date:20170805

Re: [GRASS-dev] New attempt to update GRASS for Mac

2017-08-05 Thread Michael Barton

To GRASS devs:

When I configure with paths to anaconda cairo and freetype dependencies, I get 
no errors (see below).


But when I check the configure.log, I see the same error I'm getting at the end 
of a failed build:

Undefined symbols for architecture x86_64:
  "_iconv", referenced from:
  _main in conftest-6b4e8e.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure: failed program was:
#line 4775 "configure"


It seems that configure output is not correct?

Indeed the checking for iconv begins at line 4775. Unfortunately, I cannot 
decipher what it is doing or which version of iconv it is checking (the Mac 
system one in /usr/lib or the one in anaconda).

Additionally, AFAICT, both versions of iconv that I have are 64bit. How can I 
"use -v to see invocation"?

Thanks
Michael


 configure output to shell ==

checking host system type... x86_64-apple-darwin16.7.0
checking for gcc... gcc
checking whether the C compiler (gcc  ) works... yes
checking whether the C compiler (gcc  ) is a cross-compiler... no
checking whether we are using GNU C... yes
checking whether gcc accepts -g... yes
checking for Cygwin environment... no
checking for mingw32 environment... no
checking for executable suffix... no
checking for full floating-point support... yes
checking for pwd... /bin/pwd
checking for source directory... /Users/cmbarton/grass_source/trunk
checking for build directory... /Users/cmbarton/grass_source/trunk
checking for svnversion... /opt/subversion/bin/svnversion
checking for MacOSX App... yes
checking for MacOSX architectures... no
checking for MacOSX SDK... checking for 
/Developer/SDKs/MacOSX10.8.sdk/SDKSettings.plist... yes
checking how to build libraries... shared
checking for additional include dirs...
checking for additional library dirs...
checking for a BSD compatible install... /usr/bin/install -c
checking for flex... flex
checking for yywrap in -lfl... no
checking for bison... bison -y
checking for ranlib... ranlib
checking for ar... ar
checking for env... env
checking for perl... /usr/bin/perl
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for limits.h... yes
checking for termio.h... no
checking for termios.h... yes
checking for unistd.h... yes
checking for values.h... no
checking for f2c.h... no
checking for g2c.h... no
checking for sys/ioctl.h... yes
checking for sys/mtio.h... no
checking for sys/resource.h... yes
checking for sys/time.h... yes
checking for sys/timeb.h... yes
checking for sys/types.h... yes
checking for sys/utsname.h... yes
checking for libintl.h... yes
checking for iconv.h... yes
checking for langinfo.h... yes
checking whether time.h and sys/time.h may both be included... yes
checking for off_t... yes
checking for uid_t in sys/types.h... yes
checking return type of signal handlers... void
checking for Cygwin environment... no
checking for ftime... yes
checking for gethostname... yes
checking for gettimeofday... yes
checking for lseek... yes
checking for nice... yes
checking for time... yes
checking for uname... yes
checking for seteuid... yes
checking for setpriority... yes
checking for setreuid... yes
checking for setruid... yes
checking for drand48... yes
checking for putenv... yes
checking for setenv... yes
checking for nanosleep... yes
checking whether setpgrp takes no argument... yes
checking for long long int... yes
checking for W11... no
checking for X... no
checking for library containing cuserid... no
checking for asprintf... yes
checking for atan... yes
checking for dlsym... yes
checking for iconv... no
checking for iconv in -liconv... yes
checking for socket... yes
checking for location of zlib includes...
checking for zlib.h... yes
checking for location of zlib library...
checking for deflate in -lz... yes
checking whether to use bzlib... no
checking for location of External PROJ.4 includes... 
/Applications/anaconda/include
checking for proj_api.h... yes
checking External PROJ.4 version... 492
checking for location of External PROJ.4 library... /Applications/anaconda/lib
checking for pj_get_def in -lproj... yes
checking for location of External PROJ.4 data files... 
/Applications/anaconda/share/proj
checking for /Applications/anaconda/share/proj/epsg... yes
checking for nad2bin... /Applications/anaconda/bin/nad2bin
checking whether to use regex... yes
checking for location of regex includes...
checking for regex.h... yes
checking for location of regex library...
checking for regcomp... yes
checking whether to use Readline... no
checking whether to use GDAL... yes
checking for gdal-config... /Applications/anaconda/bin/gdal-config
rm: conftest.dSYM: is a directory
checking whether to use libLAS... no
checking whether to use PDAL... no
checking whether to use NetCDF... no
checking whether to use GEOS... yes
checking for geos-config... /Applications/anaconda/bin/geos-config
checking for geos_c.h... yes
checking

Re: [GRASS-dev] New attempt to update GRASS for Mac

2017-08-05 Thread Michael Barton

I figured you are working towards an anaconda build. I'm trying something
simpler. What did you change in platform.make?

Michael Barton
School of Human Evolution Change
Center for Social Dynamics & Complexity
Arizona State University

...Sent from my iPad

On Aug 5, 2017, at 11:05 AM, Eric Hutton
> wrote:

Michael,

Those were the sorts of files I was making changes in.

Also, I just realized that I am building things slightly differently than you
and so the stuff I wrote about the temporary folder doesn't apply to you. I'm
building GRASS with conda-build so that it can be a conda installable package.

Eric
On Sat, Aug 5, 2017 at 10:39 AM Michael Barton
> wrote:
Is the place to fix this in ../include/make/Platform.make?

Michael

C. Michael Barton
Director, Center for Social Dynamics & Complexity
Professor of Anthropology, School of Human Evolution & Social Change
Head, Graduate Faculty in Complex Adaptive Systems Science
Arizona State University

voice: 480-965-6262 (SHESC), 480-965-8130/727-9746 (CSDC)
fax: 480-965-7671 (SHESC), 480-727-0709 (CSDC)
www:
http://www.public.asu.edu/~cmbarton,

http://csdc.asu.edu

On Aug 4, 2017, at 3:50 PM, Eric Hutton
> wrote:

Hi Michael

I found that if I manually add linker flags (like "-L$PREFIX/lib -liconv") I
was able to get rid of these errors. I also notice that I had to append them to
the end of the compile command (or at least after things like
"-lgrass_gis.7.2.0" - I guess it has to do with the order that the compiler
looks at libraries to resolve sysbols). Then, at runtime $PREFIX/lib needed to
appear in the LD_LIBRARY_PATH_VAR when running the tests.

I'm not sure of the best way to fix this within the grass build system (simply
adding the link flags to LDFLAGS didn't do the trick). Perhaps tweaking
Rules.make and the like would do the trick? I think the basic problem is that
conda does the entire build within a temporary folder that contains
installations of all the dependencies and that this temporary folder is not
added to all the necessary places.

Eric

On Fri, Aug 4, 2017 at 3:05 PM Michael Barton
> wrote:
After a tedious set of tests, I can say that GRASS will not build with ANY
dependency from Anaconda except SQLite. That is, I went through the
dependencies one-by-one and replaced the path to a Framework version with an
Anaconda version in my configure string. I did a make clean between each build
attempt.

All the versions are close (secondary or tertiary version number) or identical
between William's framework builds and those in Anaconda.

For FreeType and Cairo, the errors of the type I posted yesterday

ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

For the other dependencies, the errors are that the appropriate library cannot
be found, like the following for fftw:

dyld: Library not loaded: @rpath/libfftw3.3.dylib
Referenced from:
/Users/cmbarton/grass_source/trunk/dist.x86_64-apple-darwin16.7.0/lib/libgrass_gmath.7.3.svn.dylib
Reason: image not found

It seems to me like there has to be some kind of systematic reason for this not
to work. Something hardwired in a key makefile or something. The Anaconda
packages are all current builds of normal dependencies.

I am even doing it in an environment in which /Applications/anaconda/bin is
first in my PATH (which works fine if the dependencies are Frameworks).

Any thoughts on this?

Michael

voice: 480-965-6262 (SHESC),
480-965-8130/727-9746 (CSDC)
fax: 480-965-7671 (SHESC),
480-727-0709 (CSDC)
www:
http://www.public.asu.edu/~cmbarton,

Re: [GRASS-dev] [GRASS GIS] #3273: Fails to build with GCC 7

2017-08-05 Thread GRASS GIS

#3273: Fails to build with GCC 7
-+-
  Reporter:  Bas Couwenberg  |  Owner:  grass-dev@…
  Type:  defect  | Status:  new
  Priority:  critical|  Milestone:  7.2.2
 Component:  Compiling   |Version:  7.2.0
Resolution:  |   Keywords:
   CPU:  x86-64  |   Platform:  Linux
-+-

Comment (by neteler):

 Replying to [comment:5 mlennert]:
 > Replying to [comment:1 wenzeslaus]:
 > > This is probably the error message:
 > >
 > > {{{
 > > ValueError: invalid literal for int() with base 8:
 '08420217248550443400745280086994171'
 > > }}}
 > >
 >
 > Isn't this the same issue in #3331 (where it was apparently fixed) ?

 Yes, 7.2.2 will ship the fix. (also 7.0.6 if we ever release it...)

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Ticket URL: 
GRASS GIS 

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Re: [GRASS-dev] New attempt to update GRASS for Mac

2017-08-05 Thread Michael Barton

Is the place to fix this in ../include/make/Platform.make?

Michael

C. Michael Barton
Director, Center for Social Dynamics & Complexity
Professor of Anthropology, School of Human Evolution & Social Change
Head, Graduate Faculty in Complex Adaptive Systems Science
Arizona State University

voice:  480-965-6262 (SHESC), 480-965-8130/727-9746 (CSDC)
fax: 480-965-7671 (SHESC),  480-727-0709 (CSDC)
www: http://www.public.asu.edu/~cmbarton, http://csdc.asu.edu

On Aug 4, 2017, at 3:50 PM, Eric Hutton 
> wrote:

Hi Michael

I found that if I manually add linker flags (like "-L$PREFIX/lib -liconv") I 
was able to get rid of these errors. I also notice that I had to append them to 
the end of the compile command (or at least after things like 
"-lgrass_gis.7.2.0" - I guess it has to do with the order that the compiler 
looks at libraries to resolve sysbols). Then, at runtime $PREFIX/lib needed to 
appear in the LD_LIBRARY_PATH_VAR when running the tests.

I'm not sure of the best way to fix this within the grass build system (simply 
adding the link flags to LDFLAGS didn't do the trick). Perhaps tweaking 
Rules.make and the like would do the trick? I think the basic problem is that 
conda does the entire build within a temporary folder that contains 
installations of all the dependencies and that this temporary folder is not 
added to all the necessary places.

Eric

On Fri, Aug 4, 2017 at 3:05 PM Michael Barton 
> wrote:
After a tedious set of tests, I can say that GRASS will not build with ANY 
dependency from Anaconda except SQLite. That is, I went through the 
dependencies one-by-one and replaced the path to a Framework version with an 
Anaconda version in my configure string. I did a make clean between each build 
attempt.

All the versions are close (secondary or tertiary version number) or identical 
between William's framework builds and those in Anaconda.

For FreeType and Cairo, the errors of the type I posted yesterday

ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

For the other dependencies, the errors are that the appropriate library cannot 
be found, like the following for fftw:

dyld: Library not loaded: @rpath/libfftw3.3.dylib
  Referenced from: 
/Users/cmbarton/grass_source/trunk/dist.x86_64-apple-darwin16.7.0/lib/libgrass_gmath.7.3.svn.dylib
  Reason: image not found

It seems to me like there has to be some kind of systematic reason for this not 
to work. Something hardwired in a key makefile or something. The Anaconda 
packages are all current builds of normal dependencies.

I am even doing it in an environment in which /Applications/anaconda/bin is 
first in my PATH (which works fine if the dependencies are Frameworks).

Any thoughts on this?

Michael

C. Michael Barton
Director, Center for Social Dynamics & Complexity
Professor of Anthropology, School of Human Evolution & Social Change
Head, Graduate Faculty in Complex Adaptive Systems Science
Arizona State University

voice:  480-965-6262 (SHESC), 
480-965-8130/727-9746 (CSDC)
fax: 480-965-7671 (SHESC),  
480-727-0709 (CSDC)
www: 
http://www.public.asu.edu/~cmbarton,

http://csdc.asu.edu

On Aug 4, 2017, at 12:56 AM, Moritz Lennert 
> wrote:

On 04/08/17 00:33, Vaclav Petras wrote:
Well, the error (below) suggests that wrong library is either linked or 
included. You need to go through the -L and -I paths and see if you need to set 
one of these differently or add additional one for iconv. I don't see how to 
set this through ./configure (I don't see any --with-iconv-includes= or 
--with-iconv-libs=), but you can start by editing the Makefiles or the command 
itself and changing -L and -I directly.
Undefined symbols for architecture x86_64:
  "_iconv", referenced from:
  _draw_main in text3.o
  "_iconv_close", referenced from:
  _draw_main in text3.o
  "_iconv_open", referenced from:
  _draw_main in text3.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

Just guessing: Could the error be linked to the use of clang ? Have you tried 
with

Re: [GRASS-dev] [GRASS GIS] #3273: Fails to build with GCC 7

2017-08-05 Thread GRASS GIS

#3273: Fails to build with GCC 7
-+-
  Reporter:  Bas Couwenberg  |  Owner:  grass-dev@…
  Type:  defect  | Status:  new
  Priority:  critical|  Milestone:  7.2.2
 Component:  Compiling   |Version:  7.2.0
Resolution:  |   Keywords:
   CPU:  x86-64  |   Platform:  Linux
-+-

Comment (by mlennert):

 Replying to [comment:1 wenzeslaus]:
 > This is probably the error message:
 >
 > {{{
 > ValueError: invalid literal for int() with base 8:
 '08420217248550443400745280086994171'
 > }}}
 >

 Isn't this the same issue in #3331 (where it was apparently fixed) ?

--
Ticket URL: 
GRASS GIS 

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[GRASS-dev] [GRASS GIS] #3388: Legacy appstream metadata

2017-08-05 Thread GRASS GIS

#3388: Legacy appstream metadata
+-
 Reporter:  Bas Couwenberg  |  Owner:  grass-dev@…
 Type:  defect  | Status:  new
 Priority:  normal  |  Milestone:  7.2.2
Component:  Default |Version:  7.2.1
 Keywords:  appstream   |CPU:  Unspecified
 Platform:  Linux   |
+-
 The [https://www.freedesktop.org/software/appstream/docs/chap-
 Metadata.html AppSteam] metadata is installed in the legacy location
 (`/usr/share/appdata`), it should now be installed in
 `/usr/share/metainfo`.

 The `.appdata.xml` file should now be named `.metainfo.xml`, and the
 syntax has changed.

 There are a couple of validation issues reported:
 {{{
 $ appstreamcli validate gui/icons/grass.appdata.xml
 W - grass.appdata.xml:grass.desktop:4
 The component ID is not a reverse domain-name. Please update the ID
 and that of
 the accompanying .desktop file to follow the latest version of the
 Desktop-Entry
 and AppStream specifications and avoid future issues.

 E - grass.appdata.xml:grass.desktop
 The component is missing a name ( tag).

 E - grass.appdata.xml:grass.desktop:9
 The description contains an URL. This is not allowed, please use the
  tag
 to share links.

 Validation failed: errors: 2, warnings: 1
 }}}

 The changes to the AppStream metadata are likely to trigger changes to the
 `.desktop` file too (e.g. the reverse domain ID).

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GRASS GIS 

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Re: [GRASS-dev] [GRASS GIS] #3273: Fails to build with GCC 7

2017-08-05 Thread GRASS GIS

#3273: Fails to build with GCC 7
-+-
  Reporter:  Bas Couwenberg  |  Owner:  grass-dev@…
  Type:  defect  | Status:  new
  Priority:  critical|  Milestone:  7.2.2
 Component:  Compiling   |Version:  7.2.0
Resolution:  |   Keywords:
   CPU:  x86-64  |   Platform:  Linux
-+-
Changes (by martinl):

 * priority:  normal => critical


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GRASS GIS 

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Re: [GRASS-dev] openMP support in GRASS GIS

2017-08-05 Thread Jaro Hofierka


Hi Markus,

This is just a small contribution and I would like acknowledge help of 
reviewers to improve the manuscript. I believe more such grass-based 
papers in scientific journals will further promote GRASS within the 
wider scientific community.
Of course, we would welcome if this could go to the trunk version. 
Vaclav helped us is v.surf.rst and it is already there and I hope he 
could also help with r.sim.water and r.sun. He can contact me or my 
colleagues and we will provide any assistance.


Best wishes,

Jaro

Markus Neteler napísal(a):

Hi,

just saw that this article got published (congrats, Jaro and team):

Hofierka, J., Lacko, M., Zubal, S., 2017. Parallelization of
interpolation, solar radiation and water flow simulation modules in
GRASS GIS using OpenMP. Computers & Geosciences.
doi:10.1016/j.cageo.2017.07.007

Questions: since the code is already in addons, how about merging the
changes into trunk?

Markus


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Re: [GRASS-dev] New attempt to update GRASS for Mac

Re: [GRASS-dev] New attempt to update GRASS for Mac

Re: [GRASS-dev] [GRASS GIS] #3273: Fails to build with GCC 7

Re: [GRASS-dev] New attempt to update GRASS for Mac

Re: [GRASS-dev] [GRASS GIS] #3273: Fails to build with GCC 7

[GRASS-dev] [GRASS GIS] #3388: Legacy appstream metadata

Re: [GRASS-dev] [GRASS GIS] #3273: Fails to build with GCC 7

Re: [GRASS-dev] openMP support in GRASS GIS

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