[Debian-med-packaging] Bug#907819: jellyfish: FTBFS randomly (ld: cannot find -ljellyfish-2.0)

[Adrian Bunk]

Control: severity -1 minor

On Sun, Sep 02, 2018 at 03:41:11PM +0000, Santiago Vila wrote:
> Package: src:jellyfish
> Version: 2.2.8-3
> Severity: serious
> Tags: ftbfs
> 
> Dear maintainer:
> 
> I tried to build this package in sid and it failed with this error:
> 
> --------------------------------------------------------------------------------
> /usr/bin/ld: cannot find -ljellyfish-2.0
> collect2: error: ld returned 1 exit status
> error: command 'x86_64-linux-gnu-g++' failed with exit status 1
> --------------------------------------------------------------------------------
> 
> I'm building on amd64 and this error happens randomly for me
> (sometimes it fails, sometimes it does not), but it happened at least
> once in the official autobuilders in another architecture:
> 
> https://buildd.debian.org/status/fetch.php?pkg=jellyfish&arch=powerpc&ver=2.2.8-3&stamp=1531093335&raw=0
> 
> so it seems that the error is not architecture-specific and we can
> assume it will also fail randomly on the official buildds too.
>...

This powerpc build failure is completely unrelated and non-random,
that's a missing -latomic.

https://people.debian.org/~sanvila/build-logs/jellyfish/jellyfish_2.2.8-3_amd64-20180902T150417Z

...
I: NOTICE: Log filtering will replace 'build/jellyfish-La3pVw/jellyfish-2.2.8' with '<<PKGBUILDDIR>>'
...
x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/jellyfish_wrap.o -L/build/jellyfisha3pVw/jellyfish-2.2.8/debian/tmp//usr/lib/x86_64-linux-gnu -Wl,--enable-new-dtags,-R/<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu -ljellyfish-2.0 -lpthread -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_dna-jellyfish/build/_dna_jellyfish.cpython-37m-x86_64-linux-gnu.so
/usr/bin/ld: cannot find -ljellyfish-2.0


Something (libtool?) removes the "-L" from the "jellyfish-La3pVw",
this is not a problem on the buildds that use sane paths.


cu
Adrian

-- 

       "Is there not promise of rain?" Ling Tan asked suddenly out
        of the darkness. There had been need of rain for many days.
       "Only a promise," Lao Er said.
                                       Pearl S. Buck - Dragon Seed