[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)
More information about the R-help
mailing list