Subject: Re: bug#39204: r-rgdal: Reading of vector GIS data causes segfault

From: zimoun <[email-masked]>
Date: Thu, 20 Feb 2020 11:35:12 +0100

Hi Arun,

There is 2 issues in this bug report:

 1. the `check' phase is failing but the build ends with "success".
 2. a regression of r-rgdal introduced by your commit
f9d328833fc1f5d0fb76b61b12d1a3cb013932e6

About the point 1., here is what happens:

> --8<---------------cut here---------------start------------->8---
> $ guix build r-rgdal --check --no-grafts -K
> [...]
> phase `install' succeeded after 19.0 seconds
> starting phase `check'
> Testing examples for package ‘rgdal’
> /gnu/store/dnb6fzp5295fcda66dnjk2y51mcva20f-r-minimal-3.6.2/lib/R/bin/BATCH:
> line 60:   598 Segmentation fault      ${R_HOME}/bin/R -f ${in}
> ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
> [...]
> successfully built /gnu/store/7spmagnk5fycwxsigdypwkmk4kazbw7a-r-rgdal-1.4-8.drv
> note: keeping build directory `/tmp/guix-build-r-rgdal-1.4-8.drv-0'
> /gnu/store/dgkyzlasbqsxcsfk3n3bgmhrpg447f55-r-rgdal-1.4-8
> --8<---------------cut here---------------end--------------->8---

Therefore, more investigations are required to see why the upstream
test suite does not report correctly the failure.

However, the Segmentation Fault is the point 2. and introduced by the commit:

--8<---------------cut here---------------start------------->8---
commit f9d328833fc1f5d0fb76b61b12d1a3cb013932e6
Author: Arun Isaac <[email-masked]>
Date:   Thu Dec 5 01:47:47 2019 +0530

    gnu: libgeotiff: Update to 1.5.1.

    * gnu/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch:
    New file.
    * gnu/local.mk (dist_patch_DATA): Register it.
    * gnu/packages/geo.scm (libgeotiff): Update to 1.5.1.
    [inputs]: Replace proj.4 with proj.
    [sources]: Add libgeotiff-adapt-test-script-for-proj-6.2.patch
    to patches.

 gnu/local.mk                                       |  1 +
 gnu/packages/geo.scm                               | 17 +++---
 ...libgeotiff-adapt-test-script-for-proj-6.2.patch | 63 ++++++++++++++++++++++
 3 files changed, 72 insertions(+), 9 deletions(-)
 create mode 100644
gnu/packages/patches/libgeotiff-adapt-test-script-for-proj-6.2.patch
--8<---------------cut here---------------end--------------->8---

I have bisected this way:

git bisect start
git bisect bad ba7ead2b507d94397481be014d6ac0c41c7ddbfa
git bisect good 28d940961cfa1ae6dc574053aec8d03095677df8

# ba7ead2b507d94397481be014d6ac0c41c7ddbfa => bad
# 28d940961cfa1ae6dc574053aec8d03095677df8 => good
# fe0686864dc57ecdda7ecbb318d2618ac46169ae => bad
# 85c945aa97d89fdc17ec5d64c3ffa7f99ba1184b => good
# 885424bf7f6e0bc0ad5dd9353690aa82d17dd8b8 => bad
# 6f5d849a83c44ffb39c3a976aea10b7b31c24063 => good
# ce5b71f98ce39c92637876120f44868ec7ad391f => good
# 96211e3f33d1f1c35fd6377db1d8a4c6ec1a9c22 => bad
# 6cde07379f2a049b8c7f0eca90959f6c170c4102 => bad
# 87a028100c665814c3b5d622701abc6d77144faf => good
# 00d81f9866726f85241f08e444ba3932fcb38842 => good
# e72557c08f4f2fdd545106a9f4f0fc0bc9496249 => bad
# 3500d7addc2f9b2067ffd239383eb0e546be4f43 => good
# f9d328833fc1f5d0fb76b61b12d1a3cb013932e6 => bad

Please could you confirm?
If 'libgeotiff' is really the culprit, then we can try to fix it.

All the best,
simon