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 | [email protected]
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