[Debian-med-packaging] Bug#938472: Autoconf detection of libsparsehash-dev fails in sga (Was: Bug#938472: sga: Python2 removal in sid/bullseye)

[Andreas Tille]

Hi,

I dived into this more deeply and think my code snippet below was
misleading.  The configure faulure is rather:


checking google/sparse_hash_set usability... no
checking google/sparse_hash_set presence... yes
configure: WARNING: google/sparse_hash_set: present but cannot be compiled
configure: WARNING: google/sparse_hash_set:     check for missing prerequisite headers?
configure: WARNING: google/sparse_hash_set: see the Autoconf documentation
configure: WARNING: google/sparse_hash_set:     section "Present But Cannot Be Compiled"
configure: WARNING: google/sparse_hash_set: proceeding with the compiler's result
configure: WARNING:     ## -------------------------------- ##
configure: WARNING:     ## Report this to js18 at sanger.ac.uk ##
configure: WARNING:     ## -------------------------------- ##
checking for google/sparse_hash_set... no
configure: error: google sparse hash library is required: http://code.google.com/p/google-sparsehash/
<------>cd src && tail -v -n \+0 config.log
==> config.log <==


I have found an according issue upstream:

   https://github.com/jts/sga/issues/156

I tried to follow the hint given there by

--- a/debian/rules
+++ b/debian/rules
@@ -8,6 +8,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 include /usr/share/dpkg/default.mk
 
+export DEB_CXXFLAGS_MAINT_APPEND=-std=c++98
+
 %:
        dh $@ --sourcedirectory=src
 

but this does not change anything.  Is there any hint how I can
make sure that sparsehash is detected properly?

Kind regards

       Andreas.


On Thu, Sep 05, 2019 at 03:52:28PM +0200, Andreas Tille wrote:
> Control: tags -1 help
> 
> Hi,
> 
> I prepared a Python3 port in Git[1] using 2to3.  Unfortunately I get a
> configuration error which seems to be totally unrelated to the Python3
> port.  Has anybody an idea how this can be fixed:
> 
> 
> ...
> configure:4727: result: yes
> configure:4727: checking for zlib.h
> configure:4727: result: yes
> configure:4735: checking for library containing gzopen
> configure:4766: g++ -o conftest -g -O2 -fdebug-prefix-map=/build/sga-0.10.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now conftest.cpp  >&5
> /usr/bin/ld: /tmp/ccXL5EK2.o: in function `main':
> ./src/conftest.cpp:32: undefined reference to `gzopen'
> collect2: error: ld returned 1 exit status
> ...
> 
> 
> It looks pretty strange since zlib1g-dev is in Build-Depends.
> 
> Any hint is welcome
> 
>       Andreas.
> 
> 
> [1] https://salsa.debian.org/med-team/sga
> 
> -- 
> http://fam-tille.de
> 
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