[Debian-med-packaging] Bug#957581: ncbi-blast+: ftbfs with GCC-10

[Matthias Klose]

Package: src:ncbi-blast+
Version: 2.9.0-4
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/ncbi-blast+_2.9.0-4_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html

[...]
includedir='${prefix}/include'
infodir='${datarootdir}/info'
internal=''
lib_ext=''
lib_l_ext=''
lib_l_pre=''
lib_pre=''
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
loadable_ext=''
local_lbsm=''
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
make_shell=''
mandir='${datarootdir}/man'
mysql_config=''
ncbi_crypt=''
ncbi_id2proc_snp=''
ncbi_id2proc_wgs=''
ncbi_java=''
ncbi_runpath=''
ncbi_xloader_bam=''
ncbi_xloader_csra=''
ncbi_xloader_snp=''
ncbi_xloader_sra=''
ncbi_xloader_vdbgraph=''
ncbi_xloader_wgs=''
ncbi_xreader_pubseqos2=''
ncbi_xreader_pubseqos=''
ncbicntr=''
obj_ext=''
objects=''
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
runpath=''
sbindir='${exec_prefix}/sbin'
script_shell=''
serial=''
serial_ws50_rtti_kludge=''
sharedstatedir='${prefix}/com'
signature=''
sraread=''
srcdir='.'
sssutils=''
status_dir=''
sysconfdir='${prefix}/etc'
target_alias=''
top_srcdir=''
wxconf=''

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

#define NCBI_CXX_TOOLKIT 1
#define HAVE_COMMON_NCBI_BUILD_VER_H 1
#define HOST "x86_64-pc-linux-gnu"
#define HOST_CPU "x86_64"
#define HOST_VENDOR "pc"
#define HOST_OS "linux-gnu"

configure: exit 1
tail: cannot open 'BUILD/status/config.log' for reading: No such file or directory
make[1]: *** [debian/rules:68: override_dh_auto_configure-arch] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:168: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2