search for: d_fortify_sourc

Hi All, Users have contacted me because they can not build MCMCglmm from source. All are using R 3.3.0 on various machines with different compilers gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0 g++ (Ubuntu 4.8.4-2ubuntu1~14.04.3) 4.8.4 Mac OS X El Capitan (version/compiler unspecified) The issue seems to be with mixing C/C++ with the repeated error: /usr/include/c++/5/bits/cpp_type_traits.h:118:3:

...y ?/tmp/RcppDepends/lib? > * installing *source* package ?MCMCglmm? ... > ** package ?MCMCglmm? successfully unpacked and MD5 sums checked > ** libs > gcc -I/usr/share/R/include -DNDEBUG??????-fpic??-g -O2 -fstack- > protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g??-O3 -Wall -pipe -pedantic -std=gnu99??-O3 > -pipe -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set- > variable -c cs_add.c -o cs_add.o > gcc -I/usr/share/R/include -DNDEBUG??????-fpic??-g -O2 -fstack- > protector-strong -Wformat -Werror=format-security -Wdate-time > -D_...

....tar.gz * installing to library ?/tmp/RcppDepends/lib? * installing *source* package ?MCMCglmm? ... ** package ?MCMCglmm? successfully unpacked and MD5 sums checked ** libs gcc -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -Wall -pipe -pedantic -std=gnu99 -O3 -pipe -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-variable -c cs_add.c -o cs_add.o gcc -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O3 -W...

...TION' ... OK * preparing 'MCMCglmm_2.05': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * Installing *source* package ?MCMCglmm? ... ** libs g++ -m64 -I/usr/include/R -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 MCMCglmm.cc -o MCMCglmm.o MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, int*, int*, double*, double*, int*, int*, int*, i...

...TION' ... OK * preparing 'MCMCglmm_2.05': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * Installing *source* package ?MCMCglmm? ... ** libs g++ -m64 -I/usr/include/R -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 MCMCglmm.cc -o MCMCglmm.o MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, int*, int*, double*, double*, int*, int*, int*, i...

...IPTION' ... OK * preparing 'MCMCglmm_2.05': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * Installing *source* package ?MCMCglmm? ... ** libs g++ -m64 -I/usr/include/R -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 MCMCglmm.cc -o MCMCglmm.o MCMCglmm.cc: In function ?void MCMCglmm(double*, double*, double*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, int*, int*, double*, double*, int*, int*, int*, int*, int...

...yes checking for freetype-config... yes configure: using Freetype and FTGL configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -m32 -I/usr/include/R -DHAVE_PNG_H -DHAVE_FREETYPE -Iext/ftgl -I/usr/include/freetype2 -Iext -I/usr/local/include -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i686 -mtune=atom -fasynchronous-unwind-tables -c BBoxDeco.cpp...

...onfig.status* *config.status: creating src/Makevars* *Completed configuration and ready to build.* *** libs* *g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include -I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o* *g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG -I"/usr...

...c/Makevars* > > *Completed configuration and ready to build.* > > *** libs* > > *g++ -std=gnu++11 -I/usr/share/R/include -DNDEBUG > -I"/usr/local/lib/R/site-library/Rcpp/include" -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -I/usr/local/include -fpermissive -I../inst/include > -I. -DBOOST_NO_AUTO_PTR -fopenmp -fpic -g -O2 -fstack-protector-strong > -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c > RcppExports.cpp -o RcppExports.o* > > *g++ -std=gnu++11 -I/usr/share/R/inclu...

...dplyr? ... ** package ?dplyr? successfully unpacked and MD5 sums checked ** libs g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include&qu...

...** package ?dplyr? successfully unpacked and MD5 sums checked > ** libs > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/include" -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o > g++ -m64 -I/usr/include/R -DNDEBUG -I../inst/include -DCOMPILING_DPLYR -I/usr/local/include -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/BH/inclu...

Hi folks (CCing llvm-dev, but that's probably more of a cfe-dev topic), As a follow-up to that old thread about -D_FORTIFY_SOURCE=n http://lists.llvm.org/pipermail/cfe-dev/2015-November/045845.html And, more recently, to this fedora thread where clang/llvm -D_FORTIFY_SOURCE support is claimed to be only partial: https://pagure.io/fesco/issue/2020 I dig into the glibc headers in order to have a better understandin...

...39;ve diagnosed the issue correctly? __builtin___memcpy_chk works correctly, as far as I know. 100% sure. Let's have a look at the output of #include <string.h> static char dest[10]; char* square(int n) { memcpy(dest, "hello", n); return dest; } compiled with -D_FORTIFY_SOURCE=1 -O1 : https://godbolt.org/z/UvABWp Clang issues a call to memcpy, while gcc issues a call to __memcpy_chk. The call to __memcpy_chk performs extra runtime checks memcpy doesn't, and clang doesn't generate the extra checks inline either. This is a separate concern from the accuracy of __...

...t;config.h"/g > help.c.copy; mv --force help.c.copy help.c; fi /bin/sh makelist -e common.c emacs.c vi.c chared.c el.c hist.c key.c map.c parse.c prompt.c read.c refresh.c search.c sig.c term.c tty.c fcns.c help.c > editline.c gcc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,- D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer- size=4 -Werror-implicit-function-declaration -O '-D__RCSID(x)=' '- D__COPYRIGHT(x)=' '-D__RENAME(x)=' '-D_DIAGASSERT(x)=' -I. editline.c -o editline.o_a gcc -c -O2 -g -pipe -Wformat -Werror=format-security -Wp,-...

...ExtUtils/typemap -typemap typemap Zlib.xs > Zlib.xsc && mv Zlib.xsc Zlib.c gcc -c -I./zlib-src -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 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -DVERSION=\"2.024\" -DXS_VERSION=\"2.024 \" -fPIC "-I/usr/lib/perl5/5.8.8/i386-linux-thread-multi/CORE" -DGZIP_OS_CODE=3 -DUSE_PPPORT_H Zlib.c Zli...

...user/source/opus-tools-0.1.5' depbase=3D`echo src/opus_header.o | sed 's|[^/]*$|.deps/&|=3Bs|\.o$||'`=3B\ =A0=A0=A0 i686-w64-mingw32-gcc -std=3Dgnu99 -DHAVE_CONFIG_H -I. -I./src -I.= /win32=A0=A0 -I/home/user/builds/include=A0=A0 -I/home/user/builds/include/= opus=A0=A0 -DOPUSTOOLS -D_FORTIFY_SOURCE=3D2 -DHAVE_GETOPT_H -DSPX_RESAMPLE= _EXPORT=3D -DRANDOM_PREFIX=3Dopustools -DOUTSIDE_SPEEX -DFLOATING_POINT -I/= home/user/builds/include=A0 -W -Wall -Wextra -Wcast-align -Wnested-externs = -Wshadow -Wstrict-prototypes -MT src/opus_header.o -MD -MP -MF $depbase.Tpo= -c -o src/opus_header.o src/op...

On Wed, Mar 07, 2007 at 11:45:13AM +0000, richard wrote: > * configure.ac: Add -D_FORTIFY_SOURCE to AM_CXXFLAGS for GCC > builds. According to glibc CVS support for this was added in > October 2004, but it doesn't seem to be documented very well, > other than in features.h. I'd not come across this before, so I had a quick poke around. It's hardly documented *well* in...

Hi Erik, similar to what I did for libsndfile, this is to simplify the handling of adding -D_FORTIFY_SOURCE=2. Regards David

...t type 'application/x-gzip' length 71745 bytes (70 Kb) opened URL ================================================== downloaded 70 Kb * installing *source* package ?randomForest? ... ** libs gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/local/include -fpic -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -c classTree.c -o classTree.o classTree.c: In function ?predictClassTree?: classTree.c:414: warning: ?cbestsplit? may be used uninitialized in this function gcc -std=gnu99 -I/usr/lib64/R/include -I/usr/local/include -fpic -fmess...

...contrib/Hmisc_3.4-3.tar.gz' Content type 'application/x-gzip' length 519009 bytes (506 Kb) opened URL ================================================== downloaded 506 Kb /usr/lib/R/library * Installing *source* package 'Hmisc' ... ** libs gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c cidxcn.f -o cidxcn.o gfortran -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasync...