[Debian-med-packaging] Bug#831260: staden: FTBFS: conf.c:385: undefined reference to `min'

[James Bonfield]

On Thu, Jul 14, 2016 at 03:07:47PM +0200, Andreas Tille wrote:
> > > gcc -L/<<BUILDDIR>>/staden-2.0.0+b10/lib -Wl,-z,relro -Wl,--export-dynamic  -Wl,-rpath,/usr/lib/staden -o eba qual.o conf.o -L/usr/lib/x86_64-linux-gnu -lstaden-read -Wl,-z,relro -Wl,-z,now -lm -lpthread   -lcurl -lz  -lmisc   -lm      -lm 
> > > conf.o: In function `probFromQual':
> > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to `min'
> > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to `min'
> > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to `min'
> > > /<<BUILDDIR>>/staden-2.0.0+b10/eba/conf.c:385: undefined reference to `min'
> > > collect2: error: ld returned 1 exit status

I think the problem here is trying to use the old Staden release with
a much more modern io_lib release.  It's a mistake that we broke
backwards compatibility, but trivially fixed in eba itself.

See commit https://sourceforge.net/p/staden/code/4067/:
    Due to io_lib changes, change from min() to MIN().

--- a/staden/trunk/src/eba/conf.c

+++ b/staden/trunk/src/eba/conf.c
@@ -382,7 +382,7 @@
 
 char probFromQual(float qual)
 {
-    return (char)(100.0*(1.0 - min(qual,1.0)));
+    return (char)(100.0*(1.0 - MIN(qual,1.0)));
 }

There is a 2.0.0b11 release now which I think incorporates this
change.

The Staden Package as a whole is pretty much on life support.  The
only tool that gets any real updates is Gap5, and they have slowed up
a lot in the last couple years.  Things like "eba" are long since dead
really, but basic things like fixing compilation errors is OK to
solve.

James

-- 
James Bonfield (jkb at sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
                                  | Plurima gyrabant gymbolitare vabo;
  A Staden Package developer:     | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/   | Momiferique omnes exgrabure Rathi. 


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