1. mzR
  2. Commit c3b3a15623a36a1b60552ce25a2301e0a425b399
Browse code

Merge branch 'master' into devel

* master:
bump version
add netcdf static lib; potential incompatibility

From: Laurent <lg390@cam.ac.uk>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR@121358 bc3139a8-67e5-0310-9ffc-ced21a209358

Laurent Gatto authored on 26/09/2016 08:01:40
Showing 4 changed files
DESCRIPTION
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... ... 
@@ -2,7 +2,7 @@ Package: mzR
2 2 
 Type: Package
3 3 
 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files
4 4 
        (mass spectrometry data)
5 
-Version: 2.7.6
5 
+Version: 2.7.7
6 6 
 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou
7 7 
 Maintainer: Bernd Fischer <b.fischer@dkfz.de>,
8 8 
 	    Steffen Neumann <sneumann@ipb-halle.de>,
NEWS
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... ... 
@@ -1,3 +1,7 @@
1 
+CHANGES IN VERSION 2.7.7
2 
+------------------------
3 
+ o add netcdf static lib; potential incompatibility <2016-09-22 Thu>
4 
+
1 5 
 CHANGES IN VERSION 2.7.6
2 6 
 ------------------------
3 7 
  o new isolationWindow accessor <2016-09-23 Fri>
src/win/i386/libnetcdf.a
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4 8 
new file mode 100644
5 9 
Binary files /dev/null and b/src/win/i386/libnetcdf.a differ
src/win/i386/netcdf.h
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new file mode 100644
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@@ -0,0 +1,1099 @@
1 
+/*
2 
+ * Copyright 1993-2005 University Corporation for Atmospheric Research/Unidata
3 
+ *
4 
+ * Portions of this software were developed by the Unidata Program at the
5 
+ * University Corporation for Atmospheric Research.
6 
+ *
7 
+ * Access and use of this software shall impose the following obligations
8 
+ * and understandings on the user. The user is granted the right, without
9 
+ * any fee or cost, to use, copy, modify, alter, enhance and distribute
10 
+ * this software, and any derivative works thereof, and its supporting
11 
+ * documentation for any purpose whatsoever, provided that this entire
12 
+ * notice appears in all copies of the software, derivative works and
13 
+ * supporting documentation.  Further, UCAR requests that the user credit
14 
+ * UCAR/Unidata in any publications that result from the use of this
15 
+ * software or in any product that includes this software. The names UCAR
16 
+ * and/or Unidata, however, may not be used in any advertising or publicity
17 
+ * to endorse or promote any products or commercial entity unless specific
18 
+ * written permission is obtained from UCAR/Unidata. The user also
19 
+ * understands that UCAR/Unidata is not obligated to provide the user with
20 
+ * any support, consulting, training or assistance of any kind with regard
21 
+ * to the use, operation and performance of this software nor to provide
22 
+ * the user with any updates, revisions, new versions or "bug fixes."
23 
+ *
24 
+ * THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
25 
+ * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
26 
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
27 
+ * DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
28 
+ * INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
29 
+ * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
30 
+ * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
31 
+ * WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
32 
+ */
33 
+/* "$Id: netcdf.h,v 2.116 2007/01/17 22:51:41 ed Exp $" */
34 
+
35 
+#ifndef _NETCDF_
36 
+#define _NETCDF_
37 
+
38 
+#include <stddef.h> /* size_t, ptrdiff_t */
39 
+#include <errno.h>  /* netcdf functions sometimes return system errors */
40 
+
41 
+#if defined(__cplusplus)
42 
+extern "C" {
43 
+#endif
44 
+
45 
+/*
46 
+ *  The netcdf external data types
47 
+ */
48 
+typedef enum {
49 
+	NC_NAT =	0,	/* NAT = 'Not A Type' (c.f. NaN) */
50 
+	NC_BYTE =	1,	/* signed 1 byte integer */
51 
+	NC_CHAR =	2,	/* ISO/ASCII character */
52 
+	NC_SHORT =	3,	/* signed 2 byte integer */
53 
+	NC_INT =	4,	/* signed 4 byte integer */
54 
+	NC_FLOAT =	5,	/* single precision floating point number */
55 
+	NC_DOUBLE =	6	/* double precision floating point number */
56 
+} nc_type;
57 
+
58 
+
59 
+/*
60 
+ * 	Default fill values, used unless _FillValue attribute is set.
61 
+ * These values are stuffed into newly allocated space as appropriate.
62 
+ * The hope is that one might use these to notice that a particular datum
63 
+ * has not been set.
64 
+ */
65 
+#define NC_FILL_BYTE	((signed char)-127)
66 
+#define NC_FILL_CHAR	((char)0)
67 
+#define NC_FILL_SHORT	((short)-32767)
68 
+#define NC_FILL_INT	(-2147483647L)
69 
+#define NC_FILL_FLOAT	(9.9692099683868690e+36f) /* near 15 * 2^119 */
70 
+#define NC_FILL_DOUBLE	(9.9692099683868690e+36)
71 
+
72 
+
73 
+/*
74 
+ * The above values are defaults.
75 
+ * If you wish a variable to use a different value than the above
76 
+ * defaults, create an attribute with the same type as the variable
77 
+ * and the following reserved name. The value you give the attribute
78 
+ * will be used as the fill value for that variable.
79 
+ */
80 
+#define _FillValue	"_FillValue"
81 
+#define NC_FILL		0	/* argument to ncsetfill to clear NC_NOFILL */
82 
+#define NC_NOFILL	0x100	/* Don't fill data section an records */
83 
+
84 
+/*
85 
+ * 'mode' flags for ncopen
86 
+ */
87 
+#define NC_NOWRITE	0	/* default is read only */
88 
+#define NC_WRITE    	0x1	/* read & write */
89 
+
90 
+/*
91 
+ * 'mode' flags for nccreate
92 
+ */
93 
+#define NC_CLOBBER	0
94 
+#define NC_NOCLOBBER	0x4	/* Don't destroy existing file on create */
95 
+#define NC_64BIT_OFFSET 0x0200  /* Use large (64-bit) file offsets */
96 
+
97 
+/*
98 
+ * 'mode' flags for nccreate and ncopen
99 
+ */
100 
+#define NC_SHARE	0x0800	/* Share updates, limit cacheing */
101 
+#define NC_STRICT_NC3  (0x8)
102 
+
103 
+/* The following flag currently is ignored, but use in
104 
+ * nc_open() or nc_create() may someday support use of advisory
105 
+ * locking to prevent multiple writers from clobbering a file
106 
+ */
107 
+#define NC_LOCK		0x0400	/* Use locking if available */
108 
+
109 
+/*
110 
+ * Starting with version 3.6, there were two different format netCDF
111 
+ * files.  netCDF-4 introduces the third one.
112 
+ */
113 
+#define NC_FORMAT_CLASSIC (1)
114 
+#define NC_FORMAT_64BIT   (2)
115 
+#define NC_FORMAT_NETCDF4 (3)
116 
+#define NC_FORMAT_NETCDF4_CLASSIC  (4) /* create netcdf-4 files, with NC_STRICT_NC3. */
117 
+
118 
+/*
119 
+ * Let nc__create() or nc__open() figure out
120 
+ * as suitable chunk size.
121 
+ */
122 
+#define NC_SIZEHINT_DEFAULT 0
123 
+
124 
+/*
125 
+ * In nc__enddef(), align to the chunk size.
126 
+ */
127 
+#define NC_ALIGN_CHUNK ((size_t)(-1))
128 
+
129 
+/*
130 
+ * 'size' argument to ncdimdef for an unlimited dimension
131 
+ */
132 
+#define NC_UNLIMITED 0L
133 
+
134 
+/*
135 
+ * attribute id to put/get a global attribute
136 
+ */
137 
+#define NC_GLOBAL -1
138 
+
139 
+/* These are in support of the coordinate axis stuff. */
140 
+#define NC_NOAXISTYPE 0
141 
+#define NC_LATITUDE 1
142 
+#define NC_LONGITUDE 2
143 
+#define NC_GEOX 3
144 
+#define NC_GEOY 4
145 
+#define NC_GEOZ 5
146 
+#define NC_HEIGHT_UP 6
147 
+#define NC_HEIGHT_DOWN 7
148 
+#define NC_PRESSURE 8
149 
+#define NC_TIME 9
150 
+#define NC_RADAZ 10
151 
+#define NC_RADEL 11
152 
+#define NC_RADDIST 12
153 
+
154 
+/*
155 
+ * These maximums are enforced by the interface, to facilitate writing
156 
+ * applications and utilities.  However, nothing is statically allocated to
157 
+ * these sizes internally.
158 
+ */
159 
+#define NC_MAX_DIMS	1024	 /* max dimensions per file */
160 
+#define NC_MAX_ATTRS	8192	 /* max global or per variable attributes */
161 
+#define NC_MAX_VARS	8192	 /* max variables per file */
162 
+#define NC_MAX_NAME	256	 /* max length of a name */
163 
+#define NC_MAX_VAR_DIMS	NC_MAX_DIMS /* max per variable dimensions */
164 
+
165 
+/*
166 
+ * The netcdf version 3 functions all return integer error status.
167 
+ * These are the possible values, in addition to certain
168 
+ * values from the system errno.h.
169 
+ */
170 
+
171 
+#define NC_ISSYSERR(err)	((err) > 0)
172 
+
173 
+#define	NC_NOERR	0	/* No Error */
174 
+
175 
+#define NC2_ERR         (-1)    /* Returned for all errors in the v2 API. */
176 
+#define	NC_EBADID	(-33)	/* Not a netcdf id */
177 
+#define	NC_ENFILE	(-34)	/* Too many netcdfs open */
178 
+#define	NC_EEXIST	(-35)	/* netcdf file exists && NC_NOCLOBBER */
179 
+#define	NC_EINVAL	(-36)	/* Invalid Argument */
180 
+#define	NC_EPERM	(-37)	/* Write to read only */
181 
+#define	NC_ENOTINDEFINE	(-38)	/* Operation not allowed in data mode */
182 
+#define	NC_EINDEFINE	(-39)	/* Operation not allowed in define mode */
183 
+#define	NC_EINVALCOORDS	(-40)	/* Index exceeds dimension bound */
184 
+#define	NC_EMAXDIMS	(-41)	/* NC_MAX_DIMS exceeded */
185 
+#define	NC_ENAMEINUSE	(-42)	/* String match to name in use */
186 
+#define NC_ENOTATT	(-43)	/* Attribute not found */
187 
+#define	NC_EMAXATTS	(-44)	/* NC_MAX_ATTRS exceeded */
188 
+#define NC_EBADTYPE	(-45)	/* Not a netcdf data type */
189 
+#define NC_EBADDIM	(-46)	/* Invalid dimension id or name */
190 
+#define NC_EUNLIMPOS	(-47)	/* NC_UNLIMITED in the wrong index */
191 
+#define	NC_EMAXVARS	(-48)	/* NC_MAX_VARS exceeded */
192 
+#define NC_ENOTVAR	(-49)	/* Variable not found */
193 
+#define NC_EGLOBAL	(-50)	/* Action prohibited on NC_GLOBAL varid */
194 
+#define NC_ENOTNC	(-51)	/* Not a netcdf file */
195 
+#define NC_ESTS        	(-52)	/* In Fortran, string too short */
196 
+#define NC_EMAXNAME    	(-53)	/* NC_MAX_NAME exceeded */
197 
+#define NC_EUNLIMIT    	(-54)	/* NC_UNLIMITED size already in use */
198 
+#define NC_ENORECVARS  	(-55)	/* nc_rec op when there are no record vars */
199 
+#define NC_ECHAR	(-56)	/* Attempt to convert between text & numbers */
200 
+#define NC_EEDGE	(-57)	/* Start+count exceeds dimension bound */
201 
+#define NC_ESTRIDE	(-58)	/* Illegal stride */
202 
+#define NC_EBADNAME	(-59)	/* Attribute or variable name
203 
+                                         contains illegal characters */
204 
+/* N.B. following must match value in ncx.h */
205 
+#define NC_ERANGE	(-60)	/* Math result not representable */
206 
+#define NC_ENOMEM	(-61)	/* Memory allocation (malloc) failure */
207 
+
208 
+#define NC_EVARSIZE     (-62)   /* One or more variable sizes violate
209 
+				   format constraints */
210 
+#define NC_EDIMSIZE     (-63)   /* Invalid dimension size */
211 
+#define NC_ETRUNC       (-64)   /* File likely truncated or possibly corrupted */
212 
+
213 
+/*
214 
+ * The Interface
215 
+ */
216 
+
217 
+/* Declaration modifiers for DLL support (MSC et al) */
218 
+
219 
+#if defined(DLL_NETCDF) /* define when library is a DLL */
220 
+#  if defined(NC_DLL_EXPORT) /* define when building the library */
221 
+#   define MSC_EXTRA __declspec(dllexport)
222 
+#  else
223 
+#   define MSC_EXTRA __declspec(dllimport)
224 
+#  endif
225 
+#include <io.h>
226 
+#define lseek _lseeki64
227 
+#define off_t __int64
228 
+#define stat __stat64
229 
+#define fstat _fstat64
230 
+#else
231 
+#define MSC_EXTRA
232 
+#endif	/* defined(DLL_NETCDF) */
233 
+
234 
+# define EXTERNL extern MSC_EXTRA
235 
+
236 
+/* When netCDF is built as a DLL, this will export ncerr and
237 
+ * ncopts. When it is used as a DLL, it will import them. */
238 
+#if defined(DLL_NETCDF)
239 
+MSC_EXTRA int ncerr;
240 
+MSC_EXTRA int ncopts;
241 
+#endif
242 
+
243 
+EXTERNL const char *
244 
+nc_inq_libvers(void);
245 
+
246 
+EXTERNL const char *
247 
+nc_strerror(int ncerr);
248 
+
249 
+EXTERNL int
250 
+nc__create(const char *path, int cmode, size_t initialsz,
251 
+	 size_t *chunksizehintp, int *ncidp);
252 
+
253 
+EXTERNL int
254 
+nc_create(const char *path, int cmode, int *ncidp);
255 
+
256 
+EXTERNL int
257 
+nc__open(const char *path, int mode,
258 
+	size_t *chunksizehintp, int *ncidp);
259 
+
260 
+EXTERNL int
261 
+nc_open(const char *path, int mode, int *ncidp);
262 
+
263 
+EXTERNL int
264 
+nc_set_fill(int ncid, int fillmode, int *old_modep);
265 
+
266 
+EXTERNL int
267 
+nc_redef(int ncid);
268 
+
269 
+EXTERNL int
270 
+nc__enddef(int ncid, size_t h_minfree, size_t v_align,
271 
+	size_t v_minfree, size_t r_align);
272 
+
273 
+EXTERNL int
274 
+nc_enddef(int ncid);
275 
+
276 
+EXTERNL int
277 
+nc_sync(int ncid);
278 
+
279 
+EXTERNL int
280 
+nc_abort(int ncid);
281 
+
282 
+EXTERNL int
283 
+nc_close(int ncid);
284 
+
285 
+EXTERNL int
286 
+nc_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp);
287 
+
288 
+EXTERNL int
289 
+nc_inq_ndims(int ncid, int *ndimsp);
290 
+
291 
+EXTERNL int
292 
+nc_inq_nvars(int ncid, int *nvarsp);
293 
+
294 
+EXTERNL int
295 
+nc_inq_natts(int ncid, int *nattsp);
296 
+
297 
+EXTERNL int
298 
+nc_inq_unlimdim(int ncid, int *unlimdimidp);
299 
+
300 
+EXTERNL int
301 
+nc_set_default_format(int format, int *old_formatp);
302 
+
303 
+EXTERNL int
304 
+nc_inq_format(int ncid, int *formatp);
305 
+
306 
+/* Begin _dim */
307 
+
308 
+EXTERNL int
309 
+nc_def_dim(int ncid, const char *name, size_t len, int *idp);
310 
+
311 
+EXTERNL int
312 
+nc_inq_dimid(int ncid, const char *name, int *idp);
313 
+
314 
+EXTERNL int
315 
+nc_inq_dim(int ncid, int dimid, char *name, size_t *lenp);
316 
+
317 
+EXTERNL int
318 
+nc_inq_dimname(int ncid, int dimid, char *name);
319 
+
320 
+EXTERNL int
321 
+nc_inq_dimlen(int ncid, int dimid, size_t *lenp);
322 
+
323 
+EXTERNL int
324 
+nc_rename_dim(int ncid, int dimid, const char *name);
325 
+
326 
+/* End _dim */
327 
+/* Begin _att */
328 
+
329 
+EXTERNL int
330 
+nc_inq_att(int ncid, int varid, const char *name,
331 
+	   nc_type *xtypep, size_t *lenp);
332 
+
333 
+EXTERNL int
334 
+nc_inq_attid(int ncid, int varid, const char *name, int *idp);
335 
+
336 
+EXTERNL int
337 
+nc_inq_atttype(int ncid, int varid, const char *name, nc_type *xtypep);
338 
+
339 
+EXTERNL int
340 
+nc_inq_attlen(int ncid, int varid, const char *name, size_t *lenp);
341 
+
342 
+EXTERNL int
343 
+nc_inq_attname(int ncid, int varid, int attnum, char *name);
344 
+
345 
+EXTERNL int
346 
+nc_copy_att(int ncid_in, int varid_in, const char *name, int ncid_out, int varid_out);
347 
+
348 
+EXTERNL int
349 
+nc_rename_att(int ncid, int varid, const char *name, const char *newname);
350 
+
351 
+EXTERNL int
352 
+nc_del_att(int ncid, int varid, const char *name);
353 
+
354 
+/* End _att */
355 
+/* Begin {put,get}_att */
356 
+
357 
+EXTERNL int
358 
+nc_put_att(int ncid, int varid, const char *name, nc_type datatype,
359 
+	   size_t len, const void *value);
360 
+
361 
+EXTERNL int
362 
+nc_get_att(int ncid, int varid, const char *name, void *value);
363 
+
364 
+EXTERNL int
365 
+nc_put_att_text(int ncid, int varid, const char *name,
366 
+		size_t len, const char *op);
367 
+
368 
+EXTERNL int
369 
+nc_get_att_text(int ncid, int varid, const char *name, char *ip);
370 
+
371 
+EXTERNL int
372 
+nc_put_att_uchar(int ncid, int varid, const char *name, nc_type xtype,
373 
+	size_t len, const unsigned char *op);
374 
+
375 
+EXTERNL int
376 
+nc_get_att_uchar(int ncid, int varid, const char *name, unsigned char *ip);
377 
+
378 
+EXTERNL int
379 
+nc_put_att_schar(int ncid, int varid, const char *name, nc_type xtype,
380 
+	size_t len, const signed char *op);
381 
+
382 
+EXTERNL int
383 
+nc_get_att_schar(int ncid, int varid, const char *name, signed char *ip);
384 
+
385 
+EXTERNL int
386 
+nc_put_att_short(int ncid, int varid, const char *name, nc_type xtype,
387 
+	size_t len, const short *op);
388 
+
389 
+EXTERNL int
390 
+nc_get_att_short(int ncid, int varid, const char *name, short *ip);
391 
+
392 
+EXTERNL int
393 
+nc_put_att_int(int ncid, int varid, const char *name, nc_type xtype,
394 
+	size_t len, const int *op);
395 
+
396 
+EXTERNL int
397 
+nc_get_att_int(int ncid, int varid, const char *name, int *ip);
398 
+
399 
+EXTERNL int
400 
+nc_put_att_long(int ncid, int varid, const char *name, nc_type xtype,
401 
+	size_t len, const long *op);
402 
+
403 
+EXTERNL int
404 
+nc_get_att_long(int ncid, int varid, const char *name, long *ip);
405 
+
406 
+EXTERNL int
407 
+nc_put_att_float(int ncid, int varid, const char *name, nc_type xtype,
408 
+	size_t len, const float *op);
409 
+
410 
+EXTERNL int
411 
+nc_get_att_float(int ncid, int varid, const char *name, float *ip);
412 
+
413 
+EXTERNL int
414 
+nc_put_att_double(int ncid, int varid, const char *name, nc_type xtype,
415 
+	size_t len, const double *op);
416 
+
417 
+EXTERNL int
418 
+nc_get_att_double(int ncid, int varid, const char *name, double *ip);
419 
+
420 
+/* End {put,get}_att */
421 
+/* Begin _var */
422 
+
423 
+EXTERNL int
424 
+nc_def_var(int ncid, const char *name, nc_type xtype, int ndims,
425 
+	   const int *dimidsp, int *varidp);
426 
+
427 
+EXTERNL int
428 
+nc_inq_var(int ncid, int varid, char *name, nc_type *xtypep,
429 
+	   int *ndimsp, int *dimidsp, int *nattsp);
430 
+
431 
+EXTERNL int
432 
+nc_inq_varid(int ncid, const char *name, int *varidp);
433 
+
434 
+EXTERNL int
435 
+nc_inq_varname(int ncid, int varid, char *name);
436 
+
437 
+EXTERNL int
438 
+nc_inq_vartype(int ncid, int varid, nc_type *xtypep);
439 
+
440 
+EXTERNL int
441 
+nc_inq_varndims(int ncid, int varid, int *ndimsp);
442 
+
443 
+EXTERNL int
444 
+nc_inq_vardimid(int ncid, int varid, int *dimidsp);
445 
+
446 
+EXTERNL int
447 
+nc_inq_varnatts(int ncid, int varid, int *nattsp);
448 
+
449 
+EXTERNL int
450 
+nc_rename_var(int ncid, int varid, const char *name);
451 
+
452 
+EXTERNL int
453 
+nc_copy_var(int ncid_in, int varid, int ncid_out);
454 
+#ifndef ncvarcpy
455 
+/* support the old name for now */
456 
+#define ncvarcpy(ncid_in, varid, ncid_out) ncvarcopy((ncid_in), (varid), (ncid_out))
457 
+#endif
458 
+
459 
+/* End _var */
460 
+/* Begin {put,get}_var1 */
461 
+
462 
+EXTERNL int
463 
+nc_put_var1(int ncid, int varid, const size_t *indexp, const void *value);
464 
+
465 
+EXTERNL int
466 
+nc_get_var1(int ncid, int varid, const size_t *indexp, void *value);
467 
+
468 
+EXTERNL int
469 
+nc_put_var1_text(int ncid, int varid, const size_t *indexp, const char *op);
470 
+
471 
+EXTERNL int
472 
+nc_get_var1_text(int ncid, int varid, const size_t *indexp, char *ip);
473 
+
474 
+EXTERNL int
475 
+nc_put_var1_uchar(int ncid, int varid, const size_t *indexp,
476 
+	const unsigned char *op);
477 
+
478 
+EXTERNL int
479 
+nc_get_var1_uchar(int ncid, int varid, const size_t *indexp,
480 
+	unsigned char *ip);
481 
+
482 
+EXTERNL int
483 
+nc_put_var1_schar(int ncid, int varid, const size_t *indexp,
484 
+	const signed char *op);
485 
+
486 
+EXTERNL int
487 
+nc_get_var1_schar(int ncid, int varid, const size_t *indexp,
488 
+	signed char *ip);
489 
+
490 
+EXTERNL int
491 
+nc_put_var1_short(int ncid, int varid, const size_t *indexp,
492 
+	const short *op);
493 
+
494 
+EXTERNL int
495 
+nc_get_var1_short(int ncid, int varid, const size_t *indexp,
496 
+	short *ip);
497 
+
498 
+EXTERNL int
499 
+nc_put_var1_int(int ncid, int varid, const size_t *indexp, const int *op);
500 
+
501 
+EXTERNL int
502 
+nc_get_var1_int(int ncid, int varid, const size_t *indexp, int *ip);
503 
+
504 
+EXTERNL int
505 
+nc_put_var1_long(int ncid, int varid, const size_t *indexp, const long *op);
506 
+
507 
+EXTERNL int
508 
+nc_get_var1_long(int ncid, int varid, const size_t *indexp, long *ip);
509 
+
510 
+EXTERNL int
511 
+nc_put_var1_float(int ncid, int varid, const size_t *indexp, const float *op);
512 
+
513 
+EXTERNL int
514 
+nc_get_var1_float(int ncid, int varid, const size_t *indexp, float *ip);
515 
+
516 
+EXTERNL int
517 
+nc_put_var1_double(int ncid, int varid, const size_t *indexp, const double *op);
518 
+
519 
+EXTERNL int
520 
+nc_get_var1_double(int ncid, int varid, const size_t *indexp, double *ip);
521 
+
522 
+/* End {put,get}_var1 */
523 
+/* Begin {put,get}_vara */
524 
+
525 
+EXTERNL int
526 
+nc_put_vara(int ncid, int varid,
527 
+	 const size_t *start, const size_t *count, const void *value);
528 
+
529 
+EXTERNL int
530 
+nc_get_vara(int ncid, int varid,
531 
+	 const size_t *start, const size_t *count, void *value);
532 
+
533 
+EXTERNL int
534 
+nc_put_vara_text(int ncid, int varid,
535 
+	const size_t *startp, const size_t *countp, const char *op);
536 
+
537 
+EXTERNL int
538 
+nc_get_vara_text(int ncid, int varid,
539 
+	const size_t *startp, const size_t *countp, char *ip);
540 
+
541 
+EXTERNL int
542 
+nc_put_vara_uchar(int ncid, int varid,
543 
+	const size_t *startp, const size_t *countp, const unsigned char *op);
544 
+
545 
+EXTERNL int
546 
+nc_get_vara_uchar(int ncid, int varid,
547 
+	const size_t *startp, const size_t *countp, unsigned char *ip);
548 
+
549 
+EXTERNL int
550 
+nc_put_vara_schar(int ncid, int varid,
551 
+	const size_t *startp, const size_t *countp, const signed char *op);
552 
+
553 
+EXTERNL int
554 
+nc_get_vara_schar(int ncid, int varid,
555 
+	const size_t *startp, const size_t *countp, signed char *ip);
556 
+
557 
+EXTERNL int
558 
+nc_put_vara_short(int ncid, int varid,
559 
+	const size_t *startp, const size_t *countp, const short *op);
560 
+
561 
+EXTERNL int
562 
+nc_get_vara_short(int ncid, int varid,
563 
+	const size_t *startp, const size_t *countp, short *ip);
564 
+
565 
+EXTERNL int
566 
+nc_put_vara_int(int ncid, int varid,
567 
+	const size_t *startp, const size_t *countp, const int *op);
568 
+
569 
+EXTERNL int
570 
+nc_get_vara_int(int ncid, int varid,
571 
+	const size_t *startp, const size_t *countp, int *ip);
572 
+
573 
+EXTERNL int
574 
+nc_put_vara_long(int ncid, int varid,
575 
+	const size_t *startp, const size_t *countp, const long *op);
576 
+
577 
+EXTERNL int
578 
+nc_get_vara_long(int ncid, int varid,
579 
+	const size_t *startp, const size_t *countp, long *ip);
580 
+
581 
+EXTERNL int
582 
+nc_put_vara_float(int ncid, int varid,
583 
+	const size_t *startp, const size_t *countp, const float *op);
584 
+
585 
+EXTERNL int
586 
+nc_get_vara_float(int ncid, int varid,
587 
+	const size_t *startp, const size_t *countp, float *ip);
588 
+
589 
+EXTERNL int
590 
+nc_put_vara_double(int ncid, int varid,
591 
+	const size_t *startp, const size_t *countp, const double *op);
592 
+
593 
+EXTERNL int
594 
+nc_get_vara_double(int ncid, int varid,
595 
+	const size_t *startp, const size_t *countp, double *ip);
596 
+
597 
+/* End {put,get}_vara */
598 
+/* Begin {put,get}_vars */
599 
+
600 
+EXTERNL int
601 
+nc_put_vars(int ncid, int varid,
602 
+	 const size_t *start, const size_t *count, const ptrdiff_t *stride,
603 
+	 const void * value);
604 
+
605 
+EXTERNL int
606 
+nc_get_vars(int ncid, int varid,
607 
+	 const size_t *start, const size_t *count, const ptrdiff_t *stride,
608 
+	 void * value);
609 
+
610 
+EXTERNL int
611 
+nc_put_vars_text(int ncid, int varid,
612 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
613 
+	const char *op);
614 
+
615 
+EXTERNL int
616 
+nc_get_vars_text(int ncid, int varid,
617 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
618 
+	char *ip);
619 
+
620 
+EXTERNL int
621 
+nc_put_vars_uchar(int ncid, int varid,
622 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
623 
+	const unsigned char *op);
624 
+
625 
+EXTERNL int
626 
+nc_get_vars_uchar(int ncid, int varid,
627 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
628 
+	unsigned char *ip);
629 
+
630 
+EXTERNL int
631 
+nc_put_vars_schar(int ncid, int varid,
632 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
633 
+	const signed char *op);
634 
+
635 
+EXTERNL int
636 
+nc_get_vars_schar(int ncid, int varid,
637 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
638 
+	signed char *ip);
639 
+
640 
+EXTERNL int
641 
+nc_put_vars_short(int ncid, int varid,
642 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
643 
+	const short *op);
644 
+
645 
+EXTERNL int
646 
+nc_get_vars_short(int ncid, int varid,
647 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
648 
+	short *ip);
649 
+
650 
+EXTERNL int
651 
+nc_put_vars_int(int ncid, int varid,
652 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
653 
+	const int *op);
654 
+
655 
+EXTERNL int
656 
+nc_get_vars_int(int ncid, int varid,
657 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
658 
+	int *ip);
659 
+
660 
+EXTERNL int
661 
+nc_put_vars_long(int ncid, int varid,
662 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
663 
+	const long *op);
664 
+
665 
+EXTERNL int
666 
+nc_get_vars_long(int ncid, int varid,
667 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
668 
+	long *ip);
669 
+
670 
+EXTERNL int
671 
+nc_put_vars_float(int ncid, int varid,
672 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
673 
+	const float *op);
674 
+
675 
+EXTERNL int
676 
+nc_get_vars_float(int ncid, int varid,
677 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
678 
+	float *ip);
679 
+
680 
+EXTERNL int
681 
+nc_put_vars_double(int ncid, int varid,
682 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
683 
+	const double *op);
684 
+
685 
+EXTERNL int
686 
+nc_get_vars_double(int ncid, int varid,
687 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
688 
+	double *ip);
689 
+
690 
+/* End {put,get}_vars */
691 
+/* Begin {put,get}_varm */
692 
+
693 
+EXTERNL int
694 
+nc_put_varm(int ncid, int varid, const size_t *start, const size_t *count,
695 
+            const ptrdiff_t *stride, const ptrdiff_t *imapp,
696 
+	    const void *value);
697 
+
698 
+EXTERNL int
699 
+nc_get_varm(int ncid, int varid, const size_t *start, const size_t *count,
700 
+	    const ptrdiff_t *stride, const ptrdiff_t *imapp, void *value);
701 
+
702 
+EXTERNL int
703 
+nc_put_varm_text(int ncid, int varid,
704 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
705 
+	const ptrdiff_t *imapp,
706 
+	const char *op);
707 
+
708 
+EXTERNL int
709 
+nc_get_varm_text(int ncid, int varid,
710 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
711 
+	const ptrdiff_t *imapp,
712 
+	char *ip);
713 
+
714 
+EXTERNL int
715 
+nc_put_varm_uchar(int ncid, int varid,
716 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
717 
+	const ptrdiff_t *imapp,
718 
+	const unsigned char *op);
719 
+
720 
+EXTERNL int
721 
+nc_get_varm_uchar(int ncid, int varid,
722 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
723 
+	const ptrdiff_t *imapp,
724 
+	unsigned char *ip);
725 
+
726 
+EXTERNL int
727 
+nc_put_varm_schar(int ncid, int varid,
728 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
729 
+	const ptrdiff_t *imapp,
730 
+	const signed char *op);
731 
+
732 
+EXTERNL int
733 
+nc_get_varm_schar(int ncid, int varid,
734 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
735 
+	const ptrdiff_t *imapp,
736 
+	signed char *ip);
737 
+
738 
+EXTERNL int
739 
+nc_put_varm_short(int ncid, int varid,
740 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
741 
+	const ptrdiff_t *imapp,
742 
+	const short *op);
743 
+
744 
+EXTERNL int
745 
+nc_get_varm_short(int ncid, int varid,
746 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
747 
+	const ptrdiff_t *imapp,
748 
+	short *ip);
749 
+
750 
+EXTERNL int
751 
+nc_put_varm_int(int ncid, int varid,
752 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
753 
+	const ptrdiff_t *imapp,
754 
+	const int *op);
755 
+
756 
+EXTERNL int
757 
+nc_get_varm_int(int ncid, int varid,
758 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
759 
+	const ptrdiff_t *imapp,
760 
+	int *ip);
761 
+
762 
+EXTERNL int
763 
+nc_put_varm_long(int ncid, int varid,
764 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
765 
+	const ptrdiff_t *imapp,
766 
+	const long *op);
767 
+
768 
+EXTERNL int
769 
+nc_get_varm_long(int ncid, int varid,
770 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
771 
+	const ptrdiff_t *imapp,
772 
+	long *ip);
773 
+
774 
+EXTERNL int
775 
+nc_put_varm_float(int ncid, int varid,
776 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
777 
+	const ptrdiff_t *imapp,
778 
+	const float *op);
779 
+
780 
+EXTERNL int
781 
+nc_get_varm_float(int ncid, int varid,
782 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
783 
+	const ptrdiff_t *imapp,
784 
+	float *ip);
785 
+
786 
+EXTERNL int
787 
+nc_put_varm_double(int ncid, int varid,
788 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
789 
+	const ptrdiff_t *imapp,
790 
+	const double *op);
791 
+
792 
+EXTERNL int
793 
+nc_get_varm_double(int ncid, int varid,
794 
+	const size_t *startp, const size_t *countp, const ptrdiff_t *stridep,
795 
+	const ptrdiff_t * imapp,
796 
+	double *ip);
797 
+
798 
+/* End {put,get}_varm */
799 
+/* Begin {put,get}_var */
800 
+
801 
+EXTERNL int
802 
+nc_put_var_text(int ncid, int varid, const char *op);
803 
+
804 
+EXTERNL int
805 
+nc_get_var_text(int ncid, int varid, char *ip);
806 
+
807 
+EXTERNL int
808 
+nc_put_var_uchar(int ncid, int varid, const unsigned char *op);
809 
+
810 
+EXTERNL int
811 
+nc_get_var_uchar(int ncid, int varid, unsigned char *ip);
812 
+
813 
+EXTERNL int
814 
+nc_put_var_schar(int ncid, int varid, const signed char *op);
815 
+
816 
+EXTERNL int
817 
+nc_get_var_schar(int ncid, int varid, signed char *ip);
818 
+
819 
+EXTERNL int
820 
+nc_put_var_short(int ncid, int varid, const short *op);
821 
+
822 
+EXTERNL int
823 
+nc_get_var_short(int ncid, int varid, short *ip);
824 
+
825 
+EXTERNL int
826 
+nc_put_var_int(int ncid, int varid, const int *op);
827 
+
828 
+EXTERNL int
829 
+nc_get_var_int(int ncid, int varid, int *ip);
830 
+
831 
+EXTERNL int
832 
+nc_put_var_long(int ncid, int varid, const long *op);
833 
+
834 
+EXTERNL int
835 
+nc_get_var_long(int ncid, int varid, long *ip);
836 
+
837 
+EXTERNL int
838 
+nc_put_var_float(int ncid, int varid, const float *op);
839 
+
840 
+EXTERNL int
841 
+nc_get_var_float(int ncid, int varid, float *ip);
842 
+
843 
+EXTERNL int
844 
+nc_put_var_double(int ncid, int varid, const double *op);
845 
+
846 
+EXTERNL int
847 
+nc_get_var_double(int ncid, int varid, double *ip);
848 
+
849 
+#ifdef LOGGING
850 
+
851 
+#ifdef DEBUG
852 
+EXTERNL void
853 
+nc_exit(void);
854 
+#endif
855 
+
856 
+EXTERNL void
857 
+nc_set_log_level(int new_level);
858 
+/* Use this to turn off logging by calling
859 
+   nc_log_level(NC_TURN_OFF_LOGGING) */
860 
+#define NC_TURN_OFF_LOGGING (-1)
861 
+
862 
+#else /* not LOGGING */
863 
+
864 
+#define nc_set_log_level(e)
865 
+
866 
+#endif
867 
+
868 
+/* End {put,get}_var */
869 
+
870 
+/* #ifdef _CRAYMPP */
871 
+/*
872 
+ * Public interfaces to better support
873 
+ * CRAY multi-processor systems like T3E.
874 
+ * A tip of the hat to NERSC.
875 
+ */
876 
+/*
877 
+ * It turns out we need to declare and define
878 
+ * these public interfaces on all platforms
879 
+ * or things get ugly working out the
880 
+ * FORTRAN interface. On !_CRAYMPP platforms,
881 
+ * these functions work as advertised, but you
882 
+ * can only use "processor element" 0.
883 
+ */
884 
+
885 
+EXTERNL int
886 
+nc__create_mp(const char *path, int cmode, size_t initialsz, int basepe,
887 
+	 size_t *chunksizehintp, int *ncidp);
888 
+
889 
+EXTERNL int
890 
+nc__open_mp(const char *path, int mode, int basepe,
891 
+	size_t *chunksizehintp, int *ncidp);
892 
+
893 
+EXTERNL int
894 
+nc_delete(const char * path);
895 
+
896 
+EXTERNL int
897 
+nc_delete_mp(const char * path, int basepe);
898 
+
899 
+EXTERNL int
900 
+nc_set_base_pe(int ncid, int pe);
901 
+
902 
+EXTERNL int
903 
+nc_inq_base_pe(int ncid, int *pe);
904 
+
905 
+/* #endif _CRAYMPP */
906 
+
907 
+/* Begin v2.4 backward compatiblity */
908 
+/*
909 
+ * defining NO_NETCDF_2 to the preprocessor
910 
+ * turns off backward compatiblity declarations.
911 
+ */
912 
+#ifndef NO_NETCDF_2
913 
+
914 
+/*
915 
+ * Backward compatible aliases
916 
+ */
917 
+#define FILL_BYTE	NC_FILL_BYTE
918 
+#define FILL_CHAR	NC_FILL_CHAR
919 
+#define FILL_SHORT	NC_FILL_SHORT
920 
+#define FILL_LONG	NC_FILL_INT
921 
+#define FILL_FLOAT	NC_FILL_FLOAT
922 
+#define FILL_DOUBLE	NC_FILL_DOUBLE
923 
+
924 
+#define MAX_NC_DIMS	NC_MAX_DIMS
925 
+#define MAX_NC_ATTRS	NC_MAX_ATTRS
926 
+#define MAX_NC_VARS	NC_MAX_VARS
927 
+#define MAX_NC_NAME	NC_MAX_NAME
928 
+#define MAX_VAR_DIMS	NC_MAX_VAR_DIMS
929 
+
930 
+/*
931 
+ * If and when 64 integer types become ubiquitous,
932 
+ * we would like to use NC_LONG for that.
933 
+ * For now, define for backward compatibility.
934 
+ */
935 
+#define NC_LONG NC_INT
936 
+
937 
+/*
938 
+ * Global error status
939 
+ */
940 
+EXTERNL int ncerr;
941 
+
942 
+#define NC_ENTOOL       NC_EMAXNAME   /* Backward compatibility */
943 
+#define	NC_EXDR		(-32)	/* */
944 
+#define	NC_SYSERR	(-31)
945 
+
946 
+/*
947 
+ * Avoid use of this meaningless macro
948 
+ * Use sysconf(_SC_OPEN_MAX).
949 
+ */
950 
+#ifndef MAX_NC_OPEN
951 
+#define MAX_NC_OPEN 32
952 
+#endif
953 
+
954 
+/*
955 
+ * Global options variable.
956 
+ * Used to determine behavior of error handler.
957 
+ */
958 
+#define	NC_FATAL	1
959 
+#define	NC_VERBOSE	2
960 
+
961 
+EXTERNL int ncopts;	/* default is (NC_FATAL | NC_VERBOSE) */
962 
+
963 
+EXTERNL void
964 
+nc_advise(const char *cdf_routine_name, int err, const char *fmt,...);
965 
+
966 
+/*
967 
+ * C data type corresponding to a netCDF NC_LONG argument,
968 
+ * a signed 32 bit object.
969 
+ *
970 
+ * This is the only thing in this file which architecture dependent.
971 
+ */
972 
+typedef int nclong;
973 
+
974 
+EXTERNL int
975 
+nctypelen(nc_type datatype);
976 
+
977 
+EXTERNL int
978 
+nccreate(const char* path, int cmode);
979 
+
980 
+EXTERNL int
981 
+ncopen(const char* path, int mode);
982 
+
983 
+EXTERNL int
984 
+ncsetfill(int ncid, int fillmode);
985 
+
986 
+EXTERNL int
987 
+ncredef(int ncid);
988 
+
989 
+EXTERNL int
990 
+ncendef(int ncid);
991 
+
992 
+EXTERNL int
993 
+ncsync(int ncid);
994 
+
995 
+EXTERNL int
996 
+ncabort(int ncid);
997 
+
998 
+EXTERNL int
999 
+ncclose(int ncid);
1000 
+
1001 
+EXTERNL int
1002 
+ncinquire(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimp);
1003 
+
1004 
+EXTERNL int
1005 
+ncdimdef(int ncid, const char *name, long len);
1006 
+
1007 
+EXTERNL int
1008 
+ncdimid(int ncid, const char *name);
1009 
+
1010 
+EXTERNL int
1011 
+ncdiminq(int ncid, int dimid, char *name, long *lenp);
1012 
+
1013 
+EXTERNL int
1014 
+ncdimrename(int ncid, int dimid, const char *name);
1015 
+
1016 
+EXTERNL int
1017 
+ncattput(int ncid, int varid, const char *name, nc_type xtype,
1018 
+	int len, const void *op);
1019 
+
1020 
+EXTERNL int
1021 
+ncattinq(int ncid, int varid, const char *name, nc_type *xtypep, int *lenp);
1022 
+
1023 
+EXTERNL int
1024 
+ncattget(int ncid, int varid, const char *name, void *ip);
1025 
+
1026 
+EXTERNL int
1027 
+ncattcopy(int ncid_in, int varid_in, const char *name, int ncid_out,
1028 
+	int varid_out);
1029 
+
1030 
+EXTERNL int
1031 
+ncattname(int ncid, int varid, int attnum, char *name);
1032 
+
1033 
+EXTERNL int
1034 
+ncattrename(int ncid, int varid, const char *name, const char *newname);
1035 
+
1036 
+EXTERNL int
1037 
+ncattdel(int ncid, int varid, const char *name);
1038 
+
1039 
+EXTERNL int
1040 
+ncvardef(int ncid, const char *name, nc_type xtype,
1041 
+	int ndims, const int *dimidsp);
1042 
+
1043 
+EXTERNL int
1044 
+ncvarid(int ncid, const char *name);
1045 
+
1046 
+EXTERNL int
1047 
+ncvarinq(int ncid, int varid, char *name, nc_type *xtypep,
1048 
+	int *ndimsp, int *dimidsp, int *nattsp);
1049 
+
1050 
+EXTERNL int
1051 
+ncvarput1(int ncid, int varid, const long *indexp, const void *op);
1052 
+
1053 
+EXTERNL int
1054 
+ncvarget1(int ncid, int varid, const long *indexp, void *ip);
1055 
+
1056 
+EXTERNL int
1057 
+ncvarput(int ncid, int varid, const long *startp, const long *countp,
1058 
+	const void *op);
1059 
+
1060 
+EXTERNL int
1061 
+ncvarget(int ncid, int varid, const long *startp, const long *countp,
1062 
+	void *ip);
1063 
+
1064 
+EXTERNL int
1065 
+ncvarputs(int ncid, int varid, const long *startp, const long *countp,
1066 
+	const long *stridep, const void *op);
1067 
+
1068 
+EXTERNL int
1069 
+ncvargets(int ncid, int varid, const long *startp, const long *countp,
1070 
+	const long *stridep, void *ip);
1071 
+
1072 
+EXTERNL int
1073 
+ncvarputg(int ncid, int varid, const long *startp, const long *countp,
1074 
+	const long *stridep, const long *imapp, const void *op);
1075 
+
1076 
+EXTERNL int
1077 
+ncvargetg(int ncid, int varid, const long *startp, const long *countp,
1078 
+	const long *stridep, const long *imapp, void *ip);
1079 
+
1080 
+EXTERNL int
1081 
+ncvarrename(int ncid, int varid, const char *name);
1082 
+
1083 
+EXTERNL int
1084 
+ncrecinq(int ncid, int *nrecvarsp, int *recvaridsp, long *recsizesp);
1085 
+
1086 
+EXTERNL int
1087 
+ncrecget(int ncid, long recnum, void **datap);
1088 
+
1089 
+EXTERNL int
1090 
+ncrecput(int ncid, long recnum, void *const *datap);
1091 
+
1092 
+/* End v2.4 backward compatiblity */
1093 
+#endif /*!NO_NETCDF_2*/
1094 
+
1095 
+#if defined(__cplusplus)
1096 
+}
1097 
+#endif
1098 
+
1099 
+#endif /* _NETCDF_ */