Hi Andreas,
Hmmm - I'm not sure what happened with Anfo at all. I put it in BL6 by
special request and I had a working package, but in BL7 it's missing and
I can't seem to find a record (or remember) why I removed it.
It's still of interest to me since it's good for degraded environmental
DNA. I'll take a look if I get time this week - I'm preparing a course
right now so generally busy with that. I also need to upload my Galaxy
work before Stonehaven - it's not ready for Debian yet but I've made
significant progress.
Cheers,
TIM
On Wed, 2014-01-01 at 17:51 +0000, Andreas Tille wrote:
> Hi Tim,
>
> after having fixed a lot of bugs in old packages I was diving into our
> todo list and found afno. Since you commited spme packaging stuff for
> afno I guess it might be useful for BioLinux. I checked your packaging
> in SVN and tried to enhance it to latest Debian Med standards. However,
> the package FTBFSes with
>
> ...
> /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I..
> -D_FORTIFY_SOURCE=2 -pthread -g -O2 -fstack-protector
> --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o align.lo
> align.cc
> libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -D_FORTIFY_SOURCE=2 -pthread
> -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -c align.cc -fPIC -DPIC -o .libs/align.o
> In file included from index.h:22:0,
> from align.h:21,
> from align.cc:21:
> util.h: In instantiation of 'T throw_errno_if_minus1(T, const char*, const
> char*) [with T = long int]':
> util.h:107:44: required from here
> util.h:48:46: error: 'throw_errno_if_eq' was not declared in this scope, and
> no declarations were found by argument-dependent lookup at the point of
> instantiation [-fpermissive]
> { return throw_errno_if_eq( x, (T)(-1), a, b ) ; }
> ^
> util.h:55:3: note: 'template<class T> T throw_errno_if_eq(T, T, const char*,
> const char*)' declared here, later in the translation unit
> T throw_errno_if_eq( T x, T y, const char* a, const char* b = 0 )
> ^
> util.h: In instantiation of 'T throw_errno_if_minus1(T, const char*, const
> char*) [with T = int]':
> util.h:130:73: required from here
> util.h:48:46: error: 'throw_errno_if_eq' was not declared in this scope, and
> no declarations were found by argument-dependent lookup at the point of
> instantiation [-fpermissive]
> { return throw_errno_if_eq( x, (T)(-1), a, b ) ; }
> ^
> util.h:55:3: note: 'template<class T> T throw_errno_if_eq(T, T, const char*,
> const char*)' declared here, later in the translation unit
> T throw_errno_if_eq( T x, T y, const char* a, const char* b = 0 )
> ^
> make[4]: *** [align.lo] Error 1
>
>
> I wonder whether the package is worth spending more time into it (asking
> some C++ experts what might be wrong here) or whether the package might
> be not needed any more since there might be some better replacements.
>
> Kind regards and thanks for your initial work on this
>
> Andreas.
>
--
Tim Booth <tbo...@ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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