[med-svn] [Git][med-team/pftools][upstream] New upstream version 3.2.6

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / pftools


Commits:
91e9e35a by Andreas Tille at 2020-12-03T15:17:00+01:00
New upstream version 3.2.6
- - - - -


2 changed files:

- + INSTALL
- + src/C/config.h.cmake


Changes:

=====================================
INSTALL
=====================================
@@ -0,0 +1,70 @@
+REQUIREMENTS
+------------
+
+- 64bit processors
+- cmake >= 3.7
+- gcc   >= 4.6
+- gfortran (or g77 or f77)  for release 2.3 source code
+- perl  >= 5.5.3            for ps_scan.pl
+
+Optional:
+- pcre*
+- GD*
+- libpng
+- libjpeg
+- zlib
+- libharu* (hpdf)
+
+* copy of the source code is provided and could be used during build, if requested.
+
+INSTALLATION
+------------
+
+In order to compile the programs, type:
+
+BUILD:
+   git clone https://github.com/sib-swiss/pftools3.git
+   cd pftools3
+   mkdir build
+   cd build/
+   cmake ..
+
+   OPTIONS:
+   - Build static binaries:
+        cmake -DSTANDALONE=ON ..
+
+   - Build a version using 32bits integers to represent profile matrix values
+     instead of default 16bits (less problems with low/negative cutoff values,
+     might be slower & use more memory):
+        cmake -DUSE_32BIT_INTEGER=ON ..
+
+   - Change installation prefix:
+        cmake -DCMAKE_INSTALL_PREFIX:PATH=<INSTALL PATH> ..
+
+   - Compile C only code (version 3 only):
+        cmake -DC_ONLY=ON ..
+
+   - Compile with graphical support for pfcalibrateV3 (highly optional):
+        cmake -DUSE_GRAPHICS=ON -DUSE_PDF=ON ..
+
+   - Compile without regular expression support:
+        cmake -DUSE_PCRE=OFF ..
+
+   ...
+
+   example:
+        cmake -DC_ONLY=ON -DUSE_32BIT_INTEGER=ON -DUSE_PCRE=OFF ..
+
+
+COMPILE:
+   make
+
+This will create the binaries. To install the
+binaries and the corresponding manual pages type:
+
+INSTALL (see above to change install path):
+   make install
+
+CHECK/TEST:
+   make test
+


=====================================
src/C/config.h.cmake
=====================================
@@ -0,0 +1,146 @@
+#ifndef _CONFIG_H
+#define _CONFIG_H
+/*
+ ********************************************************************************
+ * SPECIFIC ARCHITECTURE
+ ********************************************************************************
+ */
+#cmakedefine USE_WINAPI
+#ifdef USE_WINAPI
+#define __USE_WINAPI__
+#endif
+
+#cmakedefine USE_AFFINITY
+#if defined(USE_AFFINITY)
+# if defined(__GNUC__) && !defined(USE_WINAPI)
+#  define _GNU_SOURCE
+# endif
+#endif
+
+/*
+ ********************************************************************************
+ * Math Library
+ ********************************************************************************
+ */
+#ifdef __INTEL_COMPILER
+# include <mathimf.h>
+#elif __IBMC__
+# include <math.h>
+# include <mass.h>
+#else
+# include <math.h>
+#endif
+
+/*
+ ********************************************************************************
+ * ALLOCA header file
+ ********************************************************************************
+ */
+#cmakedefine HAVE_ALLOCA_H
+#if !defined(HAVE_ALLOCA_H) && defined(__GNUC__)
+/* This is not defined in MinGW */
+#define alloca __builtin_alloca
+#endif
+
+/*
+ ********************************************************************************
+ * MM_MALLOC header file
+ ********************************************************************************
+ */
+#cmakedefine HAVE_MM_MALLOC_H 1
+#ifdef HAVE_MM_MALLOC_H
+# include <mm_malloc.h>
+#else
+#include <stdlib.h>
+/* We can't depend on <stdlib.h> since the prototype of posix_memalign
+   may not be visible.  */
+#ifndef __cplusplus
+extern int posix_memalign (void **, size_t, size_t);
+#else
+extern "C" int posix_memalign (void **, size_t, size_t) throw ();
+#endif
+
+static inline void * __ALWAYS_INLINE
+_mm_malloc (size_t size, size_t alignment)
+{
+  void *ptr;
+  if (alignment == 1)
+    return malloc (size);
+  if (alignment == 2 || (sizeof (void *) == 8 && alignment == 4))
+    alignment = sizeof (void *);
+  if (posix_memalign (&ptr, alignment, size) == 0)
+    return ptr;
+  else
+    return NULL;
+}
+
+static inline void __ALWAYS_INLINE
+_mm_free (void * ptr)
+{
+  free (ptr);
+}
+#endif
+
+/*
+ ********************************************************************************
+ * Haru PDF Library
+ ********************************************************************************
+ */
+#cmakedefine USE_PDF
+
+/*
+ ********************************************************************************
+ * GD Library
+ ********************************************************************************
+ */
+#cmakedefine USE_GD
+
+/*
+ ********************************************************************************
+ * PLplot Library
+ ********************************************************************************
+ */
+#cmakedefine USE_PLPLOT
+
+/*
+ ********************************************************************************
+ * Mapping database to memory or opening it through libC
+ ********************************************************************************
+ */
+#cmakedefine USE_MMAP
+#ifndef USE_MMAP
+# undef __USE_MMAP__
+# define SETUP_DATABASE_ACCESS(fileoraddress) FILE* inSequence = fopen((fileoraddress), "r")
+# define GET_DATABASE_SEQUENCE(dest, offsets, id) ReadSequenceIndex((dest), (size_t) (id), inSequence, (offsets))
+# define UNSET_DATABASE_ACCESS() fclose(inSequence)
+#else
+# include <sys/mman.h>
+# define __USE_MMAP__
+# define SETUP_DATABASE_ACCESS(fileoraddress) const char * const restrict SequenceFileMap = (fileoraddress);
+# ifndef MMAP_DEBUG
+#  define GET_DATABASE_SEQUENCE(dest, offsets) MMAP_ReadSequenceIndex((dest), SequenceFileMap, (offsets), 0)
+# else
+#  define GET_DATABASE_SEQUENCE(dest, offsets) MMAP_ReadSequenceIndex((dest), SequenceFileMap, (offsets), 0\
+                                                   ,((struct ThreadData*) _Data)->threadId, 0, *(((struct ThreadData*) _Data)->maplength))
+# endif
+# define UNSET_DATABASE_ACCESS()
+#endif
+
+/*
+ ********************************************************************************
+ * PfTools versioning
+ ********************************************************************************
+ */
+#define PF_VERSION "${VERSION}"
+#define PF_MAJOR_VERSION ${MAJOR_VERSION}
+#define PF_MINOR_VERSION ${MINOR_VERSION}
+
+/*
+ ********************************************************************************
+ * Executable build using inline functions
+ ********************************************************************************
+ */
+#ifndef BUILD_LIBRARY
+#define __USE_INLINE_FUNCTIONS__
+#endif
+#endif /* _CONFIG_H */



View it on GitLab: https://salsa.debian.org/med-team/pftools/-/commit/91e9e35a1a32e329f0c301c60fdc9939606edead

-- 
View it on GitLab: https://salsa.debian.org/med-team/pftools/-/commit/91e9e35a1a32e329f0c301c60fdc9939606edead
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201203/90046e47/attachment-0001.html>