GDAL compilation error

slackale · 10-04-2016, 03:42 PM

Hey everyone

I'm trying to compile gdal-2.1.1 from slackbuilds on slackware64 14.2 and it gives me this error

make[2]: Leaving directory '/tmp/SBo/gdal-2.1.1/swig/python'
make[1]: Leaving directory '/tmp/SBo/gdal-2.1.1/swig'
(cd scripts; make install)
make[1]: Entering directory '/tmp/SBo/gdal-2.1.1/scripts'
if test "x`pkg-config --version 2>/dev/null`" != "x" -a "x`pkg-config --variable=compatdir bash-completion`" != "x"; then \
/tmp/SBo/gdal-2.1.1/install-sh -d /tmp/SBo/package-gdal/usr`pkg-config --variable=compatdir bash-completion` ; \
cp gdal-bash-completion.sh /tmp/SBo/package-gdal/usr`pkg-config --variable=compatdir bash-completion`; \
fi
make[1]: Leaving directory '/tmp/SBo/gdal-2.1.1/scripts'
for f in LICENSE.TXT data/*.* ; do /tmp/SBo/gdal-2.1.1/install-sh -c -m 0644 $f /tmp/SBo/package-gdal/usr/share/gdal ; done
/bin/sh /tmp/SBo/gdal-2.1.1/libtool --mode=finish --silent /tmp/SBo/package-gdal/usr/lib64
/tmp/SBo/gdal-2.1.1/install-sh -d /tmp/SBo/package-gdal/usr/lib64/pkgconfig
/tmp/SBo/gdal-2.1.1/install-sh -c -m 0644 gdal.pc /tmp/SBo/package-gdal/usr/lib64/pkgconfig/gdal.pc
./config.status
config.status: creating GDALmake.opt
config.status: WARNING: 'GDALmake.opt.in' seems to ignore the --datarootdir setting
config.status: creating port/cpl_config.h
config.status: port/cpl_config.h is unchanged
config.status: executing libtool commands
(cat Doxyfile ; echo "ENABLED_SECTIONS=man"; echo "INPUT=apps swig/python/scripts"; echo "FILE_PATTERNS=*.cpp *.dox"; echo "GENERATE_HTML=NO"; echo "GENERATE_MAN=YES") | doxygen -
/bin/sh: line 1: 17604 Done ( cat Doxyfile; echo "ENABLED_SECTIONS=man"; echo "INPUT=apps swig/python/scripts"; echo "FILE_PATTERNS=*.cpp *.dox"; echo "GENERATE_HTML=NO"; echo "GENERATE_MAN=YES" )
17605 Segmentation fault | doxygen -
GNUmakefile:169: recipe for target 'man' failed
make: *** [man] Error 139

deps: geos-3.5.0, proj-4.9.2 (compiled and installed fine)

Any help would be appreciated

Thanks.

John VV · 10-04-2016, 07:27 PM

i was about to say do not build it and use one of the prebuilt
but you are on slackware

GDAL can be a pain to build and there are a few varieties
mainly the python wrapper version

as i recall the instructions are a bit old
https://trac.osgeo.org/gdal/wiki/BuildHints

and are going to need a sql database support ?

have a look at the deps needed
https://trac.osgeo.org/gdal/wiki/BuildHints

also it might not build using gcc5 or 4.9
you might need a bit older version

kjhambrick · 10-04-2016, 08:59 PM

slackale --

I've built both gdal-2.1.0 as well as gdal-2.1.1

The program does have a lot of deps (

an understatement

)

looking at your error, it would appear that your copy of `doxygen` segfaulted ?

-- kjh

This is the same 'stuff' from my do-gdal.SlackBuild.out build log ( several warnings but no segfault ):

Code:

./config.status
config.status: creating GDALmake.opt
config.status: WARNING:  'GDALmake.opt.in' seems to ignore the --datarootdir setting
config.status: creating port/cpl_config.h
config.status: port/cpl_config.h is unchanged
config.status: executing libtool commands
(cat Doxyfile ; echo "ENABLED_SECTIONS=man"; echo "INPUT=apps swig/python/scripts"; echo "FILE_PATTERNS=*.cpp *.dox"; echo "GENERATE_HTML=NO"; echo "GENERATE_MAN=YES") | doxygen -
Warning: Tag `HTML_ALIGN_MEMBERS' at line 594 of file `-' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: Tag `XML_SCHEMA' at line 826 of file `-' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: Tag `XML_DTD' at line 832 of file `-' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
/tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox:1307: warning: multiple use of section label 'gdaltransform_example' while adding section, (first occurrence: /tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox, line 1291)
/tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox:2414: warning: multiple use of section label 'gdal_grid_example' while adding section, (first occurrence: /tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox, line 2094)
/tmp/SBo/gdal-2.1.1/apps/gnm_utilities.dox:135: warning: multiple use of section label 'gnmmanage_author' while adding section, (first occurrence: /tmp/SBo/gdal-2.1.1/apps/gnm_utilities.dox, line 84)
Searching for include files...
Searching for example files...

I also installed all the optional deps before building gdal and I've got an NVidia GTX 970M running the NVidia 367.44 blob.

Code:

-rw-r--r-- 1 root root 61973 Aug 13 18:41 /var/log/packages/gdal-2.1.1-x86_64-1_SBo
-rw-r--r-- 1 root root 19999 May 29 02:38 /var/log/packages/geos-3.5.0-x86_64-1_SBo
-rw-r--r-- 1 root root 1538 May 29 02:41 /var/log/packages/proj-4.9.2-x86_64-1_SBo
-rw-r--r-- 1 root root 1184 May 29 04:42 /var/log/packages/cfitsio-3.39-x86_64-1_SBo
-rw-r--r-- 1 root root 1052 May 29 04:52 /var/log/packages/freexl-1.0.2-x86_64-1_SBo
-rw-r--r-- 1 root root 4940 Aug 31 02:37 /var/log/packages/hdf-4.2.12-x86_64-2_SBo
-rw-r--r-- 1 root root 8472 May 29 05:08 /var/log/packages/hdf5-1.8.17-x86_64-1_SBo
-rw-r--r-- 1 root root 2713 Sep 23 23:52 /var/log/packages/libwebp-0.5.1-x86_64-1_SBo
-rw-r--r-- 1 root root 4166 Aug 31 02:41 /var/log/packages/netcdf-4.4.1-x86_64-2_SBo
-rw-r--r-- 1 root root 129125 Oct  4 20:23 /var/log/packages/postgresql-9.5.4-x86_64-2_SBo
-rw-r--r-- 1 root root 112289 Jul  9 08:32 /var/log/packages/xerces-c-3.1.4-x86_64-1_SBo

This is the wrapper script I use to build gdal-2.1.x ( do-gdal.SlackBuild )

Code:

#!/bin/sh

CwdDir="`pwd`"
LogNam="$CwdDir/do-gdal.SlackBuild.out"

OPENCL=yes

export OPENCL

./gdal.SlackBuild 2>&1 |tee -a $LogNam

slackale · 10-04-2016, 09:04 PM

I managed to compile it by commenting out the lines that create the docs and man pages in the .SlackBuild, tomorrow I'll try that script and see what happens

Thank you

kjhambrick · 10-04-2016, 09:06 PM

Hmmm ...

I noticed that I left out something 'important' from my do-gdal.SlackBuild.out log ...

I do not have bash-completion installed but it appears that you do ?

Maybe bash-completion + doxygen is the culprit ?

-- kjh

This is the same snippit, including the bash-completion tests:

Code:

make[2]: Leaving directory '/tmp/SBo/gdal-2.1.1/swig/python'
make[1]: Leaving directory '/tmp/SBo/gdal-2.1.1/swig'
(cd scripts; make install)
make[1]: Entering directory '/tmp/SBo/gdal-2.1.1/scripts'
if test "x`pkg-config --version 2>/dev/null`" != "x" -a "x`pkg-config --variable=compatdir bash-completion`" != "x"; then \
        /tmp/SBo/gdal-2.1.1/install-sh -d /tmp/SBo/package-gdal/usr`pkg-config --variable=compatdir bash-completion` ; \
        cp gdal-bash-completion.sh /tmp/SBo/package-gdal/usr`pkg-config --variable=compatdir bash-completion`; \
fi
Package bash-completion was not found in the pkg-config search path.
Perhaps you should add the directory containing `bash-completion.pc'
to the PKG_CONFIG_PATH environment variable
No package 'bash-completion' found
make[1]: Leaving directory '/tmp/SBo/gdal-2.1.1/scripts'
for f in LICENSE.TXT data/*.* ; do /tmp/SBo/gdal-2.1.1/install-sh -c -m 0644 $f /tmp/SBo/package-gdal/usr/share/gdal ; done
/bin/sh /tmp/SBo/gdal-2.1.1/libtool --mode=finish --silent /tmp/SBo/package-gdal/usr/lib64
/tmp/SBo/gdal-2.1.1/install-sh -d /tmp/SBo/package-gdal/usr/lib64/pkgconfig
/tmp/SBo/gdal-2.1.1/install-sh -c -m 0644 gdal.pc /tmp/SBo/package-gdal/usr/lib64/pkgconfig/gdal.pc
./config.status
config.status: creating GDALmake.opt
config.status: WARNING:  'GDALmake.opt.in' seems to ignore the --datarootdir setting
config.status: creating port/cpl_config.h
config.status: port/cpl_config.h is unchanged
config.status: executing libtool commands
(cat Doxyfile ; echo "ENABLED_SECTIONS=man"; echo "INPUT=apps swig/python/scripts"; echo "FILE_PATTERNS=*.cpp *.dox"; echo "GENERATE_HTML=NO"; echo GENERATE_MAN=YES") | doxygen -
Warning: Tag `HTML_ALIGN_MEMBERS' at line 594 of file `-' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: Tag `XML_SCHEMA' at line 826 of file `-' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
Warning: Tag `XML_DTD' at line 832 of file `-' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
/tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox:1307: warning: multiple use of section label 'gdaltransform_example' while adding section, (first occurrence: /tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox, line 1291)
/tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox:2414: warning: multiple use of section label 'gdal_grid_example' while adding section, (first occurrence: /tmp/SBo/gdal-2.1.1/apps/gdal_utilities.dox, line 2094)
/tmp/SBo/gdal-2.1.1/apps/gnm_utilities.dox:135: warning: multiple use of section label 'gnmmanage_author' while adding section, (first occurrence: /tmp/SBo/gdal-2.1.1/apps/gnm_utilities.dox, line 84)
Searching for include files...
Searching for example files...

55020 · 10-04-2016, 10:20 PM

Hi slackale,

I suspect your problem is nothing to do with gdal or its dependencies or gcc or bash-completion (sorry everybody). From the log you supplied (thanks very much!) and as kjhambrick says the problem is quite clearly caused when 'doxygen' tries to run.

Have you recently upgraded to Slackware 14.2? Do you have some perl modules installed, either from SBo or from cpan, that you haven't rebuilt since you upgraded to 14.2?

doxygen uses perl, and because of incompatible changes in perl-5.22, it is necessary to rebuild all your added perl modules after upgrading. If you don't, it causes lots of programs that use perl to segfault when you start them. This has unfortunately bitten lots of people, and I suspect you're possibly one more victim.

kjhambrick · 10-05-2016, 05:49 AM

Thanks 55020 !

This is Great Info !!

I have added: 'rebuild ALL perl modules' to my local check list for Pat's UPGRADE.TXT File.

-- kjh

slackale · 10-05-2016, 02:59 PM

Hello

Nope, it's actually a new installation of Slackware64 14.2 and yes I installed bash-completion since the first error it gave me was about not finding that package

willysr · 10-05-2016, 05:16 PM

slackale: Do you use the latest patch from -stable or accidentally use -current mirrors?

slackale · 10-05-2016, 06:56 PM

Nope, clean installation of Slackware64 14.2, every package installed from slackbuilds org and bash-completion from slackware-install iso, also a SlackBuild