[SOLVED] GDAL install fails due to missing shared library libIlmImf

Tsuga · 06-22-2022, 08:50 PM

I did an system update via

Code:

slackpkg upgrade-all

and GDAL stopped working.

Later I used R and one of the libraries I needed indicated a problem with GDAL. I exit R.

I use

Code:

gdalinfo

and get this error:

Quote:

gdalinfo: error while loading shared libraries: libIlmImf-2_5.so.25: cannot open shared object file: No such file or directory

I searched online for "libIlmImf" and results point to OpenEXR. I use

Code:

slackpkg search openex*

and that returned:

Quote:

[ installed ] - openexr-3.1.5-x86_64-1

Not sure where to find that package, I used a find statement and

Code:

less /var/lib/pkgtools/packages/openexr-3.1.5-x86_64-1

reveals no libIlmImf. Neither does a find statement with "libIlmImf".

I'm trying to get the GDAL version on sbopkg, 3.5. It installs, but that's when I get the error. I don't know how to repair this issue.

3rensho · 06-22-2022, 10:55 PM

Did you try just rebuilding GDAL after the upgrade-all? I have found that when a previously running program fails after an update with the missing .so version error, rebuilding the app often fixes it.

henca · 06-23-2022, 01:30 AM

Quote:

Originally Posted by Tsuga

I searched online for "libIlmImf" and results point to OpenEXR.

Code:

less /var/lib/pkgtools/packages/openexr-3.1.5-x86_64-1

reveals no libIlmImf. Neither does a find statement with "libIlmImf".

On my Slackware 14.2 system it really does seem that libIlmImf used to belong to the openexr package:

Code:

/var/log/packages/openexr-2.2.0-x86_64-2_slack14.2:usr/lib64/libIlmImf-2_2.so.22.0.0
/var/log/packages/openexr-2.2.0-x86_64-2_slack14.2:usr/lib64/libIlmImf.la
/var/log/packages/openexr-2.2.0-x86_64-2_slack14.2:usr/lib64/libIlmImfUtil-2_2.so.22.0.0
/var/log/packages/openexr-2.2.0-x86_64-2_slack14.2:usr/lib64/libIlmImfUtil.la

However, things can change between versions, especially between major versions. Your gdal installation seems to depend upon a version 2 of openexr and you seem to have a version 3 of openexr installed.

regards Henrik

kjhambrick · 06-23-2022, 10:18 AM

What henca said is also true for Slackware64 15.0 + Multilib:

Code:

# whatprovides  libIlmImf
# Package: /dld/15.0/slackware/slackware-15.0-64/slackware64/l/openexr-2.5.7-x86_64-5.txz
-rwxr-xr-x root/root   3127176 2022-01-27 13:36 /usr/lib64/libIlmImf-2_5.so.25.0.6
-rwxr-xr-x root/root    176032 2022-01-27 13:36 /usr/lib64/libIlmImfUtil-2_5.so.25.0.6

# Package: /dld/15.0/multilib/15.0/slackware64-compat32/l-compat32/openexr-compat32-2.5.7-x86_64-5compat32.txz
-rwxr-xr-x root/root    182568 2022-01-27 22:24 /usr/lib/libIlmImfUtil-2_5.so.25.0.6
-rwxr-xr-x root/root   3147044 2022-01-27 22:24 /usr/lib/libIlmImf-2_5.so.25.0.6

However, in Slackware64 Current, ~/l/openexr-3.1.5-x86_64-1.txz no longer includes libIlmImf ...

HTH

-- kjh

ArTourter · 06-23-2022, 02:10 PM

Hi,

I assume from the issue you are having and the discussion in the thread that you have upgraded your slackware install to -current from 15.0. After doing such an upgrade you will have to rebuild all your sbo packages.

sbo (and therefore tools such as sbopkg) do to track slackware library changes and so you have to do that yourself. This is especially relevant with current since .so lib version bumps are very frequent. Remember that slackbuilds.org only provide scripts to build the packages and not the packages themselves.

Also, don't forget that slackbuilds.org does not officially support -current, however in this case I do happen to also use current so I test my packages on both -stable and -current. As @3rensho said in the forum, you need to rebuild gdal against the new versions of the dependent libraries (in your case, at least openexr and poppler). Note that poppler is one of these that tends to bump the .so lib version on a very regular basis so you will need to rebuild gdal (and any open packages you have that rely on it) every time it is updated.

Hope this helps

Tsuga · 06-23-2022, 02:21 PM

lol. I thought I was on 15. I honestly didn't realize that using upgrade-all would change the OS version. I thought it just updated packages, not the OS. ArTourter's explanation explains why QGIS isn't working now too. Oy vey. Thanks, everyone, for your help!

I got the GDAL to work, but after changing the libproj.so with a "ln -s" call from the version now installed (25) to the version that GDAL was looking for (22).

ArTourter · 06-24-2022, 03:26 AM

Quote:

Originally Posted by Tsuga

lol. I thought I was on 15. I honestly didn't realize that using upgrade-all would change the OS version. I thought it just updated packages, not the OS. ArTourter's explanation explains why QGIS isn't working now too. Oy vey. Thanks, everyone, for your help!

I got the GDAL to work, but after changing the libproj.so with a "ln -s" call from the version now installed (25) to the version that GDAL was looking for (22).

Upgrade-all will upgrade according to the mirrors you are pointing at. If your are pointing at the currrent tree, it will upgrade to currrent.

As for proj, please don't do this. Proj was updated and bumped the so lib version. Please rebuild the gdal package, do not simply install the old one! Same goes for qgis. Once these packages are rebuilt you will no longer have the missing lib/wrong lib version problems.

Greg

Tsuga · 06-24-2022, 08:13 PM

Sorry. What does "rebuild" mean? Does that mean to get the sbopkg package and just let it build that way? Or get the source from https://trac.osgeo.org/gdal/wiki/DownloadSource and build that?

Tonus · 06-25-2022, 01:27 AM

Rebuild is just redo the sbopkg process : it will fetch source code of theprogram, build it and install the package.

Tsuga · 06-25-2022, 09:26 AM

Thanks, Tonus.

Tsuga · 06-25-2022, 01:17 PM

I got my sbopkg package problem fixed and sbopkg is synced with remote repo again.

I used

Code:

sqg -a

to build the queue files. In sbopkg, I uninstalled PROJ and GDAL. I used

Code:

sbopkg -i GDAL

to install PROJ and GDAL again. The install has just finished and I tested with

Code:

gdalinfo

and I still get this error:

Quote:

gdalinfo
gdalinfo: error while loading shared libraries: libproj.so.22: cannot open shared object file: No such file or directory

This result seems contrary to what ArTourter indicated. What should I do to get GDAL and PROJ to play nice?

ponce · 06-25-2022, 01:40 PM

I just tried to build geos, proj and gdal on a clean system and everything went fine, also when I run gdalinfo

Code:

$ gdalinfo 
Usage: gdalinfo [--help-general] [-json] [-mm] [-stats | -approx_stats] [-hist] [-nogcp] [-nomd]
                [-norat] [-noct] [-nofl] [-checksum] [-proj4]
                [-listmdd] [-mdd domain|`all`] [-wkt_format WKT1|WKT2|...]*
                [-sd subdataset] [-oo NAME=VALUE]* [-if format]* datasetname

FAILURE: No datasource specified.

my guess is that you have installed on your system some optional dependencies of gdal that use proj too like, for example, libspatialite and, in this case, you have to rebuild those too, together with all of its dependencies (removing everything first), before rebuilding gdal.

this is one of the reasons why, whenever you have to build something from SBo, it's advisable to do it, together with all of its dependencies, on a full and clean (no other packages installed) operating system (usually virtual machines and/or chroots are used for the scope).

Tsuga · 06-25-2022, 03:09 PM

Okay. Thanks again, Ponce. I don't know why this is happening. Everything was working fine. Last week sometime, I ran

Code:

slackpkg update
slackpkg install-new
slackpkg upgrade-all

Then the R problem started. It's unclear to me what happened. Well, I guess I should go and reinstall all the sbopkg packages. I appreciate the help, Ponce.

ponce · 06-26-2022, 05:13 AM

Quote:

Originally Posted by Tsuga

Okay. Thanks again, Ponce. I don't know why this is happening. Everything was working fine. Last week sometime, I ran

Code:

slackpkg update
slackpkg install-new
slackpkg upgrade-all

Then the R problem started. It's unclear to me what happened. Well, I guess I should go and reinstall all the sbopkg packages. I appreciate the help, Ponce.

libraries upgrades are normal if you run Slackware current so you have to be prepared to rebuild whatever third-party package needed.
Slackware current is not a rolling release like archlinux, it's where development of the newer release of Slackware happen, it's not meant for general use.
if you need stability use the latest stable release, 15.0: in your case, if you have set a mirror for current in /etc/slackpkg/mirrors, instead of a downgrade to 15.0, maybe a reinstall is cleaner.

henca · 06-26-2022, 05:24 AM

Quote:

Originally Posted by Tsuga

I guess I should go and reinstall all the sbopkg packages. I appreciate the help, Ponce.

Maybe you will have to do that everytime you update current. Maybe you only need to fix those packages which needs fixing.

You can use tools like ldd or grep to find which dependencies different binaries or libraries has.

The below example is from a Slackware 14.2 system (sometimes life really gets a lot easier when running a stable version of Slacwkare)

Code:

ldd /usr/bin/gdalinfo
        linux-vdso.so.1 (0x00007ffc693ec000)
        libgdal.so.20 => /usr/lib64/../lib64/libgdal.so.20 (0x00007f17cc82c000)
        libproj.so.13 => /usr/lib64/../lib64/libproj.so.13 (0x00007f17cc5b2000)
        libpoppler.so.62 => /usr/lib64/../lib64/libpoppler.so.62 (0x00007f17cc124000)
        liblcms2.so.2 => /usr/lib64/../lib64/liblcms2.so.2 (0x00007f17cbecc000)
        libtiff.so.5 => /usr/lib64/../lib64/libtiff.so.5 (0x00007f17cbc51000)
        libnss3.so => /usr/lib64/../lib64/libnss3.so (0x00007f17cb92a000)
        libsmime3.so => /usr/lib64/../lib64/libsmime3.so (0x00007f17cb702000)
        libssl3.so => /usr/lib64/../lib64/libssl3.so (0x00007f17cb4ac000)
        libsoftokn3.so => /usr/lib64/../lib64/libsoftokn3.so (0x00007f17cb26e000)
        libnssutil3.so => /usr/lib64/../lib64/libnssutil3.so (0x00007f17cb03e000)
        libplds4.so => /usr/lib64/../lib64/libplds4.so (0x00007f17cae39000)
        libplc4.so => /usr/lib64/../lib64/libplc4.so (0x00007f17cac34000)
        libnspr4.so => /usr/lib64/../lib64/libnspr4.so (0x00007f17ca9f6000)
        libfontconfig.so.1 => /usr/lib64/../lib64/libfontconfig.so.1 (0x00007f17ca7b9000)
        libharfbuzz.so.0 => /usr/lib64/../lib64/libharfbuzz.so.0 (0x00007f17ca53b000)
        libglib-2.0.so.0 => /usr/lib64/../lib64/libglib-2.0.so.0 (0x00007f17ca204000)
        libfreetype.so.6 => /usr/lib64/../lib64/libfreetype.so.6 (0x00007f17c9f67000)
        libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f17c9cf1000)
        libjson-c.so.2 => /usr/lib64/../lib64/libjson-c.so.2 (0x00007f17c9ae7000)
        libgeos_c.so.1 => /usr/lib64/../lib64/libgeos_c.so.1 (0x00007f17c98b1000)
        libgeos-3.7.0.so => /usr/lib64/../lib64/libgeos-3.7.0.so (0x00007f17c94fd000)
        libwebp.so.6 => /usr/lib64/../lib64/libwebp.so.6 (0x00007f17c929d000)
        libsqlite3.so.0 => /usr/lib64/../lib64/libsqlite3.so.0 (0x00007f17c8fcb000)
        libexpat.so.1 => /usr/lib64/../lib64/libexpat.so.1 (0x00007f17c8d9e000)
        libxerces-c-3.1.so => not found
        libnsl.so.1 => /lib64/libnsl.so.1 (0x00007f17c8b83000)
        libidn.so.11 => /usr/lib64/../lib64/libidn.so.11 (0x00007f17c8950000)
        libicui18n.so.56 => /usr/lib64/../lib64/libicui18n.so.56 (0x00007f17c84bf000)
        libicuuc.so.56 => /usr/lib64/../lib64/libicuuc.so.56 (0x00007f17c8126000)
        libicudata.so.56 => /usr/lib64/../lib64/libicudata.so.56 (0x00007f17c6743000)
        libopenjp2.so.7 => /usr/lib64/../lib64/libopenjp2.so.7 (0x00007f17c64e6000)
        libhdf5.so.10 => /usr/local/lib/libhdf5.so.10 (0x00007f17c604b000)
        libgif.so.7 => /usr/lib64/../lib64/libgif.so.7 (0x00007f17c5e43000)
        libjpeg.so.62 => /usr/lib64/../lib64/libjpeg.so.62 (0x00007f17c5ba9000)
        libpng16.so.16 => /usr/lib64/../lib64/libpng16.so.16 (0x00007f17c5975000)
        librt.so.1 => /lib64/librt.so.1 (0x00007f17c576d000)
        libpcre.so.1 => /usr/lib64/../lib64/libpcre.so.1 (0x00007f17c54fb000)
        libcurl.so.4 => /usr/lib64/../lib64/libcurl.so.4 (0x00007f17c5269000)
        libssh2.so.1 => /usr/lib64/../lib64/libssh2.so.1 (0x00007f17c503b000)
        libldap-2.4.so.2 => /usr/lib64/../lib64/libldap-2.4.so.2 (0x00007f17c4df2000)
        libsasl2.so.3 => /usr/lib64/../lib64/libsasl2.so.3 (0x00007f17c4bd5000)
        liblber-2.4.so.2 => /usr/lib64/../lib64/liblber-2.4.so.2 (0x00007f17c49c7000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00007f17c47ac000)
        libxml2.so.2 => /usr/lib64/../lib64/libxml2.so.2 (0x00007f17c4448000)
        liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f17c4222000)
        libmysqlclient.so.18 => /usr/lib64/../lib64/libmysqlclient.so.18 (0x00007f17c3cc9000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f17c3aab000)
        libz.so.1 => /usr/lib64/../lib64/libz.so.1 (0x00007f17c3894000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00007f17c3690000)
        libssl.so.1 => /usr/lib64/../lib64/libssl.so.1 (0x00007f17c341c000)
        libcrypto.so.1 => /usr/lib64/../lib64/libcrypto.so.1 (0x00007f17c2fc4000)
        libstdc++.so.6 => /usr/lib64/../lib64/libstdc++.so.6 (0x00007f17c2c4a000)
        libm.so.6 => /lib64/libm.so.6 (0x00007f17c2940000)
        libgcc_s.so.1 => /usr/lib64/../lib64/libgcc_s.so.1 (0x00007f17c2729000)
        libc.so.6 => /lib64/libc.so.6 (0x00007f17c2360000)
        /lib64/ld-linux-x86-64.so.2 (0x0000562fb733e000)
        libxerces-c-3.1.so => not found

Above we can see that gdalinfo links to libproj, but is it really the binary that links directly to libproj or is it some other library?

Code:

grep libproj  /usr/bin/gdalinfo
Binary file /usr/bin/gdalinfo matches

Yes, it seems as if it really is the binary that directly links to libproj.

So, has the binary really recently been rebuilt from source?

Code:

ls -al  /usr/bin/gdalinfo
-rwxr-xr-x 1 root root 14608 Nov 19  2019 /usr/bin/gdalinfo*

No, my binary is from 2019. That was expected on my system where noone has messed with updating libraries and tried to rebuild packages from source. But how does things look on your system? Did you really rebuild gdal from source or did you just reinstall a previously built package?

regards Henrik