R SIG Debian - Oct 2016 - [FORGED] Re: Problem installing rgdal on a laptop running Ubuntu 16.04.1

I previously sent a cri de coeur about this problem to the r-help list 
but so far have not managed to extract a solution.  So I am trying here.
(Uh, Ubuntu *is* a "special instance" of Debian, isn't it?)

The problem is that I cannot install rgdal, and I need it.  Rather 
desperately.

I do:

     install.packages("rgdal",lib="/home/rolf/Rlib")

and get the error message:
> ** testing if installed package can be loaded
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared object
'/home/rolf/Rlib/rgdal/libs/rgdal.so':
>   /home/rolf/Rlib/rgdal/libs/rgdal.so: undefined symbol:
CPLQuietErrorHandler
> Error: loading failed
> Execution halted
I have installed libgdal-dev and (later, prompted by an email from Prof. 
John Nash) libgdal1-dev.  I also have installed libproj-dev,
as instructed by one site that I found by googling around.

No joy.

I have also gone to the Ubuntu Launchpad site and looked at the material 
there, but could not make any sense of it nor was I able to discern how 
to make use of that material.

I also tried installing gdal-bin as suggested by one site that I looked 
at; no help.

Can anyone point me in the right direction?

cheers,

Rolf Turner

P. S.  For what it's worth: my sessionInfo():

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8
  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8
  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] fortunes_1.5-4 misc_0.0-16

loaded via a namespace (and not attached):
  [1] deldir_0.1-13       Matrix_1.2-3        tools_3.3.1
  [4] mgcv_1.8-12         abind_1.4-3         spatstat_1.46-1.059
  [7] rpart_4.1-10        nlme_3.1-128        grid_3.3.1
[10] polyclip_1.5-0      lattice_0.20-33     goftest_1.0-3
[13] tensor_1.5

R. T.

-- 
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

On 10/04/2016 05:54 PM, Rolf Turner wrote:
>
> I previously sent a cri de coeur about this problem to the r-help list
> but so far have not managed to extract a solution.  So I am trying here.
> (Uh, Ubuntu *is* a "special instance" of Debian, isn't it?)
>
> The problem is that I cannot install rgdal, and I need it.  Rather
> desperately.
>
> I do:
>
>     install.packages("rgdal",lib="/home/rolf/Rlib")
>
> and get the error message:
>
>> ** testing if installed package can be loaded
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>   unable to load shared object
'/home/rolf/Rlib/rgdal/libs/rgdal.so':
>>   /home/rolf/Rlib/rgdal/libs/rgdal.so: undefined symbol:
>> CPLQuietErrorHandler
>> Error: loading failed
>> Execution halted
>
Rolf,

I would go to the cran2deb4ubuntu PPA and install r-cran-gdal from 
there.  It will install all the needed dependencies.

https://launchpad.net/~marutter/+archive/ubuntu/c2d4u

Michael

On 05/10/16 11:12, Michael Rutter wrote:

<SNIP>
> I would go to the cran2deb4ubuntu PPA and install r-cran-gdal from
> there.  It will install all the needed dependencies.
>
> https://launchpad.net/~marutter/+archive/ubuntu/c2d4u
Sorry to be a thicko, but you will have to spell things out for me a bit 
more.  I did:
> sudo add-apt-repository ppa:marutter/c2d4u
> sudo apt-get update
successfully (I think!).

Then I tried

     sudo apt-get install r-cran-gdal

and got:
> E: Unable to locate package r-cran-gdal
So what should I have said or done?  Thanks.

cheers,

Rolf

-- 
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

On 05/10/16 12:07, Michael Rutter wrote:
> Typo on my part.  Try r-cran-rgdal.
Thanks. OK, I have now done

     sudo apt-get install r-cran-rgdal

successfully.  But sad to say, it didn't help a bit.  When I try

     install.packages("rgdal",lib="/home/rolf/Rlib")

I get exactly the same error as before.  I.e.

     > undefined symbol: CPLQuietErrorHandler

Why do these things always happen to *me*?  Said he, plaintively.

cheers (not very cheerily),

Rolf


-- 
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276

On 5 October 2016 at 12:16, Rolf Turner wrote:
| 
| On 05/10/16 12:07, Michael Rutter wrote:
| 
| > Typo on my part.  Try r-cran-rgdal.
| 
| Thanks. OK, I have now done
| 
|      sudo apt-get install r-cran-rgdal
| 
| successfully.

Very good.

Now do

   IP <- installed.packages()

and convince yourself that you have rgdal. You could even do

   library(rgdal)

| But sad to say, it didn't help a bit.  When I try
| 
|      install.packages("rgdal",lib="/home/rolf/Rlib")
| 
| I get exactly the same error as before.  I.e.
| 
|      > undefined symbol: CPLQuietErrorHandler

Computers have that silly habit of being deterministic. _Installing from
source another time_ does not change the fact that you did not have your
ducks in a row in the first place.  We did not change that; Michael merely
pointed you to a different pond with different ducks, ready to roast.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

> On 10/04/2016 05:54 PM, Rolf Turner wrote:
>>
>> I previously sent a cri de coeur about this problem to the r-help list
>> but so far have not managed to extract a solution.  So I am trying
here.
>> (Uh, Ubuntu *is* a "special instance" of Debian, isn't
it?)
>>
>> The problem is that I cannot install rgdal, and I need it.  Rather
>> desperately.
>>
>> I do:
>>
>>     install.packages("rgdal",lib="/home/rolf/Rlib")
>>
>> and get the error message:
>>
>>> ** testing if installed package can be loaded
>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>   unable to load shared object
'/home/rolf/Rlib/rgdal/libs/rgdal.so':
>>>   /home/rolf/Rlib/rgdal/libs/rgdal.so: undefined symbol:
>>> CPLQuietErrorHandler
>>> Error: loading failed
>>> Execution halted
Since I (in my desperation) cross-posted to r-sig-debian and r-help, I 
am sending this "SOLVED" message to both lists.

The solution took a long while to find, but in the end it was very simple.

Quite a while back I was having problems with installing some package
(I *think* it was one of my own packages, hmm.discnp), and someone (the 
details are lost in the mists of time) advised me to create a directory 
".R" in my home directory and in it place a file "Makevars"
containing
the lines:
> FCFLAGS = -g -O2 -mtune=native -fbounds-check
> FFLAGS = -g -O2 -mtune=native -fbounds-check
> PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
This solved the problem that I was having at that time.  I had long 
forgotten the directory ".R" and *that* was  what was causing the
problem.

A *very* clever and knowledgeable young Linux whiz, who kindly agreed to 
help me with this problem, eventually tracked down the fact that it 
originated from ".R".  When I removed ".R", the problem with
rgdal (and
problems with several other packages, that subsequently surfaced) went away.

My system is now humming away smoothly.

Thanks to everyone who (futilely!) attempted to help me out.

cheers,

Rolf Turner

-- 
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276