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AIX 5.3 --enable-R-shlib --with-x ---with-iconv make error with R-2.7.0 and R-2.7.1

4 messages · Ei-ji Nakama, Fán Lóng

Original
Fán Lóng
# 
Hi guys,

I am trying to compile a 64bit version of R 2.7.0 on AIX 5.3. And I am
running into some troubles.  I also try the latest version 2.7.1 and
get the very similar errors.

The machine info:
-----------------------
$uname -srvp
AIX 3 5 powerpc
----------------------



My configuration is this:

----------------------------------------------------------
./configure \
           CC="xlc_r -q64" \
           CFLAGS="-O -qstrict" \
           CXX="xlC_r -q64" \
           CXXFLAGS="-O -qstrict" \
           F77="xlf_r -q64" \
           AR="ar -X64" \
           CPPFLAGS="-I/my_libiconv_dir/include -I/usr/lpp/X11/include/X11" \
           LDFLAGS="-L/my_libiconv_dir/lib -L/usr/lib -L/usr/X11R6/lib
-L/my_buildR_dir/R-2.7.0/lib" \
           --prefix=/my_R_dir \
           --enable-R-shlib \
           --enable-BLAS-shlib \
           --with-x \
           --with-readline=no \
           --with-libiconv-prefix="/my_libiconv_dir"
------------------------------------------------------------

I don't have the gcc and gfortran installed on the machine, so I use
the native ones. As the manual says, the AIX native iconv does not
support encodings `latin1' nor `""' and so cannot be used. I install
GNU libiconv to my_libiconv_dir follow the steps in
http://prs.ism.ac.jp/~nakama/AIX/AIX_iconv_CookBook.txt. Thanks Ei-ji
Nakama for this CookBook :)


The configuration step ends OK:

-----------------------------------------------------------

R is now configured for powerpc-ibm-aix5.3.0.0

 Source directory:          .
 Installation directory:    /rnd/homes/my/rdir/AIX/R-2.7.0

 C compiler:                xlc_r -q64 -qlanglvl=extc99  -O -qstrict
 Fortran 77 compiler:       xlf_r -q64  -g

 C++ compiler:              xlC_r -q64  -O -qstrict
 Fortran 90/95 compiler:    xlf95 -g
 Obj-C compiler:

 Interfaces supported:      X11
 External libraries:
 Additional capabilities:   iconv, MBCS, NLS
 Options enabled:           shared BLAS, R profiling, Java

 Recommended packages:      yes

configure: WARNING: you cannot build DVI versions of the R manuals
configure: WARNING: you cannot build info or HTML versions of the R manuals
configure: WARNING: you cannot build PDF versions of the R manuals
configure: WARNING: I could not determine a browser
configure: WARNING: I could not determine a PDF viewer

----------------------------------------------------------------


When trying to compile(gmake), I get the following error message.
The first for R-2.7.0 and the second for R-2.7.1.


-------------------------------------------------------------------------
make[3]: Entering directory `/my_buildR_dir/R-2.7.0/src/library/splines'
building package 'splines'
make[4]: Entering directory `/my_buildR_dir/R-2.7.0/src/library/splines/src'
make[5]: Entering directory `/my_buildR_dir/R-2.7.0/src/library/splines/src'
make[5]: `Makedeps' is up to date.
make[5]: Leaving directory `/my_buildR_dir/R-2.7.0/src/library/splines/src'
make[5]: Entering directory `/my_buildR_dir/R-2.7.0/src/library/splines/src'
xlc_r -q64 -qlanglvl=extc99 -I../../../../include
-I/my_libiconv_dir/include -I/usr/lpp/X11/include/X11      -O -qstrict
-c splines.c -o splines.o
xlc_r -q64 -qlanglvl=extc99 -Wl,-brtl -Wl,-G -Wl,-bexpall
-Wl,-bnoentry -lc -L/my_libiconv_dir/lib -L/usr/lib -L/usr/X11R6/lib
-L/my_buildR_dir/R-2.7.0/lib -o splines.so splines.o   -lm
-L../../../../lib -lR
make[5]: Leaving directory `/my_buildR_dir/R-2.7.0/src/library/splines/src'
make[4]: Leaving directory `/my_buildR_dir/R-2.7.0/src/library/splines/src'
Error in dyn.load(file, DLLpath = DLLpath, ...) :
 unable to load shared library
'/my_buildR_dir/R-2.7.0/library/stats/libs/stats.so':
 rtld: 0712-001 Symbol d1mach was referenced
     from module
/my_buildR_dir/R-2.7.0/library/stats/libs/stats.so(), but a runtime
definition
           of the symbol was not found.
rtld: 0712-001 Symbol interv was referenced
     from module
/my_buildR_dir/R-2.7.0/library/stats/libs/stats.so(), but a runtime
definition
           of the symbol was not found.
rtld: 0712-002 fatal error: exiting.
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[3]: *** [all] Error 1
make[3]: Leaving directory `/my_buildR_dir/R-2.7.0/src/library/splines'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/my_buildR_dir/R-2.7.0/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/my_buildR_dir/R-2.7.0/src'
make: *** [R] Error 1
--------------------------------------------------------------------------



------------------------------------------------------------------------
make[3]: Leaving directory `/my_buildR_dir/R-2.7.1/src/library/base'
make[3]: Entering directory `/my_buildR_dir/R-2.7.1/src/library/tools'
building package 'tools'
mkdir ../../../library/tools/R
mkdir ../../../library/tools/po
mkdir ../../../library/tools/man
make[4]: Entering directory `/my_buildR_dir/R-2.7.1/src/library/tools/src'
make[5]: Entering directory `/my_buildR_dir/R-2.7.1/src/library/tools/src'
make[5]: `Makedeps' is up to date.
make[5]: Leaving directory `/my_buildR_dir/R-2.7.1/src/library/tools/src'
make[5]: Entering directory `/my_buildR_dir/R-2.7.1/src/library/tools/src'
xlc_r -q64 -qlanglvl=extc99 -I../../../../include
-I/my_libiconv_dir/include -I/usr/lpp/X11/include/X11      -O -qstrict
-c text.c -o text.o
xlc_r -q64 -qlanglvl=extc99 -I../../../../include
-I/my_libiconv_dir/include -I/usr/lpp/X11/include/X11      -O -qstrict
-c init.c -o init.o
xlc_r -q64 -qlanglvl=extc99 -I../../../../include
-I/my_libiconv_dir/include -I/usr/lpp/X11/include/X11      -O -qstrict
-c Rmd5.c -o Rmd5.o
xlc_r -q64 -qlanglvl=extc99 -I../../../../include
-I/my_libiconv_dir/include -I/usr/lpp/X11/include/X11      -O -qstrict
-c md5.c -o md5.o
xlc_r -q64 -qlanglvl=extc99 -Wl,-brtl -Wl,-G -Wl,-bexpall
-Wl,-bnoentry -lc -L/my_libiconv_dir/lib -L/usr/lib -L/usr/X11R6/lib
-L/my_buildR_dir/R-2.7.1/lib -o tools.so text.o init.o Rmd5.o md5.o
-lm
make[5]: Leaving directory `/my_buildR_dir/R-2.7.1/src/library/tools/src'
make[4]: Leaving directory `/my_buildR_dir/R-2.7.1/src/library/tools/src'
Error in dyn.load(file, DLLpath = DLLpath, ...) :
 unable to load shared library
'/my_buildR_dir/R-2.7.1/library/tools/libs/tools.so':
 rtld: 0712-001 Symbol TYPEOF was referenced
     from module
/my_buildR_dir/R-2.7.1/library/tools/libs/tools.so(), but a runtime
definition
           of the symbol was not found.
rtld: 0712-001 Symbol LENGTH was referenced
     from module
/my_buildR_dir/R-2.7.1/library/tools/libs/tools.so(), but a runtime
definition
           of the symbol was not found.
rtld: 0712-001 Symbol R_CHAR was referenced
     from module
/my_buildR_dir/R-2.7.1/library/tools/libs/tools.so(), but a runtime
definition
           of the symbol was not found.
rtld: 0712-001 Symbol Rf_isString was referenced
     from module
/my_buildR_dir/R-2.7.1/library/tools/libs/tools.so(), but a runtime
definition
           of the symbol was not found.
rtld: 0712-002 fatal error: exiting.
Calls: ::: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
make[3]: *** [all] Error 1
make[3]: Leaving directory `/my_buildR_dir/R-2.7.1/src/library/tools'
make[2]: *** [R] Error 1
make[2]: Leaving directory `/my_buildR_dir/R-2.7.1/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/my_buildR_dir/R-2.7.1/src'
make: *** [R] Error 1
-----------------------------------------------------------------------------

You see the symbols d1mach, interv, TYPEOF, R_CHAR and Rf_isString,
were not found. As for the library dependence, I add
/my_libiconv_dir/lib to my LIBPATH to make sure libR.so etc. can find
the libiconv. Thus, stats.so and tools.so could have be loaded. I
don't know where I made a mistake. After looking up the R manual and
diving into Google for help, I've got no usable answer.

I think I really need your help.

Below environment variables may associated:
LIBPATH="/my_libiconv_dir/lib:.:/rnd/homes/my/rdir/AIX/R-2.7.0/lib/R/lib:.:/usr/lib:/lib"
PATH="/rnd/homes/my/rdir/AIX/R-2.7.0/bin:/usr/java5_64/bin:/opt/gnu/bin:/usr/java5/bin:/opt/gnu/bin:/usr/bin:/etc:/usr/sbin:/usr/ucb:/usr/bin/X11:/sbin:/usr/java14/jre/bin:/usr/java14/bin:/usr/vacpp/bin:/usr/local/bin:/usr/idebug:."
R_HOME="/rnd/homes/my/rdir/AIX/R-2.7.0"



Thank you in advance,
Foy long
Ei-ji Nakama
# 
Hi, sorry buggy English.

Did you cook this patch?
http://prs.ism.ac.jp/~nakama/AIX/aix_R-2.7.1_Rshlib_include_configure.patch

However, cooking of this patch is bad on AIX.
Therefore I put the thing which was finished with cooking.

http://prs.ism.ac.jp/~nakama/AIX/R-2.7.1.aix080701.tar.gz

I do a wish of tasting to you.

2008/7/17 F?n L?ng <foylong at gmail.com>:
``export OBJECT_MODE=64'' had better set it.
--with-libiconv-prefix are not reflected.
libjpeg and libjpeg-6b of java do conflict in my environment.
I remove PATH of the JAVA at the time of the construction.
I had the sense that GC of ld turned into recently.
Probably former specifications may be bugs.
<snip>
Because R add it in a shell of ``bin/R'', let's add LIBPATH when it
was said that there is not it.

best,
Fán Lóng
# 
Thank you, Ei-ji.

I haven't tried the aix_R-2.7.1_Rshlib_include_configure.patch for two reason:
#1 I have to compile R2.7.0 although I can reproduce the trouble on R-2.7.1.
#2 Actually, I don't know how to use this patch to R-2.7.1. Does this
need AIX admin permission?

And thanks for telling me the pacthed R-2.7.1.aix080701.tar.gz, I will
try this and let you know the result. BTW: do we also have a patched
R-2.7.0?

I will also try to export OBJECT_MODE=64 before configuring without
--with-libiconv-prefix and remove JAVA path from PATH of when
compiling R.

In a word, thank you very much for taking care of this.

Regards,
Long
On Thu, Jul 17, 2008 at 11:12 PM, Ei-ji Nakama <nakama at ki.rim.or.jp> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Fán Lóng
    

    

      
      #
    

  


  

      
Build success!

I just use the files out here:
http://prs.ism.ac.jp/~nakama/AIX/changefiles to patch my R-2.7.0 and
add export OBJECT_MODE=64 to my configure parameter. It works.

Thank you very much for your help, Ei-ji.


2008/7/17 F??n L??ng <foylong at gmail.com>: