Crashes reported on bioc-devel

[lgatto]

From [Bioc-devel] msPurity build fail on Mac OS X (morelia), @mtmorgan offers the following patch.

Index: src/cramp.cpp
===================================================================
--- src/cramp.cpp   (revision 121179)
+++ src/cramp.cpp   (working copy)
@@ -95,7 +95,7 @@
          //      if (m_runInfo->m_data.scanCount < 0) { // undeclared 
scan count
          // this will provoke reading of index, which sets scan count
          rampScanInfo* tmp = getScanHeaderInfo ( 1 );
-        free(tmp);
+        delete(tmp);
          // }
          // END HENRY
      }

It's not clear to me yet if this is really the reason for the reported problem, so I haven't applied it yet. I will once we get to the bottom of the msPurity problem.

[mtmorgan]

I'd guess that there were many of these new / delete mismatches, and a little tedious to track down!

[lgatto]

Are all free calls to be replaced by delete, or only some?

[mtmorgan]

If the memory is allocated by new(), then it needs to be deleteed; if it's allocated by malloc(), then free().

[jorainer]

These new-delete and malloc-free calls are pretty difficult to track in the code. I've tried that for some time as I was suspecting that these might cause some of the random errors we've got earlier (e.g. lgatto/MSnbase#138).

[jorainer]

do you know of an automated or semi-automated way to check for similar problems in the code? Otherwise it might be quite a task to search for them.

[lgatto]

Some file (like cramp.*, ramp.*) are very unlikely to change. pwiz changes should ideally be discussed and pushed upstream.