Community Packages

Please read this before reporting a bug:
https://wiki.archlinux.org/title/Bug_reporting_guidelines

Do NOT report bugs when a package is just outdated, or it is in the AUR. Use the 'flag out of date' link on the package page, or the Mailing List.

REPEAT: Do NOT report bugs for outdated packages!
Tasklist

FS#55026 - [gdal] 2.1.2-2 -> 2.2.0-2 => error while loading shared libraries: libhdf5.so.101

Attached to Project: Community Packages
Opened by Johnny Nielsen (Johnny.Nielsen) - Thursday, 03 August 2017, 13:43 GMT
Last edited by Evangelos Foutras (foutrelis) - Thursday, 03 August 2017, 14:33 GMT
Task Type Bug Report
Category Packages
Status Closed
Assigned To Jaroslav Lichtblau (Dragonlord)
Evangelos Foutras (foutrelis)
Bruno Pagani (ArchangeGabriel)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Greetings :o)

Please, if this is not a problem with gdal 2.1.2-2, then kindly refer me to whatever package you may think is the problem :o)

qmapshack 1.8.1-2, which depends on gdal, worked before the latest upgrade of gdal.
Note that the package (hdf5 1.10.0_patch1-2) providing the libhdf5.so* library files, was _not_ upgraded, and that the latest officially stable version of hdf5 contains the older libhdf5.so.100 .

pacman -Syyu does not solve the problem.
Upgrading hdf5 to the newer version in testing does not solve the problem, but, rather amusingly, then complains that libhdf5.so.100 (the old version) could not be found ;o)
Downgrading gdal to the previous version does not solve the problem, but seems to require downgrading of other packages too. I'm not keen to start working my way through an entire tree of downgrades :o)
Other suggestions kindly welcomed :o)

The problem
-----------
[johnny@comp ~]$ qmapshack
qmapshack: error while loading shared libraries: libhdf5.so.101: cannot open shared object file: No such file or directory

Problem investigation
---------------------
[johnny@comp ~]$ find / -name "libhdf5.so*"
(Irrelevant output snipped)
/usr/lib/libhdf5.so.100
/usr/lib/libhdf5.so
/usr/lib/libhdf5.so.100.0.1

[johnny@comp ~]$ pacman -Qo /usr/lib/libhdf5.so.100 /usr/lib/libhdf5.so /usr/lib/libhdf5.so.100.0.1
/usr/lib/libhdf5.so.100 is owned by hdf5 1.10.0_patch1-2
/usr/lib/libhdf5.so is owned by hdf5 1.10.0_patch1-2
/usr/lib/libhdf5.so.100.0.1 is owned by hdf5 1.10.0_patch1-2

[johnny@comp ~]$ pactree -r hdf5
hdf5
├─gdal
│ └─qmapshack
└─netcdf
└─gdal

[johnny@comp ~]$ less /var/log/pacman.log
(Log entries before the latest upgrade are snipped)
(gdal is the only one of the dependencies that were upgraded, marked with a '*')
[2017-08-03 05:43] [PACMAN] Running 'pacman -Syu'
[2017-08-03 05:43] [PACMAN] starting full system upgrade
[2017-08-03 05:44] [ALPM] transaction started
[2017-08-03 05:44] [ALPM] upgraded poppler (0.56.0-1 -> 0.57.0-1)
[2017-08-03 05:44] [ALPM] upgraded cups-filters (1.16.0-1 -> 1.16.0-2)
*[2017-08-03 05:44] [ALPM] upgraded gdal (2.1.2-2 -> 2.2.0-2)
[2017-08-03 05:44] [ALPM] upgraded libreoffice-still (5.3.4-1 -> 5.3.4-2)
[2017-08-03 05:44] [ALPM] upgraded poppler-qt4 (0.56.0-1 -> 0.57.0-1)
[2017-08-03 05:44] [ALPM] upgraded poppler-qt5 (0.56.0-1 -> 0.57.0-1)
[2017-08-03 05:44] [ALPM] upgraded python-setuptools (1:36.2.4-1 -> 1:36.2.7-1)
[2017-08-03 05:44] [ALPM] upgraded talloc (2.1.9-1 -> 2.1.10-1)
[2017-08-03 05:44] [ALPM] upgraded x11vnc (1:0.9.14-2 -> 1:0.9.14-3)
[2017-08-03 05:44] [ALPM] transaction completed
[2017-08-03 05:44] [ALPM] running 'gtk-update-icon-cache.hook'...
[2017-08-03 05:45] [ALPM] running 'systemd-update.hook'...
[2017-08-03 05:45] [ALPM] running 'update-desktop-database.hook'...
[2017-08-03 05:45] [ALPM] running 'update-mime-database.hook'...
[2017-08-03 05:45] [ALPM-SCRIPTLET] Unknown media type in type 'all/all'
[2017-08-03 05:45] [ALPM-SCRIPTLET] Unknown media type in type 'all/allfiles'
[end of log file]

- - -

Cheers, Johnny :o)
This task depends upon

Closed by  Evangelos Foutras (foutrelis)
Thursday, 03 August 2017, 14:33 GMT
Reason for closing:  Fixed
Additional comments about closing:  gdal 2.2.0-3
Comment by Adriano Fantini (OdinEidolon) - Thursday, 03 August 2017, 14:09 GMT
Having the same problem with other GDAL-based programs.
For example, in R:

> library(rgdal)
> Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
> unable to load shared object '/home/adriano/.R_libs/rgdal/libs/rgdal.so':
> libhdf5.so.101: cannot open shared object file: No such file or directory

Loading...