARGET_PROPERTIES(nctrunc PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE
       ${CMAKE_CURRENT_BINARY_DIR})
 
-IF(RCMERGE)
-    SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY
-      ${CMAKE_CURRENT_BINARY_DIR})
-    SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
-      ${CMAKE_CURRENT_BINARY_DIR})
-    SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE ${CMAKE_CURRENT_BINARY_DIR})
-endif()
+    IF(RCMERGE)
+        SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY
+          ${CMAKE_CURRENT_BINARY_DIR})
+        SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY_DEBUG
+          ${CMAKE_CURRENT_BINARY_DIR})
+        SET_TARGET_PROPERTIES(tst_rcmerge PROPERTIES RUNTIME_OUTPUT_DIRECTORY_RELEASE ${CMAKE_CURRENT_BINARY_DIR})
+    endif()
 
     IF(USE_HDF5)
       SET_TARGET_PROPERTIES(tst_fileinfo PROPERTIES RUNTIME_OUTPUT_DIRECTORY
@@ -189,7 +189,6 @@ endif()
   add_sh_test(ncdump tst_64bit)
   add_bin_test_no_prefix(ref_ctest)
   add_bin_test_no_prefix(ref_ctest64)
-  add_sh_test(ncdump tst_output)
   add_sh_test(ncdump tst_lengths)
   add_sh_test(ncdump tst_calendars)
   build_bin_test_no_prefix(tst_utf8)
@@ -200,15 +199,21 @@ endif()
     add_sh_test(ncdump tst_hdf5_offset)
   ENDIF(USE_HDF5)
 
+  IF(NOT MSVC AND NOT MINGW)
+      add_sh_test(ncdump tst_output)
+  ENDIF()
+
   add_sh_test(ncdump tst_null_byte_padding)
   IF(USE_STRICT_NULL_BYTE_HEADER_PADDING)
     SET_TESTS_PROPERTIES(ncdump_tst_null_byte_padding PROPERTIES WILL_FAIL TRUE)
   ENDIF(USE_STRICT_NULL_BYTE_HEADER_PADDING)
 
-  add_sh_test(ncdump tst_nccopy3)
-  IF(HAVE_BASH)
-    SET_TESTS_PROPERTIES(ncdump_tst_nccopy3 PROPERTIES RUN_SERIAL TRUE)
-  ENDIF(HAVE_BASH)
+  IF(NOT MSVC AND NOT MINGW)
+      add_sh_test(ncdump tst_nccopy3)
+      IF(HAVE_BASH)
+        SET_TESTS_PROPERTIES(ncdump_tst_nccopy3 PROPERTIES RUN_SERIAL TRUE)
+      ENDIF(HAVE_BASH)
+  ENDIF()
 
   add_sh_test(ncdump tst_nccopy3_subset)
   add_sh_test(ncdump tst_charfill)
@@ -256,10 +261,11 @@ endif()
     # formatting omits a 0.
     ###
     IF(EXTRA_TESTS)
-      add_sh_test(ncdump run_back_comp_tests)
-      IF(MSVC)
-        SET_TESTS_PROPERTIES(ncdump_run_back_comp_tests PROPERTIES WILL_FAIL TRUE)
-      ENDIF(MSVC)
+      IF(USE_HDF5)
+        IF(NOT MSVC AND NOT MINGW)
+          add_sh_test(ncdump run_back_comp_tests)
+        ENDIF()
+      ENDIF()
     ENDIF(EXTRA_TESTS)
 
     # Known failure on MSVC; the number of 0's padding
@@ -272,10 +278,11 @@ endif()
     build_bin_test_no_prefix(tst_fillbug)
     add_sh_test(ncdump_sh tst_fillbug)
 
-    add_sh_test(ncdump tst_netcdf4_4)
-    IF(MSVC AND HAVE_BASH)
-      SET_TESTS_PROPERTIES(ncdump_tst_netcdf4_4 PROPERTIES WILL_FAIL TRUE)
-    ENDIF(MSVC AND HAVE_BASH)
+    IF(HAVE_BASH)
+      IF(NOT MSVC AND NOT MINGW)
+        add_sh_test(ncdump tst_netcdf4_4)
+      ENDIF()
+    ENDIF(HAVE_BASH)
 
     ###
     # Some test reordering was required to ensure these tests
@@ -324,11 +331,11 @@ endif()
   IF(USE_HDF5)
     IF(HAVE_BASH)
       build_bin_test_no_prefix(tst_unicode)
-      IF(NOT MSVC)
+      IF(NOT MSVC AND NOT MINGW)
         # These tests do not work under windows
         add_sh_test(ncdump test_unicode_directory)
         add_sh_test(ncdump test_unicode_path)
-      ENDIF(NOT MSVC)
+      ENDIF()
     ENDIF(HAVE_BASH)
   ENDIF(USE_HDF5)