problem installing spgrass6 in R

[Tim Holland]

Dear all,

I am trying to install spgrass6 in R, but am having trouble.  I have seen a previous related post (http://n2.nabble.com/GRASS-stats-Problems-installing-spgrass6-td1930684.html#a1930684), but I believe this is a different issue as I get different error messages.  

I am installing using the command
> install.packages("spgrass6", type="source", dependencies=TRUE)

On MacOSX 10.5.8, with sessionInfo() details as follows:

R version 2.9.2 (2009-08-24)
i386-apple-darwin8.11.1
locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    
loaded via a namespace (and not attached):
[1] tools_2.9.2

I think I have the GDAL libraries installed, as I believe they are required for GRASS, which I have and which is running fine (version 6.4).  It seems like the most likely problem (based on error messages) is not having an acceptable C compiler?  If that is the issue, any guidance on how to find and install one would be very appreciated.  

Thank you for any help on this.  The error messages I get are below (sorry for so much text).

Best,
Tim



* Installing *source* package ‘bitops’ ...
** libs
** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘bitops’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/bitops’
* Installing *source* package ‘sp’ ...
** libs
** arch - i386
sh: make: command not found
ERROR: compilation failed for package ‘sp’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/sp’
* Installing *source* package ‘XML’ ...
checking for gcc... no
checking for cc... no
checking for cc... no
checking for cl... no
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details.
ERROR: configuration failed for package ‘XML’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/XML’
* Installing *source* package ‘rgdal’ ...
gdal-config: gdal-config
./configure: line 1311: gdal-config: command not found
Error: gdal-config not found
The gdal-config script distributed with GDAL could not be found.
If you have not installed the GDAL libraries, you can
download the source from  http://www.gdal.org/
If you have installed the GDAL libraries, then make sure that
gdal-config is in your path. Try typing gdal-config at a
shell prompt and see if it runs. If not, use:
 --configure-args='--with-gdal-config=/usr/local/bin/gdal-config' echo with appropriate values for your installation.

ERROR: configuration failed for package ‘rgdal’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/rgdal’
* Installing *source* package ‘spgrass6’ ...
** R
** inst
** preparing package for lazy loading
Error : package 'sp' required by 'spgrass6' could not be found
ERROR: lazy loading failed for package ‘spgrass6’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/spgrass6’

The downloaded packages are in
        ‘/private/var/folders/nX/nX5WzHJNHoC9btpEipD-dU+++TM/-Tmp-/RtmplsIEHV/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'bitops' had non-zero exit status
2: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'sp' had non-zero exit status
3: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'XML' had non-zero exit status
4: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'rgdal' had non-zero exit status
5: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'spgrass6' had non-zero exit status

[Roger Bivand]

On Mon, 28 Sep 2009, Tim Holland wrote:

>
> Dear all,
>
> I am trying to install spgrass6 in R, but am having trouble.  I have seen a
> previous related post
> (http://n2.nabble.com/GRASS-stats-Problems-installing-spgrass6-td1930684.html#a1930684),
> but I believe this is a different issue as I get different error messages.
>
> I am installing using the command
>> install.packages("spgrass6", type="source", dependencies=TRUE)
>
> On MacOSX 10.5.8, with sessionInfo() details as follows:
>
> R version 2.9.2 (2009-08-24)
> i386-apple-darwin8.11.1
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> loaded via a namespace (and not attached):
> [1] tools_2.9.2
>
> I think I have the GDAL libraries installed, as I believe they are required
> for GRASS, which I have and which is running fine (version 6.4).  It seems
> like the most likely problem (based on error messages) is not having an
> acceptable C compiler?  If that is the issue, any guidance on how to find
> and install one would be very appreciated.

Check that you do have a visible GDAL install, as well as PROJ.4. Don't
assume, it usually hurts. Until gdal-config is found, you will not make
any progress. spgrass6 does not need a C/C++ compiler (but what reasonable
Unix lacks a compiler?)

You need XML (but not bitops) and sp, which you can install as binaries,
then you need rgdal installed from source or from

http://www.kyngchaos.com/software:frameworks

Check your GRASS installation for its GDAL/PROJ.4, you do not want
clashing versions. Start from the beginning (PROJ.4, GDAL), and build from
there (rgdal, GRASS), to be sure that they match.

Hope this helps,

Roger

>
> Thank you for any help on this.  The error messages I get are below (sorry
> for so much text).
>
> Best,
> Tim
>
>
>
> * Installing *source* package ‘bitops’ ...
> ** libs
> ** arch - i386
> sh: make: command not found
> ERROR: compilation failed for package ‘bitops’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/bitops’
> * Installing *source* package ‘sp’ ...
> ** libs
> ** arch - i386
> sh: make: command not found
> ERROR: compilation failed for package ‘sp’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/sp’
> * Installing *source* package ‘XML’ ...
> checking for gcc... no
> checking for cc... no
> checking for cc... no
> checking for cl... no
> configure: error: no acceptable C compiler found in $PATH
> See `config.log' for more details.
> ERROR: configuration failed for package ‘XML’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/XML’
> * Installing *source* package ‘rgdal’ ...
> gdal-config: gdal-config
> ./configure: line 1311: gdal-config: command not found
> Error: gdal-config not found
> The gdal-config script distributed with GDAL could not be found.
> If you have not installed the GDAL libraries, you can
> download the source from  http://www.gdal.org/
> If you have installed the GDAL libraries, then make sure that
> gdal-config is in your path. Try typing gdal-config at a
> shell prompt and see if it runs. If not, use:
> --configure-args='--with-gdal-config=/usr/local/bin/gdal-config' echo with
> appropriate values for your installation.
>
> ERROR: configuration failed for package ‘rgdal’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/rgdal’
> * Installing *source* package ‘spgrass6’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : package 'sp' required by 'spgrass6' could not be found
> ERROR: lazy loading failed for package ‘spgrass6’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/spgrass6’
>
> The downloaded packages are in
>
> ‘/private/var/folders/nX/nX5WzHJNHoC9btpEipD-dU+++TM/-Tmp-/RtmplsIEHV/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Warning messages:
> 1: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'bitops' had non-zero exit status
> 2: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'sp' had non-zero exit status
> 3: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'XML' had non-zero exit status
> 4: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'rgdal' had non-zero exit status
> 5: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'spgrass6' had non-zero exit status
>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: [phone]; fax [phone]
e-mail: [hidden email]

_______________________________________________
grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[hamish-2]

Tim:
> > * Installing *source* package ‘bitops’ ...
> > ** libs
> > ** arch - i386
> > sh: make: command not found


you need to install 'make' which comes with gcc etc. from the
Xcode(?) installer.


Hamish




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grass-stats mailing list
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[Roger Bivand]

On Mon, 28 Sep 2009, Hamish wrote:

> Tim:
>>> * Installing *source* package ‘bitops’ ...
>>> ** libs
>>> ** arch - i386
>>> sh: make: command not found
>
>
> you need to install 'make' which comes with gcc etc. from the
> Xcode(?) installer.

I think Tim needs to read the available FAQs on CRAN, and read:

http://r.research.att.com/tools/

giving the recipes for setting up an OSX system for building R packages.
It isn't hard, one just needs to folloow the instructions and *never*
assume anything unless one knows more about OSX variants than the
maintainer. I think that the underlying GRASS install is broken too
(probably PATH problems) wrt. GDAL.

Roger

>
>
> Hamish
>
>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: [phone]; fax [phone]
e-mail: [hidden email]

_______________________________________________
grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[Tim Holland]

Hamish wrote:

> you need to install 'make' which comes with gcc etc. from the
> Xcode(?) installer.

Roger Bivand wrote:

I think Tim needs to read the available FAQs on CRAN, and read:

http://r.research.att.com/tools/

giving the recipes for setting up an OSX system for building R packages.
It isn't hard, one just needs to folloow the instructions and *never*
assume anything unless one knows more about OSX variants than the
maintainer. I think that the underlying GRASS install is broken too
(probably PATH problems) wrt. GDAL.

Dear all,

Thank you for the help, Hamish and Roger (on list and off).  I was missing Xcode as you suggested Hamish, so now that is installed and I got marginally further on the install: rgdal and spgrass6 still failed, but bitops, XML, and sp worked.  

I am still not sure how to test if my gdal install is broken or not, but I will follow Roger's advice and assume that is is, and reinstall everything from the ground up.  I tried running gdal-config in GRASS, and got the following output - so I think it is installed, put perhaps with PATH problems.  

GRASS 6.4.0RC4 (mapset):~ > gdal-config
Usage: gdal-config [OPTIONS]
Options:
        [--prefix[=DIR]]
        [--libs]
        [--dep-libs]
        [--cflags]
        [--datadir]
        [--version]
        [--ogr-enabled]
        [--formats]

Thanks again for the help.  The error messages I'm getting now are below.  I am mainly just writing here as an update for the info of the list (and newbies such as myself getting stuck on this in future), so unless it seems like a bad idea (in which case please correct me) I will just do the strategy of reinstalling everything.  

Best,
Tim



(part of) error transcript from R (having run install.packages("spgrass6", type="source", dependencies=TRUE)):

Error: gdal-config not found
The gdal-config script distributed with GDAL could not be found.
If you have not installed the GDAL libraries, you can
download the source from  http://www.gdal.org/
If you have installed the GDAL libraries, then make sure that
gdal-config is in your path. Try typing gdal-config at a
shell prompt and see if it runs. If not, use:
 --configure-args='--with-gdal-config=/usr/local/bin/gdal-config' echo with appropriate values for your installation.

ERROR: configuration failed for package ‘rgdal’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/rgdal’
* Installing *source* package ‘spgrass6’ ...
** R
** inst
** preparing package for lazy loading
Error : package 'rgdal' required by 'spgrass6' could not be found
ERROR: lazy loading failed for package ‘spgrass6’
* Removing ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/spgrass6’

The downloaded packages are in
        ‘/private/var/folders/nX/nX5WzHJNHoC9btpEipD-dU+++TM/-Tmp-/RtmplsIEHV/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'rgdal' had non-zero exit status
2: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
  installation of package 'spgrass6' had non-zero exit status

[Tim Holland]

I was just reading the R integration section of the KyngChaos page (http://www.kyngchaos.com/software:grass#r_integration) and it said the following:

R Integration
GRASS can be used with R (Tiger only). You should get the latest R binaries (at least 2.3.0)...

That isn't true, is it?  That it is Tiger (MacOSX 10.4) only?  Should that read Tiger and up?  I am on Leopard (10.5), so if it only works on Tiger that is a problem.  For the time being, I will assume that it can work on Leopard and will keep trying.  

Best,
Tim

[Roger Bivand]

On Tue, 29 Sep 2009, Tim Holland wrote:

>
>
>
> Hamish wrote:
>>
>>
>>> you need to install 'make' which comes with gcc etc. from the
>>> Xcode(?) installer.
>>
>>
>
>
> Roger Bivand wrote:
>>
>>
>> I think Tim needs to read the available FAQs on CRAN, and read:
>>
>> http://r.research.att.com/tools/
>>
>> giving the recipes for setting up an OSX system for building R packages.
>> It isn't hard, one just needs to folloow the instructions and *never*
>> assume anything unless one knows more about OSX variants than the
>> maintainer. I think that the underlying GRASS install is broken too
>> (probably PATH problems) wrt. GDAL.
>>
>>
>
>
> Dear all,
>
> Thank you for the help, Hamish and Roger (on list and off).  I was missing
> Xcode as you suggested Hamish, so now that is installed and I got marginally
> further on the install: rgdal and spgrass6 still failed, but bitops, XML,
> and sp worked.
>
> I am still not sure how to test if my gdal install is broken or not, but I
> will follow Roger's advice and assume that is is, and reinstall everything
> from the ground up.  I tried running gdal-config in GRASS, and got the
> following output - so I think it is installed, put perhaps with PATH
> problems.
>
> GRASS 6.4.0RC4 (mapset):~ > gdal-config
> Usage: gdal-config [OPTIONS]
> Options:
> [--prefix[=DIR]]
> [--libs]
> [--dep-libs]
> [--cflags]
> [--datadir]
> [--version]
> [--ogr-enabled]
> [--formats]
>
> Thanks again for the help.  The error messages I'm getting now are below.  I
> am mainly just writing here as an update for the info of the list (and
> newbies such as myself getting stuck on this in future), so unless it seems
> like a bad idea (in which case please correct me) I will just do the
> strategy of reinstalling everything.

Tim,

One way of handling this might be - if you will only use rgdal from
"within" GRASS, is to run the install from the rgdal source package in
that environment. Alternatively, use gdal-config within GRASS to find the
the GDAL libs (--libs) and headers (--cflags) strings to pass to the
configure arguments in install.packages() in R outside GRASS. Here rgdal
will fail after installation if the GDAL shared objects are not on the
PATH R can see.

Hope this helps,

Roger

>
> Best,
> Tim
>
>
>
> (part of) error transcript from R (having run install.packages("spgrass6",
> type="source", dependencies=TRUE)):
>
> Error: gdal-config not found
> The gdal-config script distributed with GDAL could not be found.
> If you have not installed the GDAL libraries, you can
> download the source from  http://www.gdal.org/
> If you have installed the GDAL libraries, then make sure that
> gdal-config is in your path. Try typing gdal-config at a
> shell prompt and see if it runs. If not, use:
> --configure-args='--with-gdal-config=/usr/local/bin/gdal-config' echo with
> appropriate values for your installation.
>
> ERROR: configuration failed for package ‘rgdal’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/rgdal’
> * Installing *source* package ‘spgrass6’ ...
> ** R
> ** inst
> ** preparing package for lazy loading
> Error : package 'rgdal' required by 'spgrass6' could not be found
> ERROR: lazy loading failed for package ‘spgrass6’
> * Removing
> ‘/Library/Frameworks/R.framework/Versions/2.9/Resources/library/spgrass6’
>
> The downloaded packages are in
>
> ‘/private/var/folders/nX/nX5WzHJNHoC9btpEipD-dU+++TM/-Tmp-/RtmplsIEHV/downloaded_packages’
> Updating HTML index of packages in '.Library'
> Warning messages:
> 1: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'rgdal' had non-zero exit status
> 2: In install.packages("spgrass6", type = "source", dependencies = TRUE) :
>  installation of package 'spgrass6' had non-zero exit status
>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: [phone]; fax [phone]
e-mail: [hidden email]

_______________________________________________
grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[Roger Bivand]

On Tue, 29 Sep 2009, Tim Holland wrote:

>
> I was just reading the R integration section of the KyngChaos page
> (http://www.kyngchaos.com/software:grass#r_integration) and it said the
> following:
>
> R Integration
> GRASS can be used with R (Tiger only). You should get the latest R binaries
> (at least 2.3.0)...
>
> That isn't true, is it?  That it is Tiger (MacOSX 10.4) only?  Should that
> read Tiger and up?  I am on Leopard (10.5), so if it only works on Tiger
> that is a problem.  For the time being, I will assume that it can work on
> Leopard and will keep trying.

I don't think so, as I read http://www.kyngchaos.com/software:frameworks,
and higher up on the GRASS page, it should work. Installing rgdal within
the frameworks is also a possibility, especially if the GRASS install uses
the GDAL framework.

Roger

>
> Best,
> Tim
>
>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: [phone]; fax [phone]
e-mail: [hidden email]

_______________________________________________
grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[Tim Holland]

Roger Bivand wrote:

One way of handling this might be - if you will only use rgdal from
"within" GRASS, is to run the install from the rgdal source package in
that environment. Alternatively, use gdal-config within GRASS to find the
the GDAL libs (--libs) and headers (--cflags) strings to pass to the
configure arguments in install.packages() in R outside GRASS. Here rgdal
will fail after installation if the GDAL shared objects are not on the
PATH R can see.

Dear all,

Sorry to keep asking for your time on this, but I am still running into some problems.  

I reinstalled everything from scratch, using all binaries from KyngChaos and what I think was the correct order of installation.  And I still had the same problem with spgrass6 and rgdal failing on installation.  So then I tried what Roger suggested regarding using the configure arguments in install.packages.  

In GRASS, I did the following

GRASS 6.4.0RC5 (mapset):~ > gdal-config --libs
-L/Library/Frameworks/GDAL.framework/Versions/1.6/unix/lib -lgdal
GRASS 6.4.0RC5 (mapset):~ > gdal-config --cflags
-I/Library/Frameworks/GDAL.framework/Versions/1.6/Headers

I then wanted to use those paths in R in install.packages.  I tried

>install.packages("spgrass6", type="source", dependencies=TRUE, configure.args=c("-L/Library/Frameworks/GDAL.framework/Versions/1.6/unix/lib -lgdal","-I/Library/Frameworks/GDAL.framework/Versions/1.6/Headers"))

However, I ended up with the same error messages as always regarding spgrass6 and rgdal failing to install.  Was I doing the right thing with 'configure.args'?  Was that the right syntax / the right elements?

Thanks for the help,
Best,
Tim

[Roger Bivand]

On Sun, 4 Oct 2009, Tim Holland wrote:

>
> Dear Roger,
>
> I am sorry to keep asking for your time, but I have (what I hope is) a
> fairly simple question if you have a moment.
>
> I reinstalled everything from scratch, using all binaries from KyngChaos and
> what I think was the correct order of installation.  And I still had the
> same problem with spgrass6 and rgdal failing on installation.  So now I want
> to try what you suggested about using the configure arguments in
> install.packages.
>
> In GRASS, I did the following
>
> GRASS 6.4.0RC5 (mapset):~ > gdal-config --libs
> -L/Library/Frameworks/GDAL.framework/Versions/1.6/unix/lib -lgdal
> GRASS 6.4.0RC5 (mapset):~ > gdal-config --cflags
> -I/Library/Frameworks/GDAL.framework/Versions/1.6/Headers
>
> I then wanted to use those paths in R in install.packages.  I tried
>

Install rgdal first:

install.packages("rgdal", type="source",

configure.args=c(--with-gdal-config="<where gdal-config is>",
--with-proj-include="<where the proj headers are>",
--with-proj-lib=<where the proj libs are>"))

or something like that. Didn't it seem sensible to install the rgdal OSX
binaries from kyngchaos?

Once rgdal is installed, just install spgrass6 as a source package, no
dependencies, please, and no configure arguments. These are two separate
packages, where rgdal is what spgrass6 uses to do some of its work.

Hope this helps.

Roger

>
> However, I ended up with the same error messages as always regarding
> spgrass6 and rgdal failing to install.  Was I doing the right thing with
> 'configure.args'?  Was that the right syntax / the right elements?
>
> Thanks for the help,
> Best,
> Tim
>
>
>
> Tim,
>
> One way of handling this might be - if you will only use rgdal from
> "within" GRASS, is to run the install from the rgdal source package in
> that environment. Alternatively, use gdal-config within GRASS to find the
> the GDAL libs (--libs) and headers (--cflags) strings to pass to the
> configure arguments in install.packages() in R outside GRASS. Here rgdal
> will fail after installation if the GDAL shared objects are not on the
> PATH R can see.
>
> Hope this helps,
>
> Roger
>
>
>

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: [phone]; fax [phone]
e-mail: [hidden email]

_______________________________________________
grass-stats mailing list
[hidden email]
http://lists.osgeo.org/mailman/listinfo/grass-stats

[Tim Holland]

Roger Bivand wrote:

Install rgdal first:

install.packages("rgdal", type="source",

configure.args=c(--with-gdal-config="<where gdal-config is>",
--with-proj-include="<where the proj headers are>",
--with-proj-lib=<where the proj libs are>"))

or something like that. Didn't it seem sensible to install the rgdal OSX
binaries from kyngchaos?

Once rgdal is installed, just install spgrass6 as a source package, no
dependencies, please, and no configure arguments. These are two separate
packages, where rgdal is what spgrass6 uses to do some of its work.

 Thanks again for the help.  It installed successfully! After your comment about the rgdal binaries from kyngchaos, I installed them independently (I guess until then I thought that using the 'dependencies' argument for install packages would work for rgdal automatically), and it now works.  Sorry if that should have been obvious.  
Best,
Tim