Your message dated Wed, 20 Dec 2023 19:23:40 +0100
with message-id <zymxlivbbvzsl...@laboissiere.net>
and subject line Re: Request for action on Bug#1057589, Bug#1057590, and
Bug#1058281
has caused the Debian Bug report #1057589,
regarding octave-netcdf: FTBFS: fatal: caught signal Segmentation fault --
stopping myself...
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1057589: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1057589
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:octave-netcdf
Version: 1.0.17-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules binary
dh binary --buildsystem=octave
dh_update_autotools_config -O--buildsystem=octave
dh_autoreconf -O--buildsystem=octave
dh_octave_version -O--buildsystem=octave
Checking the Octave version... ok
dh_auto_configure -O--buildsystem=octave
debian/rules execute_before_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
( cd doc ; \
makeinfo --no-split octave-netcdf.texi ; \
makeinfo --html --no-split octave-netcdf.texi ; \
texi2pdf octave-netcdf.texi || true )
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian)
(preloaded format=pdfetex)
restricted \write18 enabled.
entering extended mode
(./octave-netcdf.texi (/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2023-09-19.19]: pdf, fonts, glyphs, page headings,
tables, conditionals, indexing, sectioning, toc, environments, defuns, macros,
cross references, insertions, localization, formatting, microtype,
and turning on texinfo input format.)
(/<<PKGBUILDDIR>>/doc/version.texi)
(/<<PKGBUILDDIR>>/doc/macros.texi) [1{/var/lib/
texmf/fonts/map/pdftex/updmap/pdftex.map}] [2]
Cross reference values unknown; you must run TeX again. [3] [-1] Chapter 1
Writing index file octave-netcdf.cp
Chapter 2 [1] Chapter 3 [2]
(/<<PKGBUILDDIR>>/doc/functions.texi
Writing index file octave-netcdf.fn
Overfull \hbox (47.78485pt too wide) in paragraph at lines 38--38
[] @texttt nccreate("test.nc","temp","Dimensions",{"lon",10,"lat",20},"Format"
,"classic");[]
Underfull \hbox (badness 10000) in paragraph at lines 70--72
[]@textsl Format[]@textrm : one of the strings @texttt "@textrm CLAS-SIC@textt
t "@textrm , @texttt "@textrm 64BIT@texttt "@textrm , @texttt "@textrm NETCDF4@
texttt " @textrm or
pdfTeX warning (ext4): destination with the same identifier (name{3}) has been
already used, duplicate ignored
<to be read again>
@unvbox
@onepageout ...name{@the @pageno } xyz@fi @unvbox
@headlinebox @pagebody {#1...
<output> ...ark @onepageout {@pagecontents @PAGE }
}
<to be read again>
@vskip
@dobreak ... <#1@removelastskip @penalty #2@vskip
#1@fi
@sectionheading ...sname #2headingbreak@endcsname
@global @let @prevsectiond...
...
l.77 @subsubheading Groups
[3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13]
Warning: unbalanced parentheses in @def... [14] [15] [16] [17] [18] [19]
[20] Warning: unbalanced parentheses in @def... [21])
(/<<PKGBUILDDIR>>/doc/gpl.texi Appendix A
[22] [23] [24] [25] [26] [27] [28] [29] [30] [31]) (Index) [32]
No file octave-netcdf.cps.
[33] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/publ
ic/amsfonts/cm/cmr9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfo
nts/cm/cmsl10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm
/cmsltt10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cms
s10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pf
b></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></us
r/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on octave-netcdf.pdf (37 pages, 226722 bytes).
Transcript written on octave-netcdf.log.
This is pdfTeX, Version 3.141592653-2.6-1.40.25 (TeX Live 2023/Debian)
(preloaded format=pdfetex)
restricted \write18 enabled.
entering extended mode
(./octave-netcdf.texi (/usr/share/texmf/tex/texinfo/texinfo.tex
Loading texinfo [version 2023-09-19.19]: pdf, fonts, glyphs, page headings,
tables, conditionals, indexing, sectioning, toc, environments, defuns, macros,
cross references, insertions, localization, formatting, microtype,
and turning on texinfo input format.)
(/<<PKGBUILDDIR>>/doc/version.texi)
(/<<PKGBUILDDIR>>/doc/macros.texi) [1{/var/lib/
texmf/fonts/map/pdftex/updmap/pdftex.map}] [2]
(/<<PKGBUILDDIR>>/doc/octave-netcdf.aux)
[3] (/<<PKGBUILDDIR>>/doc/octave-netcdf.toc)
(/<<PKGBUILDDIR>>/doc/octave-netcdf.toc
[-1] [-2]) [-3]
(/<<PKGBUILDDIR>>/doc/octave-netcdf.toc)
(/<<PKGBUILDDIR>>/doc/octave-netcdf.toc)
Chapter 1
Writing index file octave-netcdf.cp
Chapter 2 [1] Chapter 3 [2]
(/<<PKGBUILDDIR>>/doc/functions.texi
Writing index file octave-netcdf.fn
Overfull \hbox (47.78485pt too wide) in paragraph at lines 38--38
[] @texttt nccreate("test.nc","temp","Dimensions",{"lon",10,"lat",20},"Format"
,"classic");[]
Underfull \hbox (badness 10000) in paragraph at lines 70--72
[]@textsl Format[]@textrm : one of the strings @texttt "@textrm CLAS-SIC@textt
t "@textrm , @texttt "@textrm 64BIT@texttt "@textrm , @texttt "@textrm NETCDF4@
texttt " @textrm or
pdfTeX warning (ext4): destination with the same identifier (name{3}) has been
already used, duplicate ignored
<to be read again>
@unvbox
@onepageout ...name{@the @pageno } xyz@fi @unvbox
@headlinebox @pagebody {#1...
<output> ...ark @onepageout {@pagecontents @PAGE }
}
<to be read again>
@vskip
@dobreak ... <#1@removelastskip @penalty #2@vskip
#1@fi
@sectionheading ...sname #2headingbreak@endcsname
@global @let @prevsectiond...
...
l.77 @subsubheading Groups
[3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13]
Warning: unbalanced parentheses in @def... [14] [15] [16] [17] [18] [19]
[20] Warning: unbalanced parentheses in @def... [21])
(/<<PKGBUILDDIR>>/doc/gpl.texi Appendix A
[22] [23] [24] [25] [26] [27] [28] [29] [30] [31]) (Index) [32]
(/<<PKGBUILDDIR>>/doc/octave-netcdf.cps
[33]) [34] )
(see the transcript file for additional information)</usr/share/texlive/texmf-d
ist/fonts/type1/public/amsfonts/cm/cmb10.pfb></usr/share/texlive/texmf-dist/fon
ts/type1/public/amsfonts/cm/cmbx12.pfb></usr/share/texlive/texmf-dist/fonts/typ
e1/public/amsfonts/cm/cmmi10.pfb></usr/share/texlive/texmf-dist/fonts/type1/pub
lic/amsfonts/cm/cmmi12.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/am
sfonts/cm/cmmi9.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/
cm/cmr10.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmr9
.pfb></usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsl10.pfb><
/usr/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsltt10.pfb></usr
/share/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmss10.pfb></usr/share
/texlive/texmf-dist/fonts/type1/public/amsfonts/cm/cmsy10.pfb></usr/share/texli
ve/texmf-dist/fonts/type1/public/amsfonts/cm/cmtt10.pfb></usr/share/texlive/tex
mf-dist/fonts/type1/public/amsfonts/cm/cmtt9.pfb>
Output written on octave-netcdf.pdf (40 pages, 290482 bytes).
Transcript written on octave-netcdf.log.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -O--buildsystem=octave
dh_auto_test -O--buildsystem=octave
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=octave
dh_prep -O--buildsystem=octave
dh_auto_install --destdir=debian/octave-netcdf/ -O--buildsystem=octave
octave --no-gui --no-history --silent --no-init-file --no-window-system
/usr/share/dh-octave/install-pkg.m
/<<PKGBUILDDIR>>/debian/octave-netcdf/usr/share/octave/packages
/<<PKGBUILDDIR>>/debian/octave-netcdf/usr/lib/x86_64-linux-gnu/octave/packages
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for gawk... no
checking for mawk... mawk
checking for a sed that does not truncate output... /usr/bin/sed
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking for mkoctfile... /usr/bin/mkoctfile --verbose
checking for nc-config... nc-config
checking for netcdf4 support... yes
checking is_cell or iscell... iscell
checking is_empty or isempty... isempty
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
octave-forge is configured with
mkoctfile: /usr/bin/mkoctfile --verbose
nc-config: nc-config
netCDF compiler flags: -I/usr/include -I/usr/include/hdf5/serial
netCDF libraries: -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
generating netcdf_constants.h
/usr/bin/mkoctfile --verbose -v -I/usr/include -I/usr/include/hdf5/serial
__netcdf__.cc -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/octave-8.4.0/octave/..
-I/usr/include/octave-8.4.0/octave -pthread -fopenmp -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -I/usr/include
-I/usr/include/hdf5/serial __netcdf__.cc -o /tmp/oct-3JqyBC.o
g++ -I/usr/include/octave-8.4.0/octave/.. -I/usr/include/octave-8.4.0/octave -pthread
-fopenmp -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -o
__netcdf__.oct /tmp/oct-3JqyBC.o -L/usr/lib/x86_64-linux-gnu
-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf -shared -Wl,-Bsymbolic -Wl,-z,relro
-L/usr/lib/x86_64-linux-gnu -shared -Wl,-Bsymbolic -flto=auto -ffat-lto-objects
-Wl,-z,relro
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
copyfile /<<PKGBUILDDIR>>/./src/__netcdf__.oct
/<<PKGBUILDDIR>>/./inst/x86_64-pc-linux-gnu-api-v58
For information about changes from previous versions of the netcdf package, run
'news netcdf'.
dh_octave_check -O--buildsystem=octave
Checking package...
Checking m files ...
[inst/test_netcdf.m]
/<<PKGBUILDDIR>>/inst/test_netcdf.m
***** test
fprintf ("\n");
test_netcdf ();
Using NetCDF library version "4.9.2 of Sep 4 2023 05:51:05 $"
run test_netcdf_constant.............. OK
run test_netcdf_create................ OK
run test_netcdf_low_level_interface... OK
run test_netcdf_unlim................. warning: variable size 0 or currently
too large to process
warning: called from
getVar at line 31 column 28
test_netcdf_unlim at line 30 column 3
test_netcdf at line 50 column 7
__test__ at line 4 column 2
test at line 682 column 11
/tmp/tmp.mXQPePYx1A at line 14 column 31
OK
run test_netcdf_datatypes............. OK
run test_netcdf_scalar_variable....... OK
run test_netcdf_attributes............ OK
run test_netcdf_high_level_interface.. OK
run test_netcdf_ncwriteschema......... OK
run test_netcdf_ncwriteschema_unlim... OK
run test_netcdf_ncwriteschema_chunking OK
run test_netcdf_ncwriteschema_group... OK
run test_netcdf_user_types............ OK
run bug_47014......................... OK
1 test, 1 passed, 0 known failure, 0 skipped
Checking C++ files ...
Run tests in debian/check.m
[test_netcdf]
Using NetCDF library version "4.9.2 of Sep 4 2023 05:51:05 $"
run test_netcdf_constant.............. OK
run test_netcdf_create................ OK
run test_netcdf_low_level_interface... OK
run test_netcdf_unlim................. warning: variable size 0 or currently
too large to process
warning: called from
getVar at line 31 column 28
test_netcdf_unlim at line 30 column 3
test_netcdf at line 50 column 7
check at line 3 column 1
/tmp/tmp.mXQPePYx1A at line 35 column 5
OK
run test_netcdf_datatypes............. OK
run test_netcdf_scalar_variable....... OK
run test_netcdf_attributes............ OK
run test_netcdf_high_level_interface.. OK
run test_netcdf_ncwriteschema......... OK
run test_netcdf_ncwriteschema_unlim... OK
run test_netcdf_ncwriteschema_chunking OK
run test_netcdf_ncwriteschema_group... OK
run test_netcdf_user_types............ OK
run bug_47014......................... OK
fatal: caught signal Segmentation fault -- stopping myself...
Segmentation fault
make: *** [debian/rules:5: binary] Error 139
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202312/
About the archive rebuild: The build was made using virtual machines
from AWS, with enough memory, enough disk, and either one or two
CPUs, using a reduced chroot with only build-essential packages.
If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Control: reassign 1057589 src:netcdf
Control: reassign 1057590 src:netcdf
Control: reassign 1058281 src:netcdf
Control: affects 1057589 octave-netcdf octave-ncarray
Control: affects 1057590 octave-netcdf octave-ncarray
Control: affects 1058281 octave-netcdf octave-ncarray
Control: found 1057589 4.9.2-2
Control: found 1057590 4.9.2-2
Control: found 1058281 4.9.2-2
Control: fixed 1057589 4.9.2-3
Control: fixed 1057590 4.9.2-3
Control: fixed 1058281 4.9.2-3
* Santiago Vila <sanv...@debian.org> [2023-12-20 12:42]:
El 20/12/23 a las 7:02, Rafael Laboissière escribió:
Hi Santiago and Lucas,
You have filed bug reports against octave-netcdf (Bug#1057590) and
octave-ncarray (Bug#1057589 and Bug#1058281). These packages FTBFS due to an
issue in the netcdf package (Bug#1058281), which has been fixed thanks to the
recent upload of version 4.9.2-3.
Would it be possible to check the build of octave-netcdf and octave-ncarray on
your systems, such that we can close the bug reports?
Hello. I confirm that both octave-netcdf and octave-ncarray build ok
in both trixie and sid, where they previously failed.
Thanks for the check, Santiago.
I'm not sure at this point if the bugs should be reassigned to netcdf
before being closed (and another affects added), so I leave that to
you.
I am hereby trying to do this. Hope I got the Control lines right.
Best,
Rafael
Thanks.
--- End Message ---
