[R] Compiling R on aix getting error

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Mar 1 08:24:50 CET 2006


You have not apparently followed the advice in the R-admin manual:

   On AIX 4.3.3 and AIX 5.1/2, it was found that the use of ``run time
   linking'' (as opposed to normal AIX style linking) was required.  For
   this, the @R{} main program must be linked to the runtime linker with
   the @option{-brtl} linker option, and shareable objects must be enabled
   for runtime linking with the @option{-G} linker option.

There is no -G or -Wl,-G on the line you show, nor was there in the past 
message you quote (and the same person is quoted in the manual as having 
succeeded).


On Wed, 1 Mar 2006, Tiong Lim wrote:

> Prof Brian Ripley wrote:
>
>> On Tue, 28 Feb 2006, Tiong Lim wrote:
>> 
>>> I am trying to compile R 2.2.1 on aix 5.3 with xlc/xlC 7.0 , but i am
>>> getting the error below. I did a search on the archive and someone had a
>>> similar error as me but I can't seem to find a fix for the error below.
>> 
>> 
>> Are you referrring to
>> 
>> http://finzi.psych.upenn.edu/R/Rhelp02a/archive/66941.html
>> 
>> ?  Unfortunately I never received a reply to those questions.
>> 
>> This appeared to be something new in AIX 5.3's headers, most likely that 
>> they have apparently started defining SOCKLEN_T.  For the R-devel version 
>> on R we changed to R_SOCKLEN_T.
>> 
>> So please try the R-devel version of R, or change all occurrences of
>> SOCKLEN_T to R_SOCKLEN_T.
>> 
>> Googling showed that several other projects had been affected by this. E.g. 
>> http://www.zsh.org/mla/workers/2004/msg01205.html
>> And socklen_t on AIX has been an age-old problem.
>> 
>> ...
>>
>>>        xlc  -I../../src/extra/zlib -I../../src/extra/bzip2
>>> -I../../src/extra/pcre   -I. -I../../src/include -I../../src/include
>>> -DHAVE_CONFIG_H   -O -qstrict  -c platform.c -o platform.o
>>> "/usr/include/netinet/in.h", line 793.1: 1506-166 (S) Definition of
>>> function socklen_t requires parentheses.
>>> "/usr/include/netinet/in.h", line 793.17: 1506-276 (S) Syntax error:
>>> possible missing '{'?
>>> "/usr/include/sys/socket.h", line 374.9: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 378.9: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 404.9: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 475.52: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 476.57: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 477.57: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 478.87: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 484.44: 1506-275 (S) Unexpected text
>>> socklen_t encountered.
>>> "/usr/include/sys/socket.h", line 485.47: 1506-275 (S) Unexpected text
>>> socklen_t encountered.
>>> "/usr/include/sys/socket.h", line 486.55: 1506-046 (S) Syntax error.
>>> "/usr/include/sys/socket.h", line 490.73: 1506-275 (S) Unexpected text
>>> socklen_t encountered.
>>> "/usr/include/sys/socket.h", line 491.49: 1506-275 (S) Unexpected text
>>> socklen_t encountered.
>>> "platform.c", line 1386.13: 1506-285 (S) The indirection operator cannot
>>> be applied to a pointer to an incomplete struct or union.
>>> "platform.c", line 1388.34: 1506-285 (S) The indirection operator cannot
>>> be applied to a pointer to an incomplete struct or union.
>>> make: The error code from the last command is 1.
>>> 
>> 
> Thanks Brian for the explanation . Compiling the development version get me 
> pass the SOCKET error . But now i get Undefined symbols errors .
> Googling I find reference 
> https://stat.ethz.ch/pipermail/r-help/2004-March/046128.html which also 
> report similar error but  no answer .
>
> Tiong
>
>
> Target "R" is up to date.
> Target "R" is up to date.
> Target "R" is up to date.
> Target "R" is up to date.
> Target "Makedeps" is up to date.
> Target "libbz2.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libpcre.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libz.a" is up to date.
> ../../../src/include/libintl.h is unchanged
> ../../../include/libintl.h is unchanged
> Target "localecharset.h" is up to date.
> Target "Makedeps" is up to date.
> Target "libintl.a" is up to date.
> Target "R" is up to date.
> Target "Makedeps" is up to date.
> Target "libappl.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libnmath.a" is up to date.
> Target "Makedeps" is up to date.
> Target "libunix.a" is up to date.
> Target "Makedeps" is up to date.
> /people/lim/R-devel/bin/exec/R is unchanged
> Target "Makedeps" is up to date.
>       xlc -q64  -Wl,-bM:SRE -Wl,-H512 -Wl,-T512 -Wl,-bnoentry -Wl,-bexpall 
> -Wl,-bI:../../../etc/R.exp -L/usr/local/lib -o R_X11.so dataentry.o devX11.o 
> rotated.o rbitmap.o -lSM -lICE -lX11 -lXt  -ljpeg -lpng -lz
> ld: 0711-317 ERROR: Undefined symbol: .Rf_error
> ld: 0711-317 ERROR: Undefined symbol: .Rf_warning
> ld: 0711-317 ERROR: Undefined symbol: .Rf_lengthgets
> ld: 0711-317 ERROR: Undefined symbol: .R_Reprotect
> ld: 0711-317 ERROR: Undefined symbol: .Rf_mkChar
> ld: 0711-317 ERROR: Undefined symbol: .SET_STRING_ELT
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isNull
> ld: 0711-317 ERROR: Undefined symbol: .SET_VECTOR_ELT
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isVector
> ld: 0711-317 ERROR: Undefined symbol: .Rf_allocVector
> ld: 0711-317 ERROR: Undefined symbol: R_NaString
> ld: 0711-317 ERROR: Undefined symbol: R_NilValue
> ld: 0711-317 ERROR: Undefined symbol: .Rf_PrintDefaults
> ld: 0711-317 ERROR: Undefined symbol: .Rf_EncodeElement
> ld: 0711-317 ERROR: Undefined symbol: .Rf_length
> ld: 0711-317 ERROR: Undefined symbol: .Rf_coerceVector
> ld: 0711-317 ERROR: Undefined symbol: .Rf_install
> ld: 0711-317 ERROR: Undefined symbol: R_GlobalEnv
> ld: 0711-317 ERROR: Undefined symbol: .Rf_GetOption
> ld: 0711-317 ERROR: Undefined symbol: .Rf_asInteger
> ld: 0711-317 ERROR: Undefined symbol: R_NaInt
> ld: 0711-317 ERROR: Undefined symbol: .log10
> ld: 0711-317 ERROR: Undefined symbol: .floor
> ld: 0711-317 ERROR: Undefined symbol: .R_strtod
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isBlankString
> ld: 0711-317 ERROR: Undefined symbol: R_NaReal
> ld: 0711-317 ERROR: Undefined symbol: .UNIMPLEMENTED
> ld: 0711-317 ERROR: Undefined symbol: .Rf_duplicate
> ld: 0711-317 ERROR: Undefined symbol: .R_ProtectWithIndex
> ld: 0711-317 ERROR: Undefined symbol: R_NamesSymbol
> ld: 0711-317 ERROR: Undefined symbol: .Rf_getAttrib
> ld: 0711-317 ERROR: Undefined symbol: .Rf_errorcall
> ld: 0711-317 ERROR: Undefined symbol: .Rf_protect
> ld: 0711-317 ERROR: Undefined symbol: .Rf_str2type
> ld: 0711-317 ERROR: Undefined symbol: R_BaseEnv
> ld: 0711-317 ERROR: Undefined symbol: .Rf_begincontext
> ld: 0711-317 ERROR: Undefined symbol: .Rf_endcontext
> ld: 0711-317 ERROR: Undefined symbol: .Rf_setAttrib
> ld: 0711-317 ERROR: Undefined symbol: .Rf_unprotect
> ld: 0711-317 ERROR: Undefined symbol: .libintl_gettext
> ld: 0711-317 ERROR: Undefined symbol: .R_setX11Routines
> ld: 0711-317 ERROR: Undefined symbol: .Rf_checkArity
> ld: 0711-317 ERROR: Undefined symbol: .vmaxget
> ld: 0711-317 ERROR: Undefined symbol: .Rf_asReal
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isValidString
> ld: 0711-317 ERROR: Undefined symbol: .Rf_warningcall
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isString
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isInteger
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isLogical
> ld: 0711-317 ERROR: Undefined symbol: .Rf_isReal
> ld: 0711-317 ERROR: Undefined symbol: .Rf_RGBpar
> ld: 0711-317 ERROR: Undefined symbol: .vmaxset
> ld: 0711-317 ERROR: Undefined symbol: .R_CheckDeviceAvailable
> ld: 0711-317 ERROR: Undefined symbol: R_interrupts_suspended
> ld: 0711-317 ERROR: Undefined symbol: .Rf_mkString
> ld: 0711-317 ERROR: Undefined symbol: .Rf_gsetVar
> ld: 0711-317 ERROR: Undefined symbol: .GEcreateDevDesc
> ld: 0711-317 ERROR: Undefined symbol: .Rf_addDevice
> ld: 0711-317 ERROR: Undefined symbol: .GEinitDisplayList
> ld: 0711-317 ERROR: Undefined symbol: R_interrupts_pending
> ld: 0711-317 ERROR: Undefined symbol: .Rf_onintr
> ld: 0711-317 ERROR: Undefined symbol: .R_alloc
> ld: 0711-317 ERROR: Undefined symbol: .Rf_findVar
> ld: 0711-317 ERROR: Undefined symbol: .Rf_elt
> ld: 0711-317 ERROR: Undefined symbol: .Rf_GetDevice
> ld: 0711-317 ERROR: Undefined symbol: .Rf_ScalarString
> ld: 0711-317 ERROR: Undefined symbol: .R_FindNamespace
> ld: 0711-317 ERROR: Undefined symbol: .Rf_eval
> ld: 0711-317 ERROR: Undefined symbol: R_InputHandlers
> ld: 0711-317 ERROR: Undefined symbol: .getInputHandler
> ld: 0711-317 ERROR: Undefined symbol: .removeInputHandler
> ld: 0711-317 ERROR: Undefined symbol: .Rf_devNumber
> ld: 0711-317 ERROR: Undefined symbol: .Rf_KillDevice
> ld: 0711-317 ERROR: Undefined symbol: .GEplayDisplayList
> ld: 0711-317 ERROR: Undefined symbol: .pow
> ld: 0711-317 ERROR: Undefined symbol: .R_ShowMessage
> ld: 0711-317 ERROR: Undefined symbol: mbcslocale
> ld: 0711-317 ERROR: Undefined symbol: .sin
> ld: 0711-317 ERROR: Undefined symbol: .cos
> ld: 0711-317 ERROR: Undefined symbol: .tan
> ld: 0711-317 ERROR: Undefined symbol: .R_ExpandFileName
> ld: 0711-317 ERROR: Undefined symbol: .R_fopen
> ld: 0711-317 ERROR: Undefined symbol: .Rf_asLogical
> ld: 0711-317 ERROR: Undefined symbol: .addInputHandler
> ld: 0711-317 ERROR: Undefined symbol: .Rprintf
> ld: 0711-317 ERROR: Undefined symbol: .R_IsNA
> ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more 
> information.
> make: The error code from the last command is 8.
>
>
> Stop.
> make: The error code from the last command is 2.
>
>
> Stop.
> make: The error code from the last command is 1.
>
>
> Stop.
> make: The error code from the last command is 1.
>
>
> Stop.
> make: The error code from the last command is 1.
>
>
> Stop.
>
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595




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