Something for our Advent calendar (Was: Bug#976254: rnahybrid: Does not build from source "multiple definition of")

[Andreas Tille <andreas@an3as.eu>]

Control: tags -1 help

Hi,

no idea why this was not catched in the usual gcc-10 rebuilds.  Any volunteer?

Kind regards

     Andreas.

On Wed, Dec 02, 2020 at 12:08:32AM +0100, Andreas Tille wrote:
> Source: rnahybrid
> Severity: serious
> Tags: ftbfs
> Justification: FTBFS
> 
> Hi,
> 
> I tried to rebuild the package but the build ends in:
> 
> ...
> gcc -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/rnahybrid-2.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,-z,relro -Wl,-z,now -o RNAeffective rnaeffective.o hybrid_core.o numerical.o energy.o input.o fasta.o random.o mt19937-1.o plot.o  -lg2 -lm 
> /usr/bin/ld: /usr/bin/ld: /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:13: multiple definition of `x'; rnahybrid.o:./src/hybrid_core.h:13: first defined here
> hybrid_core.o:./src/hybrid_core.h:/usr/bin/ld: hybrid_core.o13: multiple definition of `x'; :./src/hybrid_core.h:15: multiple definition of `y'; rnahybrid.o:./src/hybrid_core.h:15: first defined herehybrid_core.o
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r1'; rnahybrid.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r2'; rnahybrid.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r3'; rnahybrid.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:13:./src/hybrid_core.h:28: multiple definition of `r4'; rnahybrid.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o: multiple definition of `x'; :./src/hybrid_core.h:30: multiple definition of `a1'; rnahybrid.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a2'; rnahybrid.o:./src/hybrid_core.h:30: first defined herernaeffective.o:./src/hybrid_core.h:13: first defined here
> /usr/bin/ld: hybrid_core.o
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a3'; rnahybrid.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a4'; rnahybrid.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a5'; rnahybrid.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a6'; rnahybrid.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld:./src/hybrid_core.h:15: multiple definition of `y'; rnaeffective.o:./src/hybrid_core.h:15: first defined here
> /usr/bin/ld: hybrid_core.o: hybrid_core.o:./src/hybrid_core.h:23: multiple definition of `helix_start'; rnahybrid.o:./src/hybrid_core.h:23: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:23: multiple definition of `helix_end'; rnahybrid.o:./src/hybrid_core.h:23: first defined here
> /usr/bin/ld: hybrid_core.o:./src/energy.h:50: multiple definition of `canPair'; rnahybrid.o:./src/energy.h:50: first defined here
> /usr/bin/ld:./src/hybrid_core.h:28: multiple definition of `r1'; rnaeffective.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r2'; rnaeffective.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r3'; rnaeffective.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:28: multiple definition of `r4'; rnaeffective.o:./src/hybrid_core.h:28: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a1'; rnaeffective.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld: hybrid_core.o:./src/hybrid_core.h:30: multiple definition of `a2'; rnaeffective.o:./src/hybrid_core.h:30: first defined here
> /usr/bin/ld: rnacalibrate.ohybrid_core.o::./src/hybrid_core.h:./src/hybrid_core.h:3013: multiple definition of `: first defined herea3'
> ...
> 
> Kind regards
> 
>       Andreas.
> 
> 
> -- System Information:
> Debian Release: bullseye/sid
>   APT prefers unstable
>   APT policy: (500, 'unstable'), (500, 'testing'), (50, 'buildd-unstable'), (1, 'experimental')
> Architecture: amd64 (x86_64)
> 
> Kernel: Linux 5.9.0-3-amd64 (SMP w/4 CPU threads)
> Kernel taint flags: TAINT_WARN
> Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8), LANGUAGE not set
> Shell: /bin/sh linked to /usr/bin/dash
> Init: systemd (via /run/systemd/system)
> LSM: AppArmor: enabled
> 
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