[med-svn] r9732 - in trunk/packages/minc/trunk/debian: . patches
Steven Michael Robbins
smr at alioth.debian.org
Mon Feb 20 21:04:35 UTC 2012
Author: smr
Date: 2012-02-20 21:04:34 +0000 (Mon, 20 Feb 2012)
New Revision: 9732
Added:
trunk/packages/minc/trunk/debian/patches/read_file_names-refactor.patch
Removed:
trunk/packages/minc/trunk/debian/patches/mincaverage-pathmax.patch
Modified:
trunk/packages/minc/trunk/debian/changelog
trunk/packages/minc/trunk/debian/control
trunk/packages/minc/trunk/debian/patches/series
trunk/packages/minc/trunk/debian/rules
Log:
Refactor common PATH_MAX-using code, apply fix for case PATH_MAX is not defined.
Modified: trunk/packages/minc/trunk/debian/changelog
===================================================================
--- trunk/packages/minc/trunk/debian/changelog 2012-02-20 20:42:07 UTC (rev 9731)
+++ trunk/packages/minc/trunk/debian/changelog 2012-02-20 21:04:34 UTC (rev 9732)
@@ -1,3 +1,12 @@
+minc (2.1.00-5) unstable; urgency=low
+
+ * patches/mincaverage-pathmax.patch: Remove.
+ * patches/read_file_names-refactor.patch: New. Refactored duplicated
+ PATH_MAX-using code into library. Need to run autoreconf because
+ Makefile.am changed.
+
+ -- Steve M. Robbins <smr at debian.org> Mon, 20 Feb 2012 15:00:32 -0600
+
minc (2.1.00-4) unstable; urgency=low
* source/format: Set to 3.0 (quilt), so that patches are applied.
Modified: trunk/packages/minc/trunk/debian/control
===================================================================
--- trunk/packages/minc/trunk/debian/control 2012-02-20 20:42:07 UTC (rev 9731)
+++ trunk/packages/minc/trunk/debian/control 2012-02-20 21:04:34 UTC (rev 9732)
@@ -4,7 +4,7 @@
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steve M. Robbins <smr at debian.org>
-Build-Depends: debhelper (>= 9), autotools-dev, csh,
+Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf, csh,
libnetcdf-dev, zlib1g-dev, texlive-latex-base, libhdf5-dev
Standards-Version: 3.9.2
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/minc/trunk/
Deleted: trunk/packages/minc/trunk/debian/patches/mincaverage-pathmax.patch
===================================================================
--- trunk/packages/minc/trunk/debian/patches/mincaverage-pathmax.patch 2012-02-20 20:42:07 UTC (rev 9731)
+++ trunk/packages/minc/trunk/debian/patches/mincaverage-pathmax.patch 2012-02-20 21:04:34 UTC (rev 9732)
@@ -1,19 +0,0 @@
-Description: Work around missing PATH_MAX definition
-Author: Steve Robbins <smr at debian.org>
-Bug: n/a
-Forwarded: no
-
-
---- a/progs/mincaverage/mincaverage.c 2008-01-16 20:33:02.000000000 -0600
-+++ b/progs/mincaverage/mincaverage.c 2012-02-19 21:40:56.634227217 -0600
-@@ -1029,6 +1029,10 @@
- static char **read_file_names(char *filelist, int *num_files)
- {
- #define FILE_NAME_ALLOC_SIZE 10
-+#ifndef PATH_MAX
-+# define PATH_MAX 1024
-+#endif
-+
- char **files;
- int array_size;
- int nfiles;
Added: trunk/packages/minc/trunk/debian/patches/read_file_names-refactor.patch
===================================================================
--- trunk/packages/minc/trunk/debian/patches/read_file_names-refactor.patch (rev 0)
+++ trunk/packages/minc/trunk/debian/patches/read_file_names-refactor.patch 2012-02-20 21:04:34 UTC (rev 9732)
@@ -0,0 +1,593 @@
+Description: Work around missing PATH_MAX definition
+Author: Steve Robbins <smr at debian.org>
+Bug: n/a
+Forwarded: no
+
+--- minc-2.1.00.orig/Makefile.am
++++ minc-2.1.00/Makefile.am
+@@ -67,6 +67,7 @@
+ # not part of the installation.
+ #
+ noinst_HEADERS = \
++ libsrc/read_file_names.h \
+ libsrc/minc_basic.h \
+ libsrc/minc_config.h \
+ libsrc/minc_error.h \
+@@ -425,6 +426,7 @@
+ libminc2_la_LDFLAGS = -version-info 2:3:1
+ libminc2_la_SOURCES = \
+ libsrc/ParseArgv.c \
++ libsrc/read_file_names.c \
+ libsrc/dim_conversion.c \
+ libsrc/image_conversion.c \
+ libsrc/minc_convenience.c \
+--- /dev/null
++++ minc-2.1.00/libsrc/read_file_names.c
+@@ -0,0 +1,104 @@
++#if HAVE_CONFIG_H
++#include "config.h"
++#endif
++
++#include <stdio.h>
++#include <stdlib.h>
++#include <string.h>
++#include "read_file_names.h"
++
++#define FILE_NAME_ALLOC_SIZE 10
++
++#if defined(PATH_MAX)
++# define FILE_PATH_MAX PATH_MAX
++#else
++# define FILE_PATH_MAX 2046
++#endif
++
++
++
++/* ----------------------------- MNI Header -----------------------------------
++ at NAME : read_file_names
++ at INPUT : filelist - name of file from which to read names
++ at OUTPUT : num_files - number of files read in
++ at RETURNS : Pointer to a NULL-terminated array of file names
++ at DESCRIPTION: Reads in a list of file names from file filelist or stdin if
++ "-" is specified. Returns NULL if an error occurs. If
++ no error occurs, then a pointer to an empty array is
++ returned and num_files is zero.
++ at METHOD :
++ at GLOBALS :
++ at CALLS :
++ at CREATED : March 8, 1995 (Peter Neelin)
++ at MODIFIED :
++---------------------------------------------------------------------------- */
++char **read_file_names(char *filelist, int *num_files)
++{
++ char **files;
++ int array_size;
++ int nfiles;
++ FILE *fp;
++ char line[FILE_PATH_MAX+1];
++ int length;
++
++ /* Open the file */
++ if (strcmp(filelist, "-") == 0) {
++ fp = stdin;
++ }
++ else {
++ fp = fopen(filelist, "r");
++ if (fp == NULL) {
++ (void) fprintf(stderr, "Error opening file \"%s\"\n", filelist);
++ return NULL;
++ }
++ }
++
++ /* Allocate an initial array and NULL-terminate it */
++ array_size = FILE_NAME_ALLOC_SIZE;
++ files = malloc(sizeof(*files) * array_size);
++ if (files == NULL) {
++ (void) fprintf(stderr, "Error allocating memory\n");
++ return NULL;
++ }
++ nfiles = 0;
++ files[nfiles] = NULL;
++
++ /* Read in file names */
++ while (fgets(line, sizeof(line)/sizeof(line[0]), fp) != NULL) {
++
++ /* Remove a trailing newline and check that there is a name */
++ length = strlen(line);
++ if ((length > 0) && (line[length-1] == '\n')) {
++ line[length-1] = '\0';
++ length--;
++ }
++ if (length == 0) continue;
++
++ /* Make room for names if needed */
++ while (nfiles >= array_size-1) {
++ array_size += FILE_NAME_ALLOC_SIZE;
++ files = realloc(files, sizeof(*files) * array_size);
++ if (files == NULL) {
++ (void) fprintf(stderr, "Error allocating memory\n");
++ return NULL;
++ }
++ }
++
++ /* Save the name, making sure that the list is NULL-terminated */
++ files[nfiles] = strdup(line);
++ if (files[nfiles] == NULL) {
++ (void) fprintf(stderr, "Error allocating memory\n");
++ return NULL;
++ }
++ nfiles++;
++ files[nfiles] = NULL;
++ }
++
++ /* Close the file */
++ (void) fclose(fp);
++
++ /* Return the number of files */
++ *num_files = nfiles;
++
++ return files;
++}
+--- /dev/null
++++ minc-2.1.00/libsrc/read_file_names.h
+@@ -0,0 +1,18 @@
++
++
++/* ----------------------------- MNI Header -----------------------------------
++ at NAME : read_file_names
++ at INPUT : filelist - name of file from which to read names
++ at OUTPUT : num_files - number of files read in
++ at RETURNS : Pointer to a NULL-terminated array of file names
++ at DESCRIPTION: Reads in a list of file names from file filelist or stdin if
++ "-" is specified. Returns NULL if an error occurs. If
++ no error occurs, then a pointer to an empty array is
++ returned and num_files is zero.
++ at METHOD :
++ at GLOBALS :
++ at CALLS :
++ at CREATED : March 8, 1995 (Peter Neelin)
++ at MODIFIED :
++---------------------------------------------------------------------------- */
++char **read_file_names(char *filelist, int *num_files);
+--- minc-2.1.00.orig/progs/minccalc/minccalc.c
++++ minc-2.1.00/progs/minccalc/minccalc.c
+@@ -121,6 +121,7 @@
+ #include <voxel_loop.h>
+ #include <time_stamp.h>
+ #include "node.h"
++#include "read_file_names.h"
+
+ /* Constants */
+
+@@ -143,7 +144,6 @@
+ int input_vector_length, double *input_data[],
+ int output_num_buffers, int output_vector_length,
+ double *output_data[], Loop_Info *loop_info);
+-static char **read_file_names(char *filelist, int *num_files);
+ static char *read_expression_file(char *filename);
+ static int get_list_option(char *dst, char *key, int argc, char **argv);
+
+@@ -516,93 +516,6 @@
+ }
+
+ /* ----------------------------- MNI Header -----------------------------------
+- at NAME : read_file_names
+- at INPUT : filelist - name of file from which to read names
+- at OUTPUT : num_files - number of files read in
+- at RETURNS : Pointer to a NULL-terminated array of file names
+- at DESCRIPTION: Reads in a list of file names from file filelist or stdin if
+- "-" is specified. Returns NULL if an error occurs. If
+- no error occurs, then a pointer to an empty array is
+- returned and num_files is zero.
+- at METHOD :
+- at GLOBALS :
+- at CALLS :
+- at CREATED : March 8, 1995 (Peter Neelin)
+- at MODIFIED :
+----------------------------------------------------------------------------- */
+-static char **read_file_names(char *filelist, int *num_files)
+-{
+-#define FILE_NAME_ALLOC_SIZE 10
+- char **files;
+- int array_size;
+- int nfiles;
+- FILE *fp;
+- char line[PATH_MAX+1];
+- int length;
+-
+- /* Open the file */
+- if (strcmp(filelist, "-") == 0) {
+- fp = stdin;
+- }
+- else {
+- fp = fopen(filelist, "r");
+- if (fp == NULL) {
+- (void) fprintf(stderr, "Error opening file \"%s\"\n", filelist);
+- return NULL;
+- }
+- }
+-
+- /* Allocate an initial array and NULL-terminate it */
+- array_size = FILE_NAME_ALLOC_SIZE;
+- files = malloc(sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles = 0;
+- files[nfiles] = NULL;
+-
+- /* Read in file names */
+- while (fgets(line, sizeof(line)/sizeof(line[0]), fp) != NULL) {
+-
+- /* Remove a trailing newline and check that there is a name */
+- length = strlen(line);
+- if ((length > 0) && (line[length-1] == '\n')) {
+- line[length-1] = '\0';
+- length--;
+- }
+- if (length == 0) continue;
+-
+- /* Make room for names if needed */
+- while (nfiles >= array_size-1) {
+- array_size += FILE_NAME_ALLOC_SIZE;
+- files = realloc(files, sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- }
+-
+- /* Save the name, making sure that the list is NULL-terminated */
+- files[nfiles] = strdup(line);
+- if (files[nfiles] == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles++;
+- files[nfiles] = NULL;
+- }
+-
+- /* Close the file */
+- (void) fclose(fp);
+-
+- /* Return the number of files */
+- *num_files = nfiles;
+-
+- return files;
+-}
+-
+-/* ----------------------------- MNI Header -----------------------------------
+ @NAME : read_expression_file
+ @INPUT : filename - Name of file from which to read expression
+ @OUTPUT : (none)
+--- minc-2.1.00.orig/progs/mincaverage/mincaverage.c
++++ minc-2.1.00/progs/mincaverage/mincaverage.c
+@@ -105,6 +105,7 @@
+ #include <ParseArgv.h>
+ #include <time_stamp.h>
+ #include <voxel_loop.h>
++#include "read_file_names.h"
+
+ /* Constants */
+
+@@ -165,7 +166,6 @@
+ double *output_data[],
+ Loop_Info *loop_info);
+ static int get_double_list(char *dst, char *key, char *nextarg);
+-static char **read_file_names(char *filelist, int *num_files);
+
+ /* Argument variables */
+ static int clobber = FALSE;
+@@ -1010,91 +1010,3 @@
+
+ return TRUE;
+ }
+-
+-/* ----------------------------- MNI Header -----------------------------------
+- at NAME : read_file_names
+- at INPUT : filelist - name of file from which to read names
+- at OUTPUT : num_files - number of files read in
+- at RETURNS : Pointer to a NULL-terminated array of file names
+- at DESCRIPTION: Reads in a list of file names from file filelist or stdin if
+- "-" is specified. Returns NULL if an error occurs. If
+- no error occurs, then a pointer to an empty array is
+- returned and num_files is zero.
+- at METHOD :
+- at GLOBALS :
+- at CALLS :
+- at CREATED : March 8, 1995 (Peter Neelin)
+- at MODIFIED :
+----------------------------------------------------------------------------- */
+-static char **read_file_names(char *filelist, int *num_files)
+-{
+-#define FILE_NAME_ALLOC_SIZE 10
+- char **files;
+- int array_size;
+- int nfiles;
+- FILE *fp;
+- char line[PATH_MAX+1];
+- int length;
+-
+- /* Open the file */
+- if (strcmp(filelist, "-") == 0) {
+- fp = stdin;
+- }
+- else {
+- fp = fopen(filelist, "r");
+- if (fp == NULL) {
+- (void) fprintf(stderr, "Error opening file \"%s\"\n", filelist);
+- return NULL;
+- }
+- }
+-
+- /* Allocate an initial array and NULL-terminate it */
+- array_size = FILE_NAME_ALLOC_SIZE;
+- files = malloc(sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles = 0;
+- files[nfiles] = NULL;
+-
+- /* Read in file names */
+- while (fgets(line, sizeof(line)/sizeof(line[0]), fp) != NULL) {
+-
+- /* Remove a trailing newline and check that there is a name */
+- length = strlen(line);
+- if ((length > 0) && (line[length-1] == '\n')) {
+- line[length-1] = '\0';
+- length--;
+- }
+- if (length == 0) continue;
+-
+- /* Make room for names if needed */
+- while (nfiles >= array_size-1) {
+- array_size += FILE_NAME_ALLOC_SIZE;
+- files = realloc(files, sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- }
+-
+- /* Save the name, making sure that the list is NULL-terminated */
+- files[nfiles] = strdup(line);
+- if (files[nfiles] == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles++;
+- files[nfiles] = NULL;
+- }
+-
+- /* Close the file */
+- (void) fclose(fp);
+-
+- /* Return the number of files */
+- *num_files = nfiles;
+-
+- return files;
+-}
+-
+--- minc-2.1.00.orig/progs/mincconcat/mincconcat.c
++++ minc-2.1.00/progs/mincconcat/mincconcat.c
+@@ -129,6 +129,7 @@
+ #include <ParseArgv.h>
+ #include <time_stamp.h>
+ #include <voxel_loop.h>
++#include "read_file_names.h"
+
+ /* Constants */
+ #ifndef TRUE
+@@ -213,7 +214,6 @@
+ static int sort_function(const void *value1, const void *value2);
+ static void create_concat_file(int inmincid, Concat_Info *concat_info);
+ static void update_history(int mincid, char *arg_string);
+-static char **read_file_names(char *filelist, int *num_files);
+
+ /* Globals */
+ static int Sort_ascending = TRUE;
+@@ -1457,91 +1457,3 @@
+ free(string);
+
+ }
+-
+-/* ----------------------------- MNI Header -----------------------------------
+- at NAME : read_file_names
+- at INPUT : filelist - name of file from which to read names
+- at OUTPUT : num_files - number of files read in
+- at RETURNS : Pointer to a NULL-terminated array of file names
+- at DESCRIPTION: Reads in a list of file names from file filelist or stdin if
+- "-" is specified. Returns NULL if an error occurs. If
+- no error occurs, then a pointer to an empty array is
+- returned and num_files is zero.
+- at METHOD :
+- at GLOBALS :
+- at CALLS :
+- at CREATED : March 8, 1995 (Peter Neelin)
+- at MODIFIED :
+----------------------------------------------------------------------------- */
+-static char **read_file_names(char *filelist, int *num_files)
+-{
+-#define FILE_NAME_ALLOC_SIZE 10
+- char **files;
+- int array_size;
+- int nfiles;
+- FILE *fp;
+- char line[PATH_MAX+1];
+- int length;
+-
+- /* Open the file */
+- if (strcmp(filelist, "-") == 0) {
+- fp = stdin;
+- }
+- else {
+- fp = fopen(filelist, "r");
+- if (fp == NULL) {
+- (void) fprintf(stderr, "Error opening file \"%s\"\n", filelist);
+- return NULL;
+- }
+- }
+-
+- /* Allocate an initial array and NULL-terminate it */
+- array_size = FILE_NAME_ALLOC_SIZE;
+- files = malloc(sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles = 0;
+- files[nfiles] = NULL;
+-
+- /* Read in file names */
+- while (fgets(line, sizeof(line)/sizeof(line[0]), fp) != NULL) {
+-
+- /* Remove a trailing newline and check that there is a name */
+- length = strlen(line);
+- if ((length > 0) && (line[length-1] == '\n')) {
+- line[length-1] = '\0';
+- length--;
+- }
+- if (length == 0) continue;
+-
+- /* Make room for names if needed */
+- while (nfiles >= array_size-1) {
+- array_size += FILE_NAME_ALLOC_SIZE;
+- files = realloc(files, sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- }
+-
+- /* Save the name, making sure that the list is NULL-terminated */
+- files[nfiles] = strdup(line);
+- if (files[nfiles] == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles++;
+- files[nfiles] = NULL;
+- }
+-
+- /* Close the file */
+- (void) fclose(fp);
+-
+- /* Return the number of files */
+- *num_files = nfiles;
+-
+- return files;
+-}
+-
+--- minc-2.1.00.orig/progs/mincmath/mincmath.c
++++ minc-2.1.00/progs/mincmath/mincmath.c
+@@ -123,6 +123,7 @@
+ #include <ParseArgv.h>
+ #include <time_stamp.h>
+ #include <voxel_loop.h>
++#include "read_file_names.h"
+
+ /* Constants */
+
+@@ -219,7 +220,6 @@
+ int output_num_buffers, int output_vector_length,
+ double *output_data[],
+ Loop_Info *loop_info);
+-static char **read_file_names(char *filelist, int *num_files);
+
+ /* Argument variables */
+ static int clobber = FALSE;
+@@ -929,91 +929,3 @@
+
+ return;
+ }
+-
+-/* ----------------------------- MNI Header -----------------------------------
+- at NAME : read_file_names
+- at INPUT : filelist - name of file from which to read names
+- at OUTPUT : num_files - number of files read in
+- at RETURNS : Pointer to a NULL-terminated array of file names
+- at DESCRIPTION: Reads in a list of file names from file filelist or stdin if
+- "-" is specified. Returns NULL if an error occurs. If
+- no error occurs, then a pointer to an empty array is
+- returned and num_files is zero.
+- at METHOD :
+- at GLOBALS :
+- at CALLS :
+- at CREATED : March 8, 1995 (Peter Neelin)
+- at MODIFIED :
+----------------------------------------------------------------------------- */
+-static char **read_file_names(char *filelist, int *num_files)
+-{
+-#define FILE_NAME_ALLOC_SIZE 10
+- char **files;
+- int array_size;
+- int nfiles;
+- FILE *fp;
+- char line[PATH_MAX+1];
+- int length;
+-
+- /* Open the file */
+- if (strcmp(filelist, "-") == 0) {
+- fp = stdin;
+- }
+- else {
+- fp = fopen(filelist, "r");
+- if (fp == NULL) {
+- (void) fprintf(stderr, "Error opening file \"%s\"\n", filelist);
+- return NULL;
+- }
+- }
+-
+- /* Allocate an initial array and NULL-terminate it */
+- array_size = FILE_NAME_ALLOC_SIZE;
+- files = malloc(sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles = 0;
+- files[nfiles] = NULL;
+-
+- /* Read in file names */
+- while (fgets(line, sizeof(line)/sizeof(line[0]), fp) != NULL) {
+-
+- /* Remove a trailing newline and check that there is a name */
+- length = strlen(line);
+- if ((length > 0) && (line[length-1] == '\n')) {
+- line[length-1] = '\0';
+- length--;
+- }
+- if (length == 0) continue;
+-
+- /* Make room for names if needed */
+- while (nfiles >= array_size-1) {
+- array_size += FILE_NAME_ALLOC_SIZE;
+- files = realloc(files, sizeof(*files) * array_size);
+- if (files == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- }
+-
+- /* Save the name, making sure that the list is NULL-terminated */
+- files[nfiles] = strdup(line);
+- if (files[nfiles] == NULL) {
+- (void) fprintf(stderr, "Error allocating memory\n");
+- return NULL;
+- }
+- nfiles++;
+- files[nfiles] = NULL;
+- }
+-
+- /* Close the file */
+- (void) fclose(fp);
+-
+- /* Return the number of files */
+- *num_files = nfiles;
+-
+- return files;
+-}
+-
Modified: trunk/packages/minc/trunk/debian/patches/series
===================================================================
--- trunk/packages/minc/trunk/debian/patches/series 2012-02-20 20:42:07 UTC (rev 9731)
+++ trunk/packages/minc/trunk/debian/patches/series 2012-02-20 21:04:34 UTC (rev 9732)
@@ -1,4 +1,4 @@
01_mincedit-sensible-viewer.diff
03_mincview.diff
decompress-whole-file.diff
-mincaverage-pathmax.patch
+read_file_names-refactor.patch
Modified: trunk/packages/minc/trunk/debian/rules
===================================================================
--- trunk/packages/minc/trunk/debian/rules 2012-02-20 20:42:07 UTC (rev 9731)
+++ trunk/packages/minc/trunk/debian/rules 2012-02-20 21:04:34 UTC (rev 9732)
@@ -21,8 +21,13 @@
override_dh_auto_configure:
+ dh_autoreconf
dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS)
+override_dh_auto_clean:
+ dh_autoreconf_clean
+ dh_auto_clean
+
ps_docs = doc/prog_ref.ps doc/prog_guide.ps volume_io/Documentation/volume_io.ps
doc/prog_ref.ps doc/prog_guide.ps:
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