[Debian-med-packaging] You pushed new upstream source but no Debian packaging (Was: [Git][med-team/bali-phy] Pushed new tag upstream/3.1.4+dfsg)
Andreas Tille
andreas at an3as.eu
Tue May 22 07:12:50 BST 2018
Hi Benjamin,
I noticed your push of the new upstream source but no change in
packaging arrived in Git. I wonder whether you might have some not yet
pushed commits on your side. Please also note: While I'm observing the
commits I usually do not sponsor a package to the Debian mirror before I
get an explicite signal via mail asking for it. Just commiting to Git
does not have the effect that a package is uploaded automatically.
BTW, there are some issues for 3.1.2 on some architectures. You can see
an overview on the package tracker[1]. This is the relevant part of the
build log on i386:
...
[111/242] c++ -Isrc/src@@bali-phy at exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/src@@bali-phy at exe/parser_parse.cc.o' -MF 'src/src@@bali-phy at exe/parser_parse.cc.o.d' -o 'src/src@@bali-phy at exe/parser_parse.cc.o' -c ../src/parser/parse.cc
FAILED: src/src@@bali-phy at exe/parser_parse.cc.o
c++ -Isrc/src@@bali-phy at exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/src@@bali-phy at exe/parser_parse.cc.o' -MF 'src/src@@bali-phy at exe/parser_parse.cc.o.d' -o 'src/src@@bali-phy at exe/parser_parse.cc.o' -c ../src/parser/parse.cc
../src/parser/parse.cc: In constructor ‘HParser<Iterator>::HParser(HParser<Iterator>::error_handler_type&, const TokenDef&) [with TokenDef = HTokens<boost::spirit::lex::lexertl::actor_lexer<boost::spirit::lex::lexertl::position_token<boost::spirit::basic_istream_iterator<char>, boost::mpl::vector<int, char, std::__cxx11::basic_string<char> > > > >; Iterator = boost::spirit::lex::lexertl::iterator<boost::spirit::lex::lexertl::functor<boost::spirit::lex::lexertl::position_token<boost::spirit::basic_istream_iterator<char>, boost::mpl::vector<int, char, std::__cxx11::basic_string<char> > >, boost::spirit::lex::lexertl::detail::data, boost::spirit::basic_istream_iterator<char>, mpl_::bool_<true>, mpl_::bool_<true> > >]’:
../src/parser/parse.cc:563:5: note: variable tracking size limit exceeded with -fvar-tracking-assignments, retrying without
HParser(error_handler_type& error_handler, const TokenDef& tok)
^~~~~~~
virtual memory exhausted: Operation not permitted
...
I wonder whether this is a sign that balil-phy should be restricted to
64bit architectures. However the build on mips64el has another issue[2]:
...
dh_auto_test -a -O--buildsystem=meson
cd obj-mips64el-linux-gnuabi64 && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 ninja test
[1/4] Generating git-version.h with a custom command.
[1/2] Running all tests.
1/28 bali-phy version OK 0.11 s
2/28 bali-phy help OK 0.10 s
3/28 bali-phy 5d test OK 5.44 s
4/28 bali-phy 5d +A 50 TIMEOUT 30.12 s
5/28 bali-phy 5d -A 200 OK 29.63 s
6/28 model_P --help OK 0.05 s
7/28 statreport --help OK 0.04 s
8/28 stats-select --help OK 0.03 s
9/28 alignment-gild --help OK 0.03 s
10/28 alignment-consensus --help OK 0.04 s
11/28 alignment-max --help OK 0.04 s
12/28 alignment-chop-internal --help OK 0.04 s
13/28 alignment-indices --help OK 0.04 s
14/28 alignment-info --help OK 0.03 s
15/28 alignment-cat --help OK 0.03 s
16/28 alignment-translate --help OK 0.04 s
17/28 alignment-find --help OK 0.04 s
18/28 trees-consensus --help OK 0.04 s
19/28 tree-mean-lengths --help OK 0.04 s
20/28 mctree-mean-lengths --help OK 0.04 s
21/28 trees-to-SRQ --help OK 0.04 s
22/28 pickout --help OK 0.03 s
23/28 subsample --help OK 0.03 s
24/28 cut-range --help OK 0.04 s
25/28 trees-distances --help OK 0.04 s
26/28 alignment-thin --help OK 0.04 s
27/28 alignments-diff --help OK 0.03 s
28/28 bali-phy testsuite OK 359.37 s
OK: 27
FAIL: 1
SKIP: 0
TIMEOUT: 1
...
Please let me know whether I should upload 3.1.4 and what you think about the
issues on the other architectures.
Kind regards
Andreas.
[1] https://buildd.debian.org/status/package.php?p=bali-phy
[2] https://buildd.debian.org/status/fetch.php?pkg=bali-phy&arch=mips64el&ver=3.1.2%2Bdfsg-1&stamp=1525904116&raw=0
On Mon, May 14, 2018 at 12:51:53PM +0000, Benjamin Redelings wrote:
> Benjamin Redelings pushed new tag upstream/3.1.4+dfsg at Debian Med / bali-phy
>
> ---
> View it on GitLab: https://salsa.debian.org/med-team/bali-phy/tree/upstream/3.1.4+dfsg
> You're receiving this email because of your account on salsa.debian.org.
> _______________________________________________
> debian-med-commit mailing list
> debian-med-commit at alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
--
http://fam-tille.de
More information about the Debian-med-packaging
mailing list