Hi Guillaume, in the Debian bug tracking system
http://bugs.debian.org/667214 a build problem when using gcc-4.7 was reported. Below you can read some discussion about a possible fix. Michael, I can confirm that I also tried to s/uint_t/int/ in parse_dna.hpp with the same result (same error message) after I did my initial posting (that's why I did not felt a real need to send another mail). And yes, I agree that assigning negative values to unsigned variables smells like done with some purpose which might stay hidden from the first look and I would have definitely asked upstream about any problem my suggested patch might have caused. I just felt like doing some investigation into the problem might make sense. However, it seems that this does not lead to any progres. Guillaume, could you enlighten us a bit about this trick? Kind regards Andreas. On Thu, May 03, 2012 at 09:52:09AM +0200, Michael Wild wrote: > On 05/02/2012 08:33 AM, Andreas Tille wrote: > > Hi, > > > > I tried to fix the problem in the jellyfish package but the general > > hints given did not helped me really. Any more precise help to fix > > this problem: > > > > parse_dna.cc:97:3: error: narrowing conversion of '-3' from 'int' to 'const > > uint_t {aka const long unsigned int}' inside { } is ill-formed in C++11 > > [-Werror=narrowing] > > > > My first idea was to do > > > > --- jellyfish.orig/jellyfish/parse_dna.cc > > +++ jellyfish/jellyfish/parse_dna.cc > > @@ -57,7 +57,7 @@ > > } > > } > > > > - const uint_t parse_dna::codes[256] = { > > + const int parse_dna::codes[256] = { > > -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -2, -3, -3, -3, -3, -3, > > -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, > > -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -1, -3, -3, > > --- jellyfish.orig/jellyfish/parse_dna.hpp > > +++ jellyfish/jellyfish/parse_dna.hpp > > @@ -55,7 +55,7 @@ > > static uint64_t mer_string_to_binary(const char *in, uint_t klen) { > > uint64_t res = 0; > > for(uint_t i = 0; i < klen; i++) { > > - const uint_t c = parse_dna::codes[(uint_t)*in++]; > > + const int c = parse_dna::codes[(int)*in++]; > > if(c & CODE_NOT_DNA) > > return 0; > > res = (res << 2) | c; > > > > > > because it makes no sense to initialise uint with negative numbers but > > this did not changed the error message which sounds totally strange to > > me. > > > > Kind regards > > > > Andreas. > > > > You missed the declaration of parse_dna::codes in parse_dna.hpp. > > > diff --git a/jellyfish/parse_dna.cc b/jellyfish/parse_dna.cc > index ab3ec64..9ea5ae1 100644 > --- a/jellyfish/parse_dna.cc > +++ b/jellyfish/parse_dna.cc > @@ -57,7 +57,7 @@ namespace jellyfish { > } > } > > - const uint_t parse_dna::codes[256] = { > + const int parse_dna::codes[256] = { > -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -2, -3, -3, -3, -3, -3, > -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, > -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -3, -1, -3, -3, > diff --git a/jellyfish/parse_dna.hpp b/jellyfish/parse_dna.hpp > index 0435ae2..7ef8afd 100644 > --- a/jellyfish/parse_dna.hpp > +++ b/jellyfish/parse_dna.hpp > @@ -46,7 +46,7 @@ namespace jellyfish { > * '\n': map to -2. ignore > * Other ASCII: map to -3. Skip to next line > */ > - static const uint_t codes[256]; > + static const int codes[256]; > static const uint_t CODE_RESET = -1; > static const uint_t CODE_IGNORE = -2; > static const uint_t CODE_COMMENT = -3; > @@ -55,7 +55,7 @@ namespace jellyfish { > static uint64_t mer_string_to_binary(const char *in, uint_t klen) { > uint64_t res = 0; > for(uint_t i = 0; i < klen; i++) { > - const uint_t c = parse_dna::codes[(uint_t)*in++]; > + const int c = parse_dna::codes[(uint_t)*in++]; > if(c & CODE_NOT_DNA) > return 0; > res = (res << 2) | c; > > That said, assigning -3 to an unsigned int seems to be a pretty > conscious choice to me, so it might have been done on purpose to create > a wrap-around. Also, the same pattern shows up many other places (e.g. > parse_dna::CODE_RESET, parse_dna::CODE_IGNORE, ...). IMHO bad practice, > but plausible. Probably it's best to contact upstream about this and ask > what their original intention was. > > Michael > > > -- > To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org > Archive: http://lists.debian.org/4fa23929.3000...@gmail.com > > -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120503124658.gi31...@an3as.eu
