R SIG Debian - Oct 2017 - Binding with libiconv failed while compiling R-devel on Ubuntu 17.04

Dear everyone,

I posted a similar question to Stack Overflow there:
https://stackoverflow.com/questions/46907554/binding-with-libiconv-failed-while-compiling-r-devel-on-ubuntu-17-04
and I was suggested to post my question here.

I tried to compile R devel using Dirk Eddelbuettel's recipe (and many
variants of it).  Regardless of what I do, I have:
==  	[...]/src/main/sysutils.c:794: undefined reference to `libiconv'
  	[...]
  	[...]/src/main/platform.c:3052: undefined reference to `u_getVersion_54'
  	[...]
==add many other similar lines, similar to the last comment of
http://jtremblay.github.io/software_installation/2017/06/21/Install-R-3.4.0-and-RStudio-on-Ubuntu-16.04

(Of note: the offending line does not contain "libiconv" per se, but
instead "iconv(...)".)

It seems that libiconv is now in libc6. I checked that these packages are
correctly installed, and updated (with Gnome Ubuntu 17.04):
   - libc6-dev
   - libicu-dev
   - build-essential
   - fort77
   - xorg-dev
   - liblzma-dev
   - libblas-dev
   - gfortran
   - gcc-multilib
   - gobjc++
   - aptitude
   - libreadline-dev
   - libcurl4-openssl-dev
   - default-jdk
   - texlive-latex-base
   - libcairo2-dev

The configuration step regarding libiconv seems ok:
==  	checking iconv.h usability... yes
  	checking iconv.h presence... yes
  	checking for iconv.h... yes
  	checking for iconv... yes
  	checking whether iconv accepts "UTF-8", "latin1",
"ASCII" and "UCS-*"... yes
  	checking for iconvlist... no
  	checking for iconv... yes
  	checking for iconv declaration...
  			 extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char
* *outbuf, size_t *outbytesleft);
==The command iconv -l seems to work fine. This C file compiles with no problem
either:
==  	#include <iconv.h>

  	int main( int argc, char **argv ) {
  					iconv_t cd = iconv_open( "UTF-8", "ISO-8859-1" );
  					iconv_close( cd );
  					return 0;
  	}
==So libiconv seems to be indeed usable, but not during the linking.

Where should I look?

Thanks for posting here.

On 24 October 2017 at 14:14, Matthias Zytnicki wrote:
| Dear everyone,
| 
| I posted a similar question to Stack Overflow there:
https://stackoverflow.com/questions/46907554/binding-with-libiconv-failed-while-compiling-r-devel-on-ubuntu-17-04
and I was suggested to post my question here.
| 
| I tried to compile R devel using Dirk Eddelbuettel's recipe (and many
variants of it).  Regardless of what I do, I have:
| ==|   	[...]/src/main/sysutils.c:794: undefined reference to `libiconv'
|   	[...]
|   	[...]/src/main/platform.c:3052: undefined reference to
`u_getVersion_54'
|   	[...]
| ==| add many other similar lines, similar to the last comment of
http://jtremblay.github.io/software_installation/2017/06/21/Install-R-3.4.0-and-RStudio-on-Ubuntu-16.04
| 
| (Of note: the offending line does not contain "libiconv" per se, but
instead "iconv(...)".)
| 
| It seems that libiconv is now in libc6. I checked that these packages are
correctly installed, and updated (with Gnome Ubuntu 17.04):
|    - libc6-dev
|    - libicu-dev
|    - build-essential
|    - fort77
|    - xorg-dev
|    - liblzma-dev
|    - libblas-dev
|    - gfortran
|    - gcc-multilib
|    - gobjc++
|    - aptitude
|    - libreadline-dev
|    - libcurl4-openssl-dev
|    - default-jdk
|    - texlive-latex-base
|    - libcairo2-dev
| 
| The configuration step regarding libiconv seems ok:
| ==|   	checking iconv.h usability... yes
|   	checking iconv.h presence... yes
|   	checking for iconv.h... yes
|   	checking for iconv... yes
|   	checking whether iconv accepts "UTF-8", "latin1",
"ASCII" and "UCS-*"... yes
|   	checking for iconvlist... no
|   	checking for iconv... yes
|   	checking for iconv declaration...
|   			 extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft,
char * *outbuf, size_t *outbytesleft);
| ==| The command iconv -l seems to work fine. This C file compiles with no
problem either:
| ==|   	#include <iconv.h>
| 
|   	int main( int argc, char **argv ) {
|   					iconv_t cd = iconv_open( "UTF-8", "ISO-8859-1" );
|   					iconv_close( cd );
|   					return 0;
|   	}
| ==| So libiconv seems to be indeed usable, but not during the linking.
| 
| Where should I look?

Something _must be_ wrong with your machine.  We probably need more complete
details of the configure and link steps.  

Do you ever have issues with building other CRAN packages from source?

Dirk

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

Thanks for helping.

The story so far: I have been using R-devel for about one year, and installed it
with the same protocol.  Last time I compiled it, it was about 2 months ago,
with no problem.
I had not problems with packages and BioConductor working like a charm too.

Now, where I am currently stuck is the linking part:
== 	gcc -Wl,--export-dynamic -fopenmp  -L"../../lib" -L/usr/local/lib
-o R.bin Rmain.o  -lR -lRblas
 	../../lib/libR.so: undefined reference to `u_versionToString_54'
 	../../lib/libR.so: undefined reference to `u_getVersion_54'
 	../../lib/libR.so: undefined reference to `ucol_open_54'
 	../../lib/libR.so: undefined reference to `ucol_setStrength_54'
 	../../lib/libR.so: undefined reference to `libiconv'
 	../../lib/libR.so: undefined reference to `libiconv_close'
 	../../lib/libR.so: undefined reference to `ucol_strcollIter_54'
 	../../lib/libR.so: undefined reference to `_libiconv_version'
 	../../lib/libR.so: undefined reference to `libiconv_open'
 	../../lib/libR.so: undefined reference to `ucol_close_54'
 	../../lib/libR.so: undefined reference to `ucol_setAttribute_54'
 	../../lib/libR.so: undefined reference to `uloc_setDefault_54'
 	../../lib/libR.so: undefined reference to `ucol_getLocaleByType_54'
 	../../lib/libR.so: undefined reference to `uiter_setUTF8_54'
==The full trace is https://pastebin.com/7Pyn4Bwv

The configuration trace is https://pastebin.com/j1DR3WLM

I can provide any info you will consider useful.

Thanks again,

Matthias.


On Tue, 24 Oct 2017, Dirk Eddelbuettel wrote:
>
> Thanks for posting here.
>
> On 24 October 2017 at 14:14, Matthias Zytnicki wrote:
> | Dear everyone,
> |
> | I posted a similar question to Stack Overflow there:
https://stackoverflow.com/questions/46907554/binding-with-libiconv-failed-while-compiling-r-devel-on-ubuntu-17-04
and I was suggested to post my question here.
> |
> | I tried to compile R devel using Dirk Eddelbuettel's recipe (and many
variants of it).  Regardless of what I do, I have:
> | ==> |   	[...]/src/main/sysutils.c:794: undefined reference to
`libiconv'
> |   	[...]
> |   	[...]/src/main/platform.c:3052: undefined reference to
`u_getVersion_54'
> |   	[...]
> | ==> | add many other similar lines, similar to the last comment of
http://jtremblay.github.io/software_installation/2017/06/21/Install-R-3.4.0-and-RStudio-on-Ubuntu-16.04
> |
> | (Of note: the offending line does not contain "libiconv" per
se, but instead "iconv(...)".)
> |
> | It seems that libiconv is now in libc6. I checked that these packages are
correctly installed, and updated (with Gnome Ubuntu 17.04):
> |    - libc6-dev
> |    - libicu-dev
> |    - build-essential
> |    - fort77
> |    - xorg-dev
> |    - liblzma-dev
> |    - libblas-dev
> |    - gfortran
> |    - gcc-multilib
> |    - gobjc++
> |    - aptitude
> |    - libreadline-dev
> |    - libcurl4-openssl-dev
> |    - default-jdk
> |    - texlive-latex-base
> |    - libcairo2-dev
> |
> | The configuration step regarding libiconv seems ok:
> | ==> |   	checking iconv.h usability... yes
> |   	checking iconv.h presence... yes
> |   	checking for iconv.h... yes
> |   	checking for iconv... yes
> |   	checking whether iconv accepts "UTF-8", "latin1",
"ASCII" and "UCS-*"... yes
> |   	checking for iconvlist... no
> |   	checking for iconv... yes
> |   	checking for iconv declaration...
> |   			 extern size_t iconv (iconv_t cd, char * *inbuf, size_t
*inbytesleft, char * *outbuf, size_t *outbytesleft);
> | ==> | The command iconv -l seems to work fine. This C file compiles
with no problem either:
> | ==> |   	#include <iconv.h>
> |
> |   	int main( int argc, char **argv ) {
> |   					iconv_t cd = iconv_open( "UTF-8", "ISO-8859-1"
);
> |   					iconv_close( cd );
> |   					return 0;
> |   	}
> | ==> | So libiconv seems to be indeed usable, but not during the
linking.
> |
> | Where should I look?
>
> Something _must be_ wrong with your machine.  We probably need more
complete
> details of the configure and link steps.
>
> Do you ever have issues with building other CRAN packages from source?
>
> Dirk
>
> -- 
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
>