[med-svn] [Git][med-team/plink2][upstream] New upstream version 2.00~a3-220218+dfsg

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / plink2


Commits:
5c4d7d84 by Andreas Tille at 2022-02-20T21:24:51+01:00
New upstream version 2.00~a3-220218+dfsg
- - - - -


4 changed files:

- include/plink2_base.cc
- include/plink2_base.h
- plink2.cc
- plink2_cmdline.cc


Changes:

=====================================
include/plink2_base.cc
=====================================
@@ -23,7 +23,7 @@ namespace plink2 {
 
 uintptr_t g_failed_alloc_attempt_size = 0;
 
-#if (__GNUC__ <= 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)
+#if (((__GNUC__ == 4) && (__GNUC_MINOR__ < 7)) || (__GNUC__ >= 11)) && !defined(__APPLE__)
 BoolErr pgl_malloc(uintptr_t size, void* pp) {
   *S_CAST(unsigned char**, pp) = S_CAST(unsigned char*, malloc(size));
   if (likely(*S_CAST(unsigned char**, pp))) {


=====================================
include/plink2_base.h
=====================================
@@ -2010,12 +2010,16 @@ extern uintptr_t g_failed_alloc_attempt_size;
 // number is printed as well; see e.g.
 //   https://stackoverflow.com/questions/15884793/how-to-get-the-name-or-file-and-line-of-caller-method
 
-#if (__GNUC__ == 4) && (__GNUC_MINOR__ < 7) && !defined(__APPLE__)
+#if (((__GNUC__ == 4) && (__GNUC_MINOR__ < 7)) || (__GNUC__ >= 11)) && !defined(__APPLE__)
 // putting this in the header file caused a bunch of gcc 4.4 strict-aliasing
 // warnings, while not doing so seems to inhibit some malloc-related compiler
 // optimizations, bleah
 // compromise: header-inline iff gcc version >= 4.7 (might not be the right
 // cutoff?)
+// update (18 Feb 2022): looks like inlined pgl_malloc is not compiled as
+// intended by gcc 11, due to new ipa-modref pass?  Open to suggestions on how
+// to fix this; maybe it's now necessary to define type-specific malloc
+// wrappers, ugh...
 BoolErr pgl_malloc(uintptr_t size, void* pp);
 #else
 // Unfortunately, defining the second parameter to be of type void** doesn't do


=====================================
plink2.cc
=====================================
@@ -71,7 +71,7 @@ static const char ver_str[] = "PLINK v2.00a3"
 #ifdef USE_MKL
   " Intel"
 #endif
-  " (17 Feb 2022)";
+  " (18 Feb 2022)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""
@@ -10944,13 +10944,7 @@ int main(int argc, char** argv) {
     reterr = kPglRetWriteFail;
   }
   if (bigstack_ua) {
-    if (g_debug_on) {
-      fputs("--debug: Trying to free bigstack_ua.\n", stdout);
-    }
     free(bigstack_ua);
   }
-  if (g_debug_on) {
-    fputs("--debug: Exiting.\n", stdout);
-  }
   return S_CAST(int32_t, reterr);
 }


=====================================
plink2_cmdline.cc
=====================================
@@ -526,15 +526,9 @@ BoolErr CleanupLogfile(uint32_t print_end_time) {
   }
   BoolErr ret_boolerr = 0;
   if (g_logfile) {
-    if (g_debug_on) {
-      printf("--debug: g_log_failed = %u.\n", g_log_failed);
-    }
     if (!g_log_failed) {
       logputs_silent("\n");
       logputs_silent(g_logbuf);
-      if (g_debug_on) {
-        fputs("--debug: Trying to close log.\n", stdout);
-      }
       if (unlikely(fclose(g_logfile))) {
         fflush(stdout);
         fprintf(stderr, "Error: Failed to finish writing to log: %s.\n", strerror(errno));



View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/5c4d7d84642085afb135dfe023039aec73732e8f

-- 
View it on GitLab: https://salsa.debian.org/med-team/plink2/-/commit/5c4d7d84642085afb135dfe023039aec73732e8f
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