Re: Fasta3 is non-free just because of some Smith Waterman implementation (Was: Please choose a free license for fasta3 components)

2019-08-20 Thread Erik Sjölund
Hi Andreas, Regarding "Alex has once contacted upstream" note the sad news from https://cryptogenomicon.org/2019/03/11/farrars-striped-simd-smith-waterman/ Kind regards, Erik On Mon, Aug 19, 2019 at 10:06 PM Andreas Tille wrote: > > Hi Steffen, > > you have uploaded fasta3. When I wanted to up

Re: [Debian-med-packaging] Bug#934600: gffread in cufflinks seems to be the same codebase but older

2019-08-20 Thread Alex Mestiashvili
On 8/20/19 7:16 AM, Andreas Tille wrote: > Hi Alexandre, > > it looks as if the gffread code in cufflinks would be the > same code base but the code in gffread source seems to be > more recent. What do you think? > > Kind regards > > Andreas. > > - Forwarded message from Debian te

[Help] libgtextutils: ftbfs with GCC-9

2019-08-20 Thread Andreas Tille
Control: tags -1 help Hi, any hint how to deal with ... g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswi

Re: Fasta3 is non-free just because of some Smith Waterman implementation (Was: Please choose a free license for fasta3 components)

2019-08-20 Thread Steffen Möller
That is truly sad, indeed. Many thanks go to his widow and to Prof. Eddy for caring. It is also an opportunity to think about how we as a community can grow. A donation box for instance would never be enough to feed the kids, but it would be something like a nice gesture about work and his creator

Re: [Debian-med-packaging] Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-08-20 Thread Olivier Sallou
On 8/20/19 1:24 PM, Andreas Tille wrote: > Control: tags -1 help > > Hi, > > any hint how to deal with this is a test file. In test, there is explicit conversion to string: line = reader.line_string() ; //first line - with explicit method to get the string which works fine as expected In gcc

Re: Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-08-20 Thread Andreas Tille
Hi Olivier, I'm just forwarding this to Debian Mentors list to get a wider audience. I'd prefer a fix over simply removing the test ... Thanks for your analysis anyway Andreas. On Tue, Aug 20, 2019 at 03:36:48PM +0200, Olivier Sallou wrote: > > On 8/20/19 1:24 PM, Andreas Tille wrote: > >

Re: [Debian-med-packaging] Bug#925745: [Help] libgtextutils: ftbfs with GCC-9

2019-08-20 Thread Olivier Sallou
On 8/20/19 3:41 PM, Andreas Tille wrote: > Hi Olivier, > > I'm just forwarding this to Debian Mentors list to get a wider audience. > I'd prefer a fix over simply removing the test ... commenting in text_line_reader.h:         // operator const std::string& () const { return line_string()

Re: [MoM] FAST progress (was Re: [MoM] fast: Add further dependencies to enable chroot / cowbuilder to build)

2019-08-20 Thread Andreas Tille
Hi Shayan, On Tue, Aug 20, 2019 at 07:14:33PM +0100, Shayan Doust wrote: > > Welcome back :). :-) > I've probably checked gatb-core at least a dozen times before you sent > this to me. I just never checked debian/patch as I didn't think this was > some cmake thing :). Talked to upstream and th