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_NAMEC;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)
