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gpertea / gclib

GCLib - Genomic C++ library of reusable code for bioinformatics projects
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g++ warnings - #8

Open smoe opened 4 years ago

smoe commented 4 years ago

Hello,

Admittedly, I do not see any immediate need to address any of these warnings.

Kind regards, Steffen

$ gcc --version
gcc (Debian 10.2.0-3) 10.2.0
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/home/moeller/git/med-team/libgclib=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp  -fPIC -DPIC -o .libs/libgclib_la-GStr.o
In file included from gff.cpp:1:
gff.h:229:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  229 |      struct {
      |             ^
gff.h:232:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  232 |      struct {
      |             ^
gff.h:328:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  328 |     struct {
      |            ^
gff.h:691:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  691 |       struct {
      |              ^
gff.h:1150:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
 1150 |     struct {
      |            ^
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GMapSeg]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GMapSeg]’
gff.h:127:50:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GMapSeg’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:70:7: note: ‘class GMapSeg’ declared here
   70 | class GMapSeg:public GSeg {
      |       ^~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GSeg]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GSeg]’
gff.h:311:92:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.h:6,
                 from gff.cpp:1:
GBase.h:308:7: note: ‘class GSeg’ declared here
  308 | class GSeg {
      |       ^~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GeneCDS]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GeneCDS]’
gff.h:1351:31:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GeneCDS’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:1340:7: note: ‘class GeneCDS’ declared here
 1340 | class GeneCDS: public GSeg {
      |       ^~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GffExon]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GffExon]’
gff.cpp:2315:16:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GffExon’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:629:7: note: ‘class GffExon’ declared here
  629 | class GffExon : public GSeg {
      |       ^~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GSegMatch]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GSegMatch]’
GList.hh:191:76:   required from ‘GArray<OBJ>::GArray(int (*)(pointer, pointer)) [with OBJ = GSegMatch; GCompareProc = int(void*, void*); pointer = void*]’
gff.h:1351:31:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSegMatch’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:1328:7: note: ‘class GSegMatch’ declared here
 1328 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
      |       ^~~~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSegMatch]’:
GVec.hh:437:9:   required from ‘void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSegMatch]’
GVec.hh:69:44:   required from ‘void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSegMatch]’
GList.hh:234:21:   required from ‘int GArray<OBJ>::Add(OBJ*) [with OBJ = GSegMatch]’
GList.hh:51:36:   required from ‘int GArray<OBJ>::Add(OBJ&) [with OBJ = GSegMatch]’
gff.h:1364:22:   required from here
GVec.hh:358:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSegMatch’; use assignment or value-initialization instead [-Wclass-memaccess]
  358 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:1328:7: note: ‘class GSegMatch’ declared here
 1328 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
      |       ^~~~~~~~~
gpertea commented 4 years ago

Thank you for pointing these out, had no idea ISO C++ is denying the convenience of anonymous structs. It's not that hard to adjust the code to fix it and I'll do it, just seems unnecessarily limiting.

The memset thing puzzles me, I saw it flagged before when using sanitizers but I cannot yet figure out why the compiler doesn't see that's conditional code there (template based), memset should only be called for the primitive types I am allowing there, yet somehow I keep getting that warning for GSeg. I have to dig a bit deeper there -- thank you for compiling this on such a new compiler to expose these issues.