Get rid of compiler warnings

[plexoos]

Our build system currently asks the compiler to print many useful warnings (-Wall). This sounds like a good idea since warnings may indicate problematic places in the code, obsolete features, or the use of nonstandard extension of C/C++. However, it appears that the reported warnings have been ignored for quite a long time. Currently there are about 3,000 warnings reported by gcc 4.8.5. A goal to address all the warnings should be recognized and a zero-warning policy should be enforced for all future code modifications.

A list of warnings sorted by their frequency in the build log (gcc 4.8.5, root 5):

                                                                      msg  count   freq
0         deprecated conversion from string constant to [-Wwrite-strings]    798  27.0%
1      may be used uninitialized in this function [-Wmaybe-uninitialized]    435  14.7%
2   deleting object of polymorphic class type which has non-virtual de...    403  13.6%
3                   variable set but not used [-Wunused-but-set-variable]    341  11.5%
4                                     unused variable [-Wunused-variable]    293   9.9%
5      format expects argument of type, but argument has type [-Wformat=]    210   7.1%
6   comparison between signed and unsigned integer expressions [-Wsign...     73   2.5%
7   iteration invokes undefined behavior [-Waggressive-loop-optimizati...     56   1.9%
8                        operation on may be undefined [-Wsequence-point]     54   1.8%
9                           declaration of shadows a member of [-Wshadow]     41   1.4%
10           converting to non-pointer type from NULL [-Wconversion-null]     30   1.0%
11                                  unused parameter [-Wunused-parameter]     25   0.8%
12                       ignoring #pragma omp section [-Wunknown-pragmas]     22   0.7%
13                                      was hidden [-Woverloaded-virtual]     20   0.7%
14                 array subscript is above array bounds [-Warray-bounds]     14   0.5%
15  dereferencing type-punned pointer will break strict-aliasing rules...     13   0.4%
16                               defined but not used [-Wunused-variable]     12   0.4%
17                                  will be initialized after [-Wreorder]     11   0.4%
18                               defined but not used [-Wunused-function]      9   0.3%
19                unknown conversion type character in format [-Wformat=]      8   0.3%
20               control reaches end of non-void function [-Wreturn-type]      7   0.2%
21  argument to in call is the same pointer type as the destination; e...      7   0.2%
22                    too many arguments for format [-Wformat-extra-args]      7   0.2%
23  type qualifiers ignored on function return type [-Wignored-qualifi...      6   0.2%
24                            value computed is not used [-Wunused-value]      6   0.2%
25             suggest explicit braces to avoid ambiguous [-Wparentheses]      6   0.2%
26                               statement has no effect [-Wunused-value]      5   0.2%
27                                             within comment [-Wcomment]      5   0.2%
28  base class should be explicitly initialized in the copy constructo...      4   0.1%
29  comparison with string literal results in unspecified behaviour [-...      4   0.1%
30  cast to pointer from integer of different size [-Wint-to-pointer-c...      4   0.1%
31                      suggest parentheses around within [-Wparentheses]      3   0.1%
32                     the address of will always evaluate as [-Waddress]      3   0.1%
33    suggest parentheses around comparison in operand of [-Wparentheses]      3   0.1%
34           extra tokens at end of #endif directive [enabled by default]      2   0.1%
35       large integer implicitly truncated to unsigned type [-Woverflow]      2   0.1%
36         typedef locally defined but not used [-Wunused-local-typedefs]      2   0.1%
37                                         redefined [enabled by default]      2   0.1%
38                                    repeated flag in format [-Wformat=]      2   0.1%
39  argument to in call is the same expression as the destination; did...      2   0.1%
40                      ignoring #pragma omp parallel [-Wunknown-pragmas]      2   0.1%
41     no return statement in function returning non-void [-Wreturn-type]      2   0.1%
42                 use of length modifier with type character [-Wformat=]      1   0.0%
43                          initialized and declared [enabled by default]      1   0.0%
44  field precision specifier expects argument of type, but argument h...      1   0.0%
45            zero-length gnu_printf format string [-Wformat-zero-length]      1   0.0%
46                         format expects a matching argument [-Wformat=]      1   0.0%
47                            label defined but not used [-Wunused-label]      1   0.0%