[Debian-med-packaging] Bug#976254: Something for our Advent calendar (Was: Bug#976254: rnahybrid: Does not build from source "multiple definition of")

Wed Dec 2 14:13:17 GMT 2020

Hi,

That is a common problem with legacy code being compiled with gcc-10, since
it defaults to "-fno-common". It can be solved for legacy packages by
passing "CFLAGS=-fcommon" to the `configure` (e.g `./configure
CFLAGS=-fcommon`), then `make` will succeed.
More information from https://gcc.gnu.org/gcc-10/porting_to.html:

> Default to -fno-common
> A common mistake in C is omitting extern when declaring a global variable
in a header file. If the header is included by several files it results in
multiple definitions of the same variable. In previous GCC versions this
error is ignored. GCC 10 defaults to -fno-common, which means a linker
> error will now be reported. To fix this, use extern in header files when
declaring global variables, and ensure each global is defined in exactly
one C file. If tentative definitions of particular variables need to be
placed in a common block, __attribute__((__common__)) can be used to force
> that behavior even in code compiled without -fcommon. As a workaround,
legacy C code where all tentative definitions should be placed into a
common block can be compiled with -fcommon.

Regards,
Hamid Nassiby

On Wed, Dec 2, 2020 at 12:51 PM Andreas Tille <andreas at an3as.eu> wrote:

> 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
> >
> > _______________________________________________
> > Debian-med-packaging mailing list
> > Debian-med-packaging at alioth-lists.debian.net
> >
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
>
> --
> http://fam-tille.de
>
>
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