Bug#929264: Segmentation fault in grdpaste

[Joachim Breitner]

Package: gmt
Version: 5.4.5+dfsg-1
Severity: normal

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Hi,

this sequence of commands causes a segementation fault. This is a
regression; this is from a project from a few years back and worked
then:

wget -c http://dds.cr.usgs.gov/srtm/version2_1/SRTM3/Eurasia/N45E0{06,07}.hgt.zip
unzip N45E006.hgt.zip
gmt xyz2grd N45E006.hgt -R6/7/45/46 -I3s -di-32768 -ZTLhw -GN45E006.grd
gmt grd2xyz N45E006.grd >N45E006.txt
gmt surface N45E006.txt -RN45E006.grd -T0.35 -GN45E006.grd
unzip N45E007.hgt.zip
gmt xyz2grd N45E007.hgt -R7/8/45/46 -I3s -di-32768 -ZTLhw -GN45E007.grd
gmt grd2xyz N45E007.grd >N45E007.txt
gmt surface N45E007.txt -RN45E007.grd -T0.35 -GN45E007.grd
cp N45E006.grd 45tmp.grd
gmt grdpaste 45tmp.grd N45E007.grd -G45tmp.grd
ERROR: Caught signal number 11 (Segmentation fault) at
/usr/lib/x86_64-linux-gnu/libnetcdf.so.13(NC_check_nulls+0xc7)[0x7f9dbb8af9a7]
[0x0]
Stack backtrace:
/usr/lib/x86_64-linux-gnu/libgmt.so.5(sig_handler+0x2ac)[0x7f9dbb9f006c]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x12670)[0x7f9dbb4c9670]
/usr/lib/x86_64-linux-gnu/libnetcdf.so.13(NC_check_nulls+0xc7)[0x7f9dbb8af9a7]
/usr/lib/x86_64-linux-gnu/libnetcdf.so.13(+0x2df9f)[0x7f9dbb8aff9f]
/usr/lib/x86_64-linux-gnu/libnetcdf.so.13(nc_get_varm_float+0xf)[0x7f9dbb8b133f]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(+0x91c24)[0x7f9dbba54c24]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(gmt_nc_read_grd+0x826)[0x7f9dbba55bb6]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(gmtlib_read_grd+0x9e)[0x7f9dbba37ede]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(+0x488e8)[0x7f9dbba0b8e8]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(GMT_Read_Data+0x4c3)[0x7f9dbba0d213]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(GMT_grdpaste+0x3e0)[0x7f9dbbbaddc0]
/usr/lib/x86_64-linux-gnu/libgmt.so.5(GMT_Call_Module+0xc0)[0x7f9dbb9faf50]
gmt(main+0x5c6)[0x55ef48806716]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xeb)[0x7f9db8ca709b]
gmt(_start+0x2a)[0x55ef48806cda]

Cheers,
Joachim

- -- System Information:
Debian Release: buster/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.19.0-2-amd64 (SMP w/8 CPU cores)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8), LANGUAGE=de_DE.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages gmt depends on:
ii  gmt-common                       5.4.5+dfsg-1
ii  libatlas3-base [liblapack.so.3]  3.10.3-8
ii  libblas3 [libblas.so.3]          3.8.0-2
ii  libc6                            2.28-5
ii  libcurl3-gnutls                  7.63.0-1
ii  libfftw3-single3                 3.3.8-2
ii  libgdal20                        2.4.0+dfsg-1+b1
ii  libgmt5                          5.4.5+dfsg-1
ii  libhdf5-103                      1.10.4+repack-9
ii  liblapack3 [liblapack.so.3]      3.8.0-2
ii  libnetcdf13                      1:4.6.2-1
ii  libpcre3                         2:8.39-11
ii  libsz2                           1.0.2-1
ii  zlib1g                           1:1.2.11.dfsg-1

Versions of packages gmt recommends:
ii  gmt-dcw                          1.1.4-2
ii  gmt-doc                          5.4.5+dfsg-1
ii  gmt-gshhg-full [gmt-gshhg-data]  2.3.7-4
ii  gmt-gshhg-high [gmt-gshhg-data]  2.3.7-4
ii  gmt-gshhg-low [gmt-gshhg-data]   2.3.7-4

Versions of packages gmt suggests:
pn  gmt-examples  <none>

- -- no debconf information

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