[Debian-med-packaging] Bug#978784: clustalw: ftbfs with autoconf 2.70

[Matthias Klose]

Package: src:clustalw
Version: 2.1+lgpl-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/clustalw_2.1+lgpl-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 

[...]
      |                                                              ^~~~~~~~~~~~~~
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
      |                                                                  ^~~~~~~~~~~~~~
In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
                 from ./pairwise/../alignment/Alignment.h:42,
                 from ./pairwise/PairwiseAlignBase.h:10,
                 from ./pairwise/FastPairwiseAlign.h:9,
                 from ./pairwise/FastPairwiseAlign.cpp:10:
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
      |                                                              ^~~~~~~~~~~~~~
./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
      |                                                                  ^~~~~~~~~~~~~~
In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
                 from ./fileInput/../alignment/Alignment.h:42,
                 from ./fileInput/FileReader.h:12,
                 from ./fileInput/FileReader.cpp:29:
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
      |                                                              ^~~~~~~~~~~~~~
./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
      |                                                                  ^~~~~~~~~~~~~~
In file included from ./fileInput/FileReader.cpp:29:
./fileInput/FileReader.h:42:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   42 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
      |                                      ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
                 from ./fileInput/FileReader.h:11,
                 from ./fileInput/FileReader.cpp:29:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./fileInput/FileReader.cpp: In member function ‘int clustalw::FileReader::readSeqs(clustalw::Alignment*, int, std::string*)’:
./fileInput/FileReader.cpp:155:5: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  155 |     auto_ptr<FileParser> fileParser; // Means we dont need to delete it!
      |     ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
                 from ./fileInput/FileReader.h:11,
                 from ./fileInput/FileReader.cpp:29:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./fileInput/FileReader.cpp: At global scope:
./fileInput/FileReader.cpp:426:42: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  426 | void FileReader::checkInfile(int *nseqs, auto_ptr<FileParser>& fileParser)
      |                                          ^~~~~~~~
In file included from /usr/include/c++/10/memory:83,
                 from ./fileInput/FileReader.h:11,
                 from ./fileInput/FileReader.cpp:29:
/usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
make[4]: *** [Makefile:696: FullPairwiseAlign.o] Error 1
make[4]: *** Waiting for unfinished jobs....
make[4]: *** [Makefile:710: FastPairwiseAlign.o] Error 1
make[4]: *** [Makefile:724: MSFFileParser.o] Error 1
make[4]: *** [Makefile:738: FileReader.o] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[3]: *** [Makefile:1412: all-recursive] Error 1
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:516: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: *** [Makefile:364: all-recursive] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 returned exit code 2
make: *** [debian/rules:6: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2