Bug 386825 – dev-lang/R-2.13.1 *** stack smashing detected ***: R - terminated when compiling

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Anton Kochkov 2011-10-11 18:12:20 UTC]

Created attachment 289605 [details]
full build log

ake[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/po'
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/po'
you should 'make docs' now ...
make[1]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/doc'
*** stack smashing detected ***: R - terminated
R: stack smashing attack in function <unknown> - terminated
Report to http://bugs.gentoo.org/
/bin/sh: line 1:  8890 Done                    echo "options(warn=1);saveRDS(tools:::prepare_Rd(tools::parse_Rd(\"./NEWS.Rd\"), stages = 'install'), 'NEWS.rds')"
      8891 Killed                  | ../bin/R --vanilla --slave
make[1]: *** [NEWS.rds] Error 137
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/doc'
make: [docs] Error 2 (ignored)
make[1]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library'
make[2]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library'
installing parsed Rd
make[3]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library'
*** stack smashing detected ***: R - terminated
R: stack smashing attack in function <unknown> - terminated
Report to http://bugs.gentoo.org/
/bin/sh: line 2:  8938 Done                    echo "options(warn=1);tools:::.install_package_Rd_objects('./stats',   '../../library/stats')"
      8939 Killed                  | R_DEFAULT_PACKAGES=NULL ../../bin/R --vanilla --slave
make[3]: *** [stats.Rdts] Error 1
make[3]: *** Waiting for unfinished jobs....
*** stack smashing detected ***: R - terminated
R: stack smashing attack in function <unknown> - terminated
Report to http://bugs.gentoo.org/
/bin/sh: line 2:  8937 Done                    echo "options(warn=1);tools:::.install_package_Rd_objects('./base',   '../../library/base')"
      8940 Killed                  | R_DEFAULT_PACKAGES=NULL ../../bin/R --vanilla --slave
make[3]: *** [base.Rdts] Error 1
make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library'
make[2]: *** [Rdobjects] Error 2
make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library'
make[1]: *** [docs] Error 2
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library'
make: [docs] Error 2 (ignored)
make[1]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library/Recommended'
make[2]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library/Recommended'
begin installing recommended package MASS
begin installing recommended package lattice
* installing *source* package ‘lattice’ ...
*** stack smashing detected ***: R - terminated
R: stack smashing attack in function <unknown> - terminated
Report to http://bugs.gentoo.org/
/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/bin/INSTALL: line 34:  8961 Done                    echo 'tools:::.install_packages()'
      8962 Killed                  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
make[2]: *** [lattice.ts] Error 1
make[2]: *** Waiting for unfinished jobs....
* installing *source* package ‘MASS’ ...
** libs
make[3]: Entering directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/temp/Rtmp0fpjra/R.INSTALL266f90ba/MASS/src'
i686-pc-linux-gnu-gcc -std=gnu99 -I/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/include  -I/usr/local/include    -fpic  -O2 -march=core2 -mfpmath=sse -mmmx 
-msse -msse2 -mssse3 -pipe -c MASS.c -o MASS.o
i686-pc-linux-gnu-gcc -std=gnu99 -I/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/include  -I/usr/local/include    -fpic  -O2 -march=core2 -mfpmath=sse -mmmx 
-msse -msse2 -mssse3 -pipe -c lqs.c -o lqs.o
i686-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o MASS.so MASS.o lqs.o -L/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/lib -lR
make[3]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/temp/Rtmp0fpjra/R.INSTALL266f90ba/MASS/src'
installing to /var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/library/MASS/libs
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** stack smashing detected ***: R - terminated
R: stack smashing attack in function <unknown> - terminated
Report to http://bugs.gentoo.org/
/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/bin/INSTALL: line 34:  8959 Done                    echo 'tools:::.install_packages()'
      8960 Killed                  | R_DEFAULT_PACKAGES= LC_COLLATE=C "${R_HOME}/bin/R" $myArgs --slave --args ${args}
make[2]: *** [MASS.ts] Error 1
make[2]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library/Recommended'
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory `/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1/src/library/Recommended'
make: *** [stamp-recommended] Error 2
 * ERROR: dev-lang/R-2.13.1-r1 failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of 'emerge --info =dev-lang/R-2.13.1-r1',
 * the complete build log and the output of 'emerge -pqv =dev-lang/R-2.13.1-r1'.
 * The complete build log is located at '/var/tmp/portage/dev-lang/R-2.13.1-r1/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/dev-lang/R-2.13.1-r1/temp/environment'.
 * S: '/var/tmp/portage/dev-lang/R-2.13.1-r1/work/R-2.13.1'

>>> Failed to emerge dev-lang/R-2.13.1-r1, Log file:

>>>  '/var/tmp/portage/dev-lang/R-2.13.1-r1/temp/build.log'


emerge --info https://bugs.gentoo.org/attachment.cgi?id=288639

[Comment 1 Jason C 2011-10-23 23:39:40 UTC]

I'm building a new machine with amd64 and hardened and was also unable to build R-2.31.1-r1 with the same problem as listed.

[Comment 2 Justin Lecher (RETIRED) 2011-11-21 16:20:26 UTC]

same with 2.14.0?

[Comment 3 Anton Kochkov 2011-11-21 22:10:26 UTC]

(In reply to comment #2)
> same with 2.14.0?

2.14 - works ok - bug is fixed