[Debian-med-packaging] Bug#976906: libpll: FTBFS on ppc64el: lex_utree.l:22:10: fatal error: parse_utree.h: No such file or directory

Lucas Nussbaum lucas at debian.org
Wed Dec 9 08:37:42 GMT 2020 

Source: libpll
Version: 0.3.2-3
Severity: serious
Justification: FTBFS on ppc64el
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201209 ftbfs-bullseye ftbfs-ppc64el

Hi,

During a rebuild of all packages in sid, your package failed to build
on ppc64el. At the same time, it did not fail on amd64.

I'm marking this bug as severity:serious since your package currently has
ppc64el binary packages in unstable (so this is a regression).

Relevant part (hopefully):
> /bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c -o libpll_la-lex_utree.lo `test -f 'lex_utree.c' || echo './'`lex_utree.c
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c fasta.c  -fPIC -DPIC -o .libs/libpll_la-fasta.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c pll.c  -fPIC -DPIC -o .libs/libpll_la-pll.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c likelihood.c  -fPIC -DPIC -o .libs/libpll_la-likelihood.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c maps.c  -fPIC -DPIC -o .libs/libpll_la-maps.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c output.c  -fPIC -DPIC -o .libs/libpll_la-output.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c utree.c  -fPIC -DPIC -o .libs/libpll_la-utree.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c utree_moves.c  -fPIC -DPIC -o .libs/libpll_la-utree_moves.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c models.c  -fPIC -DPIC -o .libs/libpll_la-models.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c parsimony.c  -fPIC -DPIC -o .libs/libpll_la-parsimony.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c core_partials.c  -fPIC -DPIC -o .libs/libpll_la-core_partials.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c derivatives.c  -fPIC -DPIC -o .libs/libpll_la-derivatives.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c utree_svg.c  -fPIC -DPIC -o .libs/libpll_la-utree_svg.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c gamma.c  -fPIC -DPIC -o .libs/libpll_la-gamma.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c rtree.c  -fPIC -DPIC -o .libs/libpll_la-rtree.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c list.c  -fPIC -DPIC -o .libs/libpll_la-list.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c partials.c  -fPIC -DPIC -o .libs/libpll_la-partials.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c compress.c  -fPIC -DPIC -o .libs/libpll_la-compress.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c core_pmatrix.c  -fPIC -DPIC -o .libs/libpll_la-core_pmatrix.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c core_likelihood.c  -fPIC -DPIC -o .libs/libpll_la-core_likelihood.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c fast_parsimony.c  -fPIC -DPIC -o .libs/libpll_la-fast_parsimony.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c core_derivatives.c  -fPIC -DPIC -o .libs/libpll_la-core_derivatives.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c phylip.c  -fPIC -DPIC -o .libs/libpll_la-phylip.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c hardware.c  -fPIC -DPIC -o .libs/libpll_la-hardware.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c random.c  -fPIC -DPIC -o .libs/libpll_la-random.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c stepwise.c  -fPIC -DPIC -o .libs/libpll_la-stepwise.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c lex_rtree.c  -fPIC -DPIC -o .libs/libpll_la-lex_rtree.o
> libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -c lex_utree.c  -fPIC -DPIC -o .libs/libpll_la-lex_utree.o
> lex_utree.l:22:10: fatal error: parse_utree.h: No such file or directory
>    22 | #include "parse_utree.h"
>       |          ^~~~~~~~~~~~~~~
> compilation terminated.
> lex_rtree.l:22:10: fatal error: parse_rtree.h: No such file or directory
>    22 | #include "parse_rtree.h"
>       |          ^~~~~~~~~~~~~~~
> compilation terminated.
> make[3]: *** [Makefile:873: libpll_la-lex_utree.lo] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/12/09/libpll_0.3.2-3_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.

About the archive rebuild: The rebuild was done on a Power8 cluster part of the
Grid'5000 testbed. Hardware specs: https://www.grid5000.fr/w/Grenoble:Hardware#drac

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