Oracle R Distribution (ORD) ld: fatal: file /opt/ORD/R/lib/libR.so: wrong ELF class: ELFCLASS64

Hello Team,

                 Thank you for response. very much appreciate. As i am not aware of ORD and its process.

what customer done:   CU installed latest ORD 3.3.0 (its a Solaris 10 package installed in solaris 11) have curl 7.49,so CU removed curl 7.49 libraries of ORD and linked with Solaris 11  SRU 23.5 of curl 7.45 libraries.so till now ORD (solaris 10 pkg) is working fine in solaris 11.3 OS.

                    when CU installed solaris studio 12.6 and  started ORD and execute below commands.

> sessionInfo()

    Oracle Distribution of R version 3.3.0 (2016-05-03)

    Platform: sparc-sun-solaris2.10 (64-bit)

    Running under: Solaris 11

    locale:

    [1] C

    attached base packages:

   [1] stats     graphics  grDevices utils     datasets  methods   base    

> system("which cc")

     /opt/developerstudio/bin/cc

> system("‘which cc‘ -V")

     cc: Studio 12.6 Sun C 5.15 SunOS_sparc 2017/05/30

> system("which ld")

     /usr/ccs/bin/ld

> system("‘which ld‘ -V")

     ld: Software Generation Utilities - Solaris Link Editors: 5.11-1.2560

> drat::addRepo("jr-packages")                       -----------------------------> CU wants to install

> install.packages("jrIntroduction", dependencies=TRUE)

     Installing package into ’/usr/lib/sparcv9/R/library’

      (as ’lib’ is unspecified)

      Warning in install.packages("jrIntroduction", dependencies = TRUE) :

      ’lib = "/usr/lib/sparcv9/R/library"’ is not writable

      Would you like to use a personal library instead?  (y/n) y

      /opt/developerstudio/bin/cc -I/usr/lib/sparcv9/R/include -DNDEBUG      -KPIC  -m32 -c rawmatch.c -o rawmatch.o

     /opt/developerstudio/bin/cc -G -L/usr/lib/sparcv9/R/lib -o mime.so rawmatch.o -L/usr/lib/sparcv9/R/lib -lR

ld: fatal: file /usr/lib/sparcv9/R/lib/libR.so: wrong ELF class: ELFCLASS64

gmake: *** [mime.so] Error 2

ERROR: compilation failed for package ’mime’

* removing ’/disk/home/michael/R/mime’

* installing *source* package ’stringi’ ...

** package ’stringi’ successfully unpacked and MD5 sums checked

                  Please refere link CU explained issue brefily  http://cloud.tel.co.uk:8192/dropbox/SR_3-15757052521_03.pdf

what Customer wants: ORD source code which support Solaris 11.3 for make and compile which should install perfectly without error.

Regards

Pavan Aketi

Hello Team,

            As suggested please find the below link which CU has given output for Makeconf & library_path. please let me know if you can able to open the link or not.

           I have copied data in below. please check and provide me a solution

      http://cloud.tel.co.uk:8192/dropbox/SR_3-15757052521_04.pdf

21/09/2017

11:56:11 1 SR_3-15757052521_04

SR #3-15757052521: Oracle R Distribution (ORD) ld: fatal: libR.so wrong ELF class

      GALAXY Sun SPARC T4-1 128 GB RAM Serial #103425876. Host ID: 862a2754

                              Hypervisor 1.15.5.a

        SunOS Release 5.11 Version 11.3 64-bit SPARC  CSN: 13068DY261

                         (Oracle Solaris 11.3.24.0.0)

     Sun SysFW 8.9.5.a Oracle Solaris 11.3 SPARCT4-1 Rev 1.2 sun4v 2.85 GHz

      Oracle(R) Integrated Lights Out Manager Version 3.2.6.4a r110875

   OpenBoot  4.38.5  U-Boot 1.1.4 Custom AST2100 U-Boot 3.0 r110875

AST2200 264 MHz 128 MB SDRAM 64 MB FLASH ARM Linux Kernel Image Linux-2.6.27.43

  Copyright (c) 1983, 2016, Oracle and/or its affiliates.  All rights reserved.

                            Assembled 09 August 2016

Terminal type is xterm; 24 rows; 80 columns; Display is localhost:10.0

Thu Sep 21 11:08:29 BST 2017 on /dev/pts/32 from

You have new mail.

GNU bash, version 4.4.11(1)-release (sparc-sun-solaris2.11)

GALAXY 11:07:10 $ echo $PATH

/home/michael/bin:/usr/sbin:/usr/gnu/bin:/usr/lib/sparcv9/R/bin:/usr/ccs/bin:/usr/bin:

/opt/local/sbin:/usr/perl5/5.12/bin:/opt/local/bin:/usr/dt/bin:/usr/lib/mailman/bin:

/u01/app/oracle/product/12.1.0/dbhome_1/bin:/u01/app/oracle/product/12.1.0/dbhome_1/../grid/bin:

/u01/app/oracle/product/12.1.0/dbhome_1/../grid/suptools/orachk:

/u01/app/oracle/product/12.1.0/dbhome_1/../grid/suptools/tfa/release/tfa_home/bin:

/usr/mysql/5.5/bin:/usr/xpg4/bin:/usr/bin:/usr/ucb:/usr/sfw/bin:/opt/sfw/bin:

/opt/developerstudio/bin:/opt/oppenoffice.org/ure/bin:/usr/X/bin:/usr/X/lib/xdm:/opt/Minitab:

/opt/Adobe/Reader7/bin:/opt/Adobe/Reader8/bin:/opt/applixware:/opt/csw/bin:/opt/csw/sbin:

GALAXY 11:07:16 $ echo $LD_LIBRARY_PATH

/usr/X/lib:/usr/X11/lib:/lib/sparcv9:/usr/lib/sparcv9:/u01/app/oracle/product/12.1.0/dbhome_1/lib:

/u01/app/oracle/product/12.1.0/dbhome_1/network/lib:/usr/lib/sparcv9/R/lib:/usr/lib:/usr/xpg4/lib:

/usr/dt/lib:/opt/local/lib:/opt/developerstudio/lib:/opt/developerstudio/lib/compilers/rtlibs/usr/lib/sparcv9:

/opt/ooo-dev/basis3.4/program:/opt/ooo-dev/ure/lib:/opt/ooo-dev3/basis-link/ure-link/lib:/opt/hpnpl/lib:

/opt/hpnp/lib:/opt/sfw/lib/thunderbird:/usr/java1.1/lib/sparc/native_threads:/u01/app/oracle/../grid/lib:

/usr/oracle/instantclient/12.1/lib:/opt/csw/lib:

GALAXY 11:07:34 $ file /usr/lib/sparcv9/R/bin/exec/R

/usr/lib/sparcv9/R/bin/exec/R:  ELF 64-bit MSB executable SPARCV9 Version 1, dynamically linked, not stripped

GALAXY 11:09:40 $ ldd /usr/lib/sparcv9/R/bin/exec/R

        liblzma.so.5 =>         /usr/lib/sparcv9/liblzma.so.5

        libz.so.1 =>            /lib/sparcv9/libz.so.1

        libR.so =>              /usr/lib/sparcv9/R/lib/libR.so

        libmtsk.so.1 =>         /lib/sparcv9/libmtsk.so.1

        libthread.so.1 =>       /lib/sparcv9/libthread.so.1

        libc.so.1 =>            /lib/sparcv9/libc.so.1

        libpthread.so.1 =>      /lib/sparcv9/libpthread.so.1

        libfai.so.3 =>          /u01/app/oracle/product/12.1.0/dbhome_1/lib/libfai.so.3

        libfai2.so.3 =>         /u01/app/oracle/product/12.1.0/dbhome_1/lib/libfai2.so.3

        libfui.so.2 =>          /u01/app/oracle/product/12.1.0/dbhome_1/lib/libfui.so.2

        libfsu.so.1 =>          /u01/app/oracle/product/12.1.0/dbhome_1/lib/libfsu.so.1

        libm.so.2 =>            /lib/sparcv9/libm.so.2

        libreadline.so.6 =>     /u01/app/oracle/product/12.1.0/dbhome_1/lib/libreadline.so.6

        libncurses.so.5 =>      /usr/lib/sparcv9/libncurses.so.5

        libpcre.so.1 =>         /u01/app/oracle/product/12.1.0/dbhome_1/lib/libpcre.so.1

        libbz2.so.1.0 =>        /u01/app/oracle/product/12.1.0/dbhome_1/lib/libbz2.so.1.0

        libnsl.so.1 =>          /lib/sparcv9/libnsl.so.1

        libsocket.so.1 =>       /lib/sparcv9/libsocket.so.1

        librt.so.1 =>           /lib/sparcv9/librt.so.1

        libdl.so.1 =>           /lib/sparcv9/libdl.so.1

        libcurl.so.4 =>         /usr/lib/sparcv9/libcurl.so.4

        libiconv.so.2 =>        /u01/app/oracle/product/12.1.0/dbhome_1/lib/libiconv.so.2

        libsunperf.so.8 =>      /u01/app/oracle/product/12.1.0/dbhome_1/lib/libsunperf.so.8

        libkstat.so.1 =>        /lib/sparcv9/libkstat.so.1

        libsunmath.so.1 =>      /lib/sparcv9/libsunmath.so.1

        libmp.so.2 =>           /lib/sparcv9/libmp.so.2

        libucrypto.so.1 =>      /lib/sparcv9/libucrypto.so.1

        libidn.so.11 =>         /usr/lib/sparcv9/libidn.so.11

        libssh2.so.1 =>         /usr/lib/sparcv9/libssh2.so.1

        libssl.so.1.0.0 =>      /lib/sparcv9/libssl.so.1.0.0

        libcrypto.so.1.0.0 =>   /lib/sparcv9/libcrypto.so.1.0.0

        libgssapi_krb5.so.2 =>  /usr/lib/sparcv9/libgssapi_krb5.so.2

        liblber-2.4.so.2 =>     /usr/lib/sparcv9/liblber-2.4.so.2

        libldap_r-2.4.so.2 =>   /usr/lib/sparcv9/libldap_r-2.4.so.2

        libpicl.so.1 =>         /usr/lib/sparcv9/libpicl.so.1

        libelf.so.1 =>          /lib/sparcv9/libelf.so.1

        libcryptoutil.so.1 =>   /lib/sparcv9/libcryptoutil.so.1

        libkrb5.so.3 =>         /usr/lib/sparcv9/libkrb5.so.3

        libk5crypto.so.3 =>     /usr/lib/sparcv9/libk5crypto.so.3

        libcom_err.so.3 =>      /usr/lib/sparcv9/libcom_err.so.3

        libkwarn.so.1 =>        /usr/lib/sparcv9/libkwarn.so.1

21/09/2017

11:56:11 2 SR_3-15757052521_04

SR #3-15757052521: Oracle R Distribution (ORD) ld: fatal: libR.so wrong ELF class

        libkrb5support.so.0 =>  /usr/lib/sparcv9/libkrb5support.so.0

        libresolv.so.2 =>       /lib/sparcv9/libresolv.so.2

        libsasl.so.1 =>         /usr/lib/sparcv9/libsasl.so.1

GALAXY 11:36:48 $ ls -l $R_HOME/etc/Makeconf

-rw-r--r-- 1 root root 5203 Mar 12  2017 /usr/lib/sparcv9/R/etc/Makeconf

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

: Unmodified -- the same Makeconf as packaged with ORD 3.3.0

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

GALAXY 11:36:52 $ cat $R_HOME/etc/Makeconf

# etc/Makeconf.  Generated from Makeconf.in by configure.

#

# ${R_HOME}/etc/Makeconf

#

# R was configured using the following call

# (not including env. vars and site configuration)

# configure  ’--enable-R-shlib’ ’--with-blas=-xlic_lib=sunperf -lsunmath ’ ’--with-lapack’ ’--with-tcltk=no’ ’-

-with-ICU=no’ ’--enable-prebuilt-html’ ’--with-cairo’ ’--with-internal-tzcode’ ’--disable-long-double’ ’CC=/opt

/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/cc -xc99 -m64’ ’CXX=/opt/SunProd/studio12u4/solarisstudio12

.4-151845-20/bin/CC -m64 -std=c++03’ ’F77=/opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/f95 -m64’ ’FC

=/opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/f95 -m64’ ’CFLAGS=-xlibmieee -DLINK_SIZE=2’ ’CPPFLAGS=

## This fails if it contains spaces, or if it is quoted

include $(R_SHARE_DIR)/make/vars.mk

AR = ar

BLAS_LIBS = -xlic_lib=sunperf -lsunmath

C_VISIBILITY =

CC = /opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/cc -xc99 -m64

CFLAGS = -xlibmieee -DLINK_SIZE=2 $(LTO)

CPICFLAGS = -KPIC

CPPFLAGS =

CXX = /opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/CC -m64 -std=c++03

CXXCPP = $(CXX) -E

CXXFLAGS = -g $(LTO)

CXXPICFLAGS = -KPIC

CXX1X = /opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/CC -m64 -std=c++03

CXX1XFLAGS = -g

CXX1XPICFLAGS = -KPIC

CXX1XSTD =  -std=c++11

DYLIB_EXT = .so

DYLIB_LD = $(CC)

DYLIB_LDFLAGS = -G -fopenmp# $(CFLAGS) $(CPICFLAGS)

DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)

ECHO = echo

ECHO_C =

ECHO_N = -n

ECHO_T =

## NB, set FC before F77 as on Solaris make, setting FC sets F77

FC = /opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/f95 -m64

FCFLAGS = -g $(LTO)

## additional libs needed when linking with $(FC), e.g. on Solaris

FCLIBS =

F77 = /opt/SunProd/studio12u4/solarisstudio12.4-151845-20/bin/f95 -m64

F77_VISIBILITY =

FFLAGS = -g $(LTO)

FLIBS =  -llzma -lz -R/opt/SunProd/studio12u4/solarisstudio12.4-151845-20/lib/sparcv9 -lifai -lsunimath -lfai -

lfai2 -lfui -lfsu -lsunmath -lmtsk -lm

FCPICFLAGS = -PIC

FPICFLAGS = -PIC

FOUNDATION_CPPFLAGS =

FOUNDATION_LIBS =

JAR =

JAVA =

JAVAC =

JAVAH =

## JAVA_HOME might be used in the next three.

## They are for packages ’JavaGD’ and ’rJava’

JAVA_HOME =

JAVA_CPPFLAGS =

JAVA_LIBS =

JAVA_LD_LIBRARY_PATH =

LAPACK_LIBS =

## we only need this is if it is external, as otherwise link to R

LIBINTL=

LIBM = -lm

LIBR0 = -L$(R_HOME)/lib$(R_ARCH)

LIBR1 = -lR

21/09/2017

11:56:11 3 SR_3-15757052521_04

SR #3-15757052521: Oracle R Distribution (ORD) ld: fatal: libR.so wrong ELF class

LIBR = -L$(R_HOME)/lib$(R_ARCH) -lR

LIBS =  -lpcre -llzma -lbz2 -lz -lnsl -lsocket -lrt -lsunmath -ldl -lm -lcurl -liconv

## needed by R CMD config

LIBnn = lib

LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"

LDFLAGS =

LTO =

## needed to build applications linking to static libR

MAIN_LD = $(CC)

MAIN_LDFLAGS = -fopenmp

MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS)

MKINSTALLDIRS = $(R_HOME)/bin/mkinstalldirs

OBJC =

OBJCFLAGS = -g -O2 $(LTO)

OBJC_LIBS =

OBJCXX =

R_ARCH =

RANLIB = ranlib

SAFE_FFLAGS = -g

SED = /usr/xpg4/bin/sed

SHELL = /bin/bash

SHLIB_CFLAGS =

SHLIB_CXXFLAGS =

SHLIB_CXXLD = $(CXX)

SHLIB_CXXLDFLAGS = -G

SHLIB_CXX1XLD = $(CXX1X) $(CXX1XSTD)

SHLIB_CXX1XLDFLAGS = -G

SHLIB_EXT = .so

SHLIB_FCLD = $(FC)

SHLIB_FCLDFLAGS = -G

SHLIB_FFLAGS =

SHLIB_LD = $(CC)

SHLIB_LDFLAGS = -G# $(CFLAGS) $(CPICFLAGS)

SHLIB_LIBADD =

## We want to ensure libR is picked up from $(R_HOME)/lib

## before e.g. /usr/local/lib if a version is already installed.

SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)

SHLIB_OPENMP_CFLAGS = -fopenmp

SHLIB_OPENMP_CXXFLAGS = -fopenmp

SHLIB_OPENMP_FCFLAGS = -fopenmp

SHLIB_OPENMP_FFLAGS = -fopenmp

STRIP_LIBS =

STRIP_STATIC_LIBS =

TCLTK_CPPFLAGS =

TCLTK_LIBS =

YACC = bison -y

## for linking to libR.a

STATIC_LIBR = #  "$(R_HOME)/lib$(R_ARCH)/libR.a"  $(BLAS_LIBS) $(FLIBS)  $(LIBINTL) -lreadline -lncurses  $(LIB

S)

R_XTRA_CFLAGS =

R_XTRA_CPPFLAGS =  -I$(R_INCLUDE_DIR) -DNDEBUG

R_XTRA_CXXFLAGS =

R_XTRA_FFLAGS =

ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)

ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CPPFLAGS) $(CLINK_CPPFLAGS)

ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)

ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)

ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)

ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)

## LIBR here as a couple of packages use this without SHLIB_LINK

ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)

.SUFFIXES:

.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o

.c.o:

.c.d:

.m.d:

.cc.o:

.cpp.o:

.cc.d:

21/09/2017

11:56:11 4 SR_3-15757052521_04

SR #3-15757052521: Oracle R Distribution (ORD) ld: fatal: libR.so wrong ELF class

.cpp.d:

.m.o:

.mm.o:

.M.o:

.f.o:

.f95.o:

.f90.o:

GALAXY 11:37:20 $

Regards

Pavan Aketi