[Debian-med-packaging] Bug#978843: jellyfish: ftbfs with autoconf 2.70

[Matthias Klose]

Package: src:jellyfish
Version: 2.3.0-6
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/jellyfish_2.3.0-6_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 

[...]
am__untar='$${TAR-tar} xf -'
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='${prefix}/share/info'
install_sh='${SHELL} /<<PKGBUILDDIR>>/install-sh'
libdir='${prefix}/lib/x86_64-linux-gnu'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='/var'
mandir='${prefix}/share/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${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 "jellyfish"
#define PACKAGE_TARNAME "jellyfish"
#define PACKAGE_VERSION "2.3.0"
#define PACKAGE_STRING "jellyfish 2.3.0"
#define PACKAGE_BUGREPORT "gmarcais at umd.edu"
#define PACKAGE_URL ""
#define PACKAGE "jellyfish"
#define VERSION "2.3.0"
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define STDC_HEADERS 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
#define HAVE_HTSLIB 1

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 --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 returned exit code 2
make[1]: *** [debian/rules:50: override_dh_auto_configure] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:21: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2