[R] Fwd: RSPerl buffer overflow

Ido M. Tamir tamir at imp.univie.ac.at
Thu Mar 22 09:32:09 CET 2007


Hi,

I installed RSPerl (RSPerl_0.91-2.tar.gz) and after
loading the library I get a buffer overflow.

below is the output from R and below that the
messages during the installation.

Its on an AMD opteron system running Fedora Core5
R version 2.4.1 (2006-12-18).

Thank you very much for your help.

Ido

> sessionInfo()

R version 2.4.1 (2006-12-18)
x86_64-redhat-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;
LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=
C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "methods"
[7] "base"



[Previously saved workspace restored]

> library("RSPerl")

*** buffer overflow detected ***: /usr/lib64/R/bin/exec/R terminated
======= Backtrace: =========
/lib64/libc.so.6(__chk_fail+0x2f)[0x385f3df24f]
/lib64/libc.so.6[0x385f3de809]
/lib64/libc.so.6(_IO_default_xsputn+0x8e)[0x385f369a3e]
/lib64/libc.so.6(_IO_vfprintf+0x36e4)[0x385f344294]
/lib64/libc.so.6(__vsprintf_chk+0x9d)[0x385f3de8ad]
/lib64/libc.so.6(__sprintf_chk+0x80)[0x385f3de7f0]
/usr/lib64/R/library/RSPerl/libs/RSPerl.so(RS_PerlEvalString+0x12e)
[0x2aaaae5ca31e]
/usr/lib64/R/lib/libR.so[0x350558468a]
/usr/lib64/R/lib/libR.so(Rf_eval+0x606)[0x35055b1fa6]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so[0x35055b5c50]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so[0x3505537228]
/usr/lib64/R/lib/libR.so[0x35055df063]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so[0x35055b5c50]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x36d)[0x35055b1d0d]
/usr/lib64/R/lib/libR.so(Rf_eval+0x546)[0x35055b1ee6]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_applyClosure+0x286)[0x35055b3ed6]
/usr/lib64/R/lib/libR.so(Rf_eval+0x2fc)[0x35055b1c9c]
/usr/lib64/R/lib/libR.so[0x35055b2408]
/usr/lib64/R/lib/libR.so(Rf_eval+0x48c)[0x35055b1e2c]
/usr/lib64/R/lib/libR.so[0x35055b2408]
/usr/lib64/R/lib/libR.so(Rf_eval+0x48c)[0x35055b1e2c]
/usr/lib64/R/lib/libR.so[0x35055b50d8]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
/usr/lib64/R/lib/libR.so[0x35055b2a72]
/usr/lib64/R/lib/libR.so(Rf_eval+0x452)[0x35055b1df2]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fd:00
87064596                           /usr/lib64/R/bin/exec/R
00500000-00502000 rw-p 00000000 fd:00
87064596                           /usr/lib64/R/bin/exec/R
00502000-01b45000 rw-p 00502000 00:00 0                                  
[heap]
3505100000-350510d000 r-xp 00000000 fd:00
26279979                       /lib64/libgcc_s-4.1.1-20070108.so.1
350510d000-350520c000 ---p 0000d000 fd:00
26279979                       /lib64/libgcc_s-4.1.1-20070108.so.1
350520c000-350520d000 rw-p 0000c000 fd:00
26279979                       /lib64/libgcc_s-4.1.1-20070108.so.1
3505300000-3505396000 r-xp 00000000 fd:00
49948505                       /usr/lib64/libgfortran.so.1.0.0
3505396000-3505495000 ---p 00096000 fd:00
49948505                       /usr/lib64/libgfortran.so.1.0.0
3505495000-3505497000 rw-p 00095000 fd:00
49948505                       /usr/lib64/libgfortran.so.1.0.0
3505500000-3505725000 r-xp 00000000 fd:00
50989646                       /usr/lib64/R/lib/libR.so
3505725000-3505824000 ---p 00225000 fd:00
50989646                       /usr/lib64/R/lib/libR.so
3505824000-3505838000 rw-p 00224000 fd:00
50989646                       /usr/lib64/R/lib/libR.so
3505838000-35058d1000 rw-p 3505838000 00:00 0
385f100000-385f11a000 r-xp 00000000 fd:00
91291670                       /lib64/ld-2.4.so
385f219000-385f21a000 r--p 00019000 fd:00
91291670                       /lib64/ld-2.4.so
385f21a000-385f21b000 rw-p 0001a000 fd:00
91291670                       /lib64/ld-2.4.so
385f300000-385f43f000 r-xp 00000000 fd:00
91291679                       /lib64/libc-2.4.so
385f43f000-385f53e000 ---p 0013f000 fd:00
91291679                       /lib64/libc-2.4.so
385f53e000-385f542000 r--p 0013e000 fd:00
91291679                       /lib64/libc-2.4.so
385f542000-385f543000 rw-p 00142000 fd:00
91291679                       /lib64/libc-2.4.so
385f543000-385f548000 rw-p 385f543000 00:00 0
385f600000-385f680000 r-xp 00000000 fd:00
91291778                       /lib64/libm-2.4.so
385f680000-385f77f000 ---p 00080000 fd:00
91291778                       /lib64/libm-2.4.so
385f77f000-385f780000 r--p 0007f000 fd:00
91291778                       /lib64/libm-2.4.so
385f780000-385f781000 rw-p 00080000 fd:00
91291778                       /lib64/libm-2.4.so
385f800000-385f802000 r-xp 00000000 fd:00
91291713                       /lib64/libdl-2.4.so
385f802000-385f902000 ---p 00002000 fd:00
91291713                       /lib64/libdl-2.4.so
385f902000-385f903000 r--p 00002000 fd:00
91291713                       /lib64/libdl-2.4.so
385f903000-385f904000 rw-p 00003000 fd:00
91291713                       /lib64/libdl-2.4.so
385fa00000-385fa32000 r-xp 00000000 fd:00
113246301                      /usr/lib64/libreadline.so.5.0
385fa32000-385fb31000 ---p 00032000 fd:00
113246301                      /usr/lib64/libreadline.so.5.0
385fb31000-385fb39000 rw-p 00031000 fd:00
113246301                      /usr/lib64/libreadline.so.5.0
385fb39000-385fb3a000 rw-p 385fb39000 00:00 0
3860200000-3860214000 r-xp 00000000 fd:00
49939208                       /usr/lib64/libz.so.1.2.3
3860214000-3860313000 ---p 00014000 fd:00
49939208                       /usr/lib64/libz.so.1.2.3
3860313000-3860314000 rw-p 00013000 fd:00
49939208                       /usr/lib64/libz.so.1.2.3
3860400000-3860412000 r-xp 00000000 fd:00
91291860                       /lib64/libpthread-2.4.so
3860412000-3860512000 ---p 00012000 fd:00
91291860                       /lib64/libpthread-2.4.so
3860512000-3860513000 r--p 00012000 fd:00
91291860                       /lib64/libpthread-2.4.so
3860513000-3860514000 rw-p 00013000 fd:00
91291860                       /lib64/libpthread-2.4.so
3860514000-3860518000 rw-p 3860514000 00:00 0
3860600000-386072c000 r-xp 00000000 fd:00
54034480                      
 /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/libperl.so
 386072c000-386082b000 ---p 0012c000 fd:00
54034480                      
 /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/libperl.so
 386082b000-3860834000 rw-p 0012b000 fd:00
54034480                      
 /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE/libperl.so
 3860834000-3860836000 rw-p 3860834000 00:00 0
3862d00000-3862d4e000 r-xp 00000000 fd:00
113246305                      /usr/lib64/libncurses.so.5.5
3862d4e000-3862e4e000 ---p 0004e000 fd:00
113246305                      /usr/lib64/libncurses.so.5.5
3862e4e000-3862e5c000 rw-p 0004e000 fd:00
113246305                      /usr/lib64/libncurses.so.5.5
3862e5c000-3862e5d000 rw-p 3862e5c000 00:00 0
3864800000-3864813000 r-xp 00000000 fd:00
91291980                       /lib64/libnsl-2.4.so
3864813000-3864913000 ---p 00013000 fd:00
91291980                       /lib64/libnsl-2.4.so
3864913000-3864914000 r--p 00013000 fd:00
91291980                       /lib64/libnsl-2.4.so
3864914000-3864915000 rw-p 00014000 fd:00
91291980                       /lib64/libnsl-2.4.so
3864915000-3864917000 rw-p 3864915000 00:00 0
3864c00000-3864c11000 r-xp 00000000 fd:00 91291864       Aborted

******************************************************************

[root at MCP dl]# R CMD INSTALL -c RSPerl_0.91-2.tar.gz
* Installing *source* package 'RSPerl' ...
No support for any of the Perl modules from calling Perl from R.
*****************************************************

       Set PERL5LIB to /usr/lib64/R/library/RSPerl/perl

*****************************************************
Using '/usr/bin/perl' as the perl executable
Perl modules:
Adding R package to list of Perl modules to enable callbacks to R from Perl
modules:  R; linking:
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
Support R in Perl: yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/RSUtils.S
config.status: creating inst/scripts/RSPerl.csh
config.status: creating inst/scripts/RSPerl.bsh
config.status: creating src/RinPerlMakefile
config.status: creating src/Makefile.PL
config.status: creating cleanup
config.status: creating src/R.pm
config.status: creating R/perl5lib.R
making RinPerlMakefile
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c Converters.c -o
 Converters.o
Converters.c: In function 'fromPerl':
Converters.c:297: warning: unused variable 'tmp'
Converters.c: In function 'GetRScalar':
Converters.c:421: warning: unused variable 'mg'
Converters.c: In function 'makeForeignPerlReference':
Converters.c:567: warning: unused variable 'key'
Converters.c:565: warning: unused variable 'n'
Converters.c: In function 'getForeignPerlReference':
Converters.c:715: warning: unused variable 'key'
Converters.c:714: warning: unused variable 'el'
Converters.c:713: warning: unused variable 'table'
Converters.c: In function 'directConvertFromPerl':
Converters.c:1058: warning: unused variable 'classes'
Converters.c: In function 'RS_GetPerlReferenceObjects':
Converters.c:636: warning: 'ans' may be used uninitialized in this function
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c Reflectance.c -o
 Reflectance.o
Reflectance.c: In function 'RS_getStashFromCode':
Reflectance.c:52: warning: unused variable 'classes'
Reflectance.c:49: warning: unused variable 'ref'
Reflectance.c: In function 'computeRSPerlClassVector':
Reflectance.c:402: warning: unused variable 'z'
Reflectance.c:401: warning: unused variable 'ixval'
Reflectance.c:400: warning: unused variable 'ival'
Reflectance.c:399: warning: unused variable 'xvalue'
Reflectance.c:427: warning: unused variable 'obj'
Reflectance.c:426: warning: unused variable 'tt'
Reflectance.c:442: warning: operation on 'classes' may be undefined
Reflectance.c: In function 'isHomogeneous':
Reflectance.c:513: warning: 'el' may be used uninitialized in this function
Reflectance.c: In function 'RS_getPerlType':
Reflectance.c:140: warning: 'el' may be used uninitialized in this function
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c ForeignReference.c -o
 ForeignReference.o
ForeignReference.c: In function 'RPerl_createRProxy':
ForeignReference.c:212: warning: value computed is not used
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c UserConverters.c -o
 UserConverters.o
UserConverters.c: In function 'RPerl_addConverter':
UserConverters.c:264: warning: 'className' may be used uninitialized in this
function
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c GeneralConverters.c -o
 GeneralConverters.o
making libPerlConverter.so
/usr/lib64/R/bin/R CMD SHLIB -o libPerlConverter.so Converters.c
 Reflectance.c ForeignReference.c UserConverters.o GeneralConverters.o
make[1]: Entering directory `/tmp/R.INSTALL.Z15223/RSPerl/src'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o libPerlConverter.so Converters.o
Reflectance.o ForeignReference.o UserConverters.o
GeneralConverters.o -Wl,-E
 -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE
  /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/DynaLoader/DynaLoader
.a -L/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -lperl -lresolv
 -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc   -L/usr/lib64/R/lib -lR
 make[1]: Leaving directory `/tmp/R.INSTALL.Z15223/RSPerl/src'
if test ! -d /usr/lib64/R/library/RSPerl/libs ; then
mkdir /usr/lib64/R/library/RSPerl/libs ; fi
cp libPerlConverter.so /usr/lib64/R/library/RSPerl/libs
/usr/bin/perl Makefile.PL PREFIX=/usr/lib64/R/library/RSPerl
LIB=/usr/lib64/R/library/RSPerl/perl
Warning: -L. changed to -L/tmp/R.INSTALL.Z15223/RSPerl/src/.
Writing Makefile.perl for R
make -f Makefile.perl
make[1]: Entering directory `/tmp/R.INSTALL.Z15223/RSPerl/src'
cp R.pm blib/lib/R.pm
AutoSplitting blib/lib/R.pm (blib/lib/auto/R)
cp RReferences.pm blib/lib/RReferences.pm
/usr/bin/perl /usr/lib/perl5/5.8.8/ExtUtils/xsubpp  -typemap
 /usr/lib/perl5/5.8.8/ExtUtils/typemap   R.xs > R.xsc && mv R.xsc R.c
gcc -c  -I. -I/usr/lib64/R/include -D_REENTRANT -D_GNU_SOURCE
 -fno-strict-aliasing -pipe -Wdeclaration-after-statement
 -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
 -I/usr/include/gdbm -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions
 -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  
 -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC
 "-I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE"  -g -D_R_=1
 -DUSE_R=1 R.c
R.c: In function 'XS_R_call':
R.c:115: warning: unused variable 'RETVAL'
R.xs:103: warning: unused variable 'addLocal'
R.c: In function 'XS_R_callWithNames':
R.c:267: warning: unused variable 'RETVAL'
R.xs:243: warning: unused variable 'addLocal'
R.xs: In function 'XS_R_initRSession':
R.xs:385: warning: implicit declaration of function 'Rf_initEmbeddedR'
R.c: In function 'XS_R_eval':
R.c:441: warning: unused variable 'RETVAL'
R.xs: In function 'XS_R_setConverter':
R.xs:475: warning: implicit declaration of function 'addPerlConverterRoutine'
R.c:522: warning: unused variable 'RETVAL'
R.c: In function 'XS_R_deleteRReference':
R.c:546: warning: unused variable 'RETVAL'
R.c: In function 'XS_R_setDebug':
R.c:567: warning: unused variable 'RETVAL'
R.c: In function 'XS_R_library':
R.c:593: warning: unused variable 'RETVAL'
R.c: In function 'XS_R_rnorm':
R.c:623: warning: unused variable 'RETVAL'
Running Mkbootstrap for R ()
chmod 644 R.bs
rm -f blib/arch/auto/R/R.so
gcc  -shared R.o  -o blib/arch/auto/R/R.so      \
   -L/tmp/R.INSTALL.Z15223/RSPerl/src -L/usr/lib64/R/library/RSPerl/libs
 -lPerlConverter -L/usr/lib64/R/lib -lR         \

chmod 755 blib/arch/auto/R/R.so
cp R.bs blib/arch/auto/R/R.bs
chmod 644 blib/arch/auto/R/R.bs
Manifying blib/man3/R.3pm
Manifying blib/man3/RReferences.3pm
make[1]: Leaving directory `/tmp/R.INSTALL.Z15223/RSPerl/src'
Manifying blib/man3/R.3pm
Manifying blib/man3/RReferences.3pm
Installing
 /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/auto/R/R.so
 Installing
 /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/auto/R/R.bs Files
 found in blib/arch: installing files in blib/lib into architecture dependent
 library tree
Installing /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/R.pm
Installing
 /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/RReferences.pm
 Installing
 /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/auto/R/autosplit.
ix Installing /usr/lib64/R/library/RSPerl/share/man/man3/RReferences.3pm
 Installing /usr/lib64/R/library/RSPerl/share/man/man3/R.3pm
Writing
 /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/auto/R/.packlist
 Appending installation info
to /usr/lib64/R/library/RSPerl/perl/x86_64-linux-thread-multi/perllocal.pod
Finished configuration
** libs
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c RPerlElements.c -o
 RPerlElements.o
RPerlElements.c: In function ‘RS_PerlHashElement’:
RPerlElements.c:56: warning: ‘depth’ may be used uninitialized in this
function
RPerlElements.c: In function ‘RS_PerlArrayElement’:
RPerlElements.c:11: warning: ‘depth’ may be used uninitialized in this
function
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c RPerlEval.c -o RPerlEval.o
RPerlEval.c: In function ‘RS_PerlEvalString’:
RPerlEval.c:18: warning: unused variable ‘interp’
RPerlEval.c: In function ‘RS_PerlGet’:
RPerlEval.c:123: warning: unused variable ‘interp’
RPerlEval.c: In function ‘RS_PerlCallModified’:
RPerlEval.c:297: warning: value computed is not used
RPerlEval.c:203: warning: unused variable ‘interp’
RPerlEval.c: In function ‘RS_PerlCall’:
RPerlEval.c:372: warning: unused variable ‘interp’
RPerlEval.c: In function ‘RS_PerlPackage’:
RPerlEval.c:555: warning: unused variable ‘sv’
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c RPerlInit.c -o RPerlInit.o
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c RPerlNew.c -o RPerlNew.o
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c RPerlReference.c -o
 RPerlReference.o
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c RPerlVars.c -o RPerlVars.o
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c Utils.c -o Utils.o
gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/lib64/R/include -I.
  -D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe
 -Wdeclaration-after-statement -I/usr/local/include -D_LARGEFILE_SOURCE
 -D_FILE_OFFSET_BITS=64 -I/usr/include/gdbm
  -I/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE  -DPERL_POLLUTE  
 -D_R_=1 -DUSE_R=1 -DUSE_TOPLEVEL_EXEC=1 -I/usr/local/include    -fpic  -O2
 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
 --param=ssp-buffer-size=4 -m64 -mtune=generic -c xsinit.c -o xsinit.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o RSPerl.so Converters.o
ForeignReference.o GeneralConverters.o R.o Reflectance.o RPerlElements.o
RPerlEval.o RPerlInit.o RPerlNew.o RPerlReference.o RPerlVars.o
UserConverters.o Utils.o
xsinit.o -Wl,-E
 -Wl,-rpath,/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE
  /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/DynaLoader/DynaLoader
.a -L/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/CORE -lperl -lresolv
 -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc   -L/usr/lib64/R/lib -lR ** R
** inst
** help
 >>> Building/Updating help pages for package 'RSPerl'
     Formats: text html latex example
  Perl                              text    html    latex   example
  PerlClear                         text    html    latex   example
  PerlDiscard                       text    html    latex   example
  PerlExists                        text    html    latex   example
  PerlExpr                          text    html    latex   example
  PerlFile                          text    html    latex   example
  PerlGetArray                      text    html    latex   example
  PerlGetCode                       text    html    latex   example
  PerlInit                          text    html    latex   example
  PerlInterpreter                   text    html    latex   example
  PerlLength                        text    html    latex   example
  PerlNames                         text    html    latex   example
  PerlNew                           text    html    latex   example
  PerlNewArray                      text    html    latex   example
  PerlPackage                       text    html    latex   example
  PerlReferenceDollar               text    html    latex   example
  PerlReferenceObjects              text    html    latex   example
  PerlReferenceSubset               text    html    latex   example
  PerlSetHash                       text    html    latex   example
  PerlStashInfo                     text    html    latex   example
  PerlTerminate                     text    html    latex   example
  PerlType                          text    html    latex   example
  PerlTypes                         text    html    latex
  PerlUndef                         text    html    latex   example
  addConverter                      text    html    latex   example
  foreignReference                  text    html    latex   example
  getNumPerlConverters              text    html    latex   example
  getPerlClasses                    text    html    latex   example
  getPerlScript                     text    html    latex   example
  mkRef                             text    html    latex   example
  parseEval                         text    html    latex   example
  perlInitArgs                      text    html    latex   example
  perlModuleLoaded                  text    html    latex   example
  referenceHandlerGenerator         text    html    latex   example
  setPerlHandler                    text    html    latex   example
** building package indices ...
Removing additional files
* DONE (RSPerl)



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