[Debian-med-packaging] Bug#978841: infernal: ftbfs with autoconf 2.70

[Matthias Klose]

Package: src:infernal
Version: 1.1.3-5
Severity: normal
Tags: sid bookworm
User: doko at debian.org
Usertags: ftbfs-ac270

[This bug report is not targeted to the upcoming bullseye release]

The package fails to build in a test rebuild on at least amd64 with
autoconf 2.70, but succeeds to build with autoconf 2.69. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://qa-logs.debian.net/2020/09/26.ac270/infernal_1.1.3-5_unstable_ac270.log
The last lines of the build log are at the end of this report.

To build with autoconf 2.70, please install the autoconf package from
experimental:  apt-get -t=experimental install autoconf 

[...]
VMX_CFLAGS=''
ac_ct_CC='gcc'
ax_pthread_config=''
bindir='${exec_prefix}/bin'
build='x86_64-pc-linux-gnu'
build_alias='x86_64-linux-gnu'
build_cpu='x86_64'
build_os='linux-gnu'
build_vendor='pc'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host='x86_64-pc-linux-gnu'
host_alias=''
host_cpu='x86_64'
host_os='linux-gnu'
host_vendor='pc'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${prefix}/share/info'
libdir='${prefix}/lib/x86_64-linux-gnu'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='/var'
mandir='${prefix}/share/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr'
program_transform_name='s,x,x,'
psdir='${docdir}'
runstatedir='/run'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "Infernal"
#define PACKAGE_TARNAME "infernal"
#define PACKAGE_VERSION "1.1.3"
#define PACKAGE_STRING "Infernal 1.1.3"
#define PACKAGE_BUGREPORT "eric.nawrocki at nih.gov"
#define PACKAGE_URL ""
#define INFERNAL_DATE "Nov 2019"
#define INFERNAL_COPYRIGHT "Copyright (C) 2019 Howard Hughes Medical Institute."
#define INFERNAL_LICENSE "Freely distributed under the BSD open source license."
#define INFERNAL_VERSION "1.1.3"
#define INFERNAL_URL "http://eddylab.org/infernal/"
#define HMMER_DATE "Nov 2019"
#define HMMER_COPYRIGHT "Copyright (C) 2019 Howard Hughes Medical Institute."
#define HMMER_LICENSE "Freely distributed under the BSD open source license."
#define HMMER_VERSION "3.3"
#define HMMER_URL "http://hmmer.org/"
#define EASEL_DATE "Nov 2019"
#define EASEL_COPYRIGHT "Copyright (C) 2019 Howard Hughes Medical Institute."
#define EASEL_LICENSE "Freely distributed under the BSD open source license."
#define EASEL_VERSION "0.46"
#define EASEL_URL "http://bioeasel.org/"
#define eslDEBUGLEVEL 0

configure: exit 2
dh_auto_configure: error: ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking returned exit code 2
make: *** [debian/rules:13: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2