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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:

...> R_LIBS_USER=/tmp/RcppDepends/lib R CMD INSTALL > MCMCglmm_2.22.1.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/inc...

I am trying to work through the usage of thinlto for distributed builds. Here is the simple thinlto usage, just add -flto=thin everywhere, easy: clang++ -flto=thin -O3 -c -o CreateWay_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else CreateWay_.cpp clang++ -flto=thin -O3 -c -o Places_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else Places_.cpp clang++ -flto=thin -O3 -c -o RegBounds_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else...

...CMD INSTALL MCMCglmm_2.22.1.tar.gz R_LIBS_USER=/tmp/RcppDepends/lib R CMD INSTALL MCMCglmm_2.22.1.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 -...

...t lists.llvm.org<mailto:llvm-dev at lists.llvm.org>> wrote: I am trying to work through the usage of thinlto for distributed builds. Here is the simple thinlto usage, just add -flto=thin everywhere, easy: clang++ -flto=thin -O3 -c -o CreateWay_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else CreateWay_.cpp clang++ -flto=thin -O3 -c -o Places_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else Places_.cpp clang++ -flto=thin -O3 -c -o RegBounds_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else...

...cking for gluProject in -lGLU... yes checking for freetype-config... no configure: creating ./config.status config.status: creating src/Makevars ** libs *** arch - x86_64 g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -I/System/Library/Frameworks/OpenGL.framework/Headers -DHAVE_PNG_H -DDarwin -DNO_GL_PREFIX -I/usr/X11R6/include -Iext -I/usr/local/include -g -O2 -fPIC -g -O2 -c ABCLineSet.cpp -o ABCLineSet.o g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framewor...

On Fri, Jul 20, 2001 at 03:01:54PM -0700, Josh Coalson wrote: > --- Matt Zimmerman <mdz@debian.org> wrote: > > > > automake will include ltmain.sh in the source distribution, so it > > should be > > used even if it isn't installed on the build system. In fact, it > > seems to > > always use the distributed version, and not the installed one

...t lists.llvm.org<mailto:llvm-dev at lists.llvm.org>> wrote: I am trying to work through the usage of thinlto for distributed builds. Here is the simple thinlto usage, just add -flto=thin everywhere, easy: clang++ -flto=thin -O3 -c -o CreateWay_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else CreateWay_.cpp clang++ -flto=thin -O3 -c -o Places_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else Places_.cpp clang++ -flto=thin -O3 -c -o RegBounds_.o -DSPEC_CPU -DNDEBUG -DSPEC_CPU_LITTLE_ENDIAN -Wno-dangling-else...

...FLAC' /bin/sh ../../libtool --mode=compile gcc -DPACKAGE=\"flac\" -DVERSION=\"1.0\" -DFLAC__CPU_IA32=1 -DFLAC__ALIGN_MALLOC_DATA=1 -DFLAC__HAS_NASM=1 -DSIZEOF_SHORT=2 -DSIZEOF_INT=4 -DSIZEOF_LONG=4 -DSIZEOF_LONG_LONG=8 -I. -I. -I./include -I ../../include -Wall -W -O3 -DNDEBUG -fomit-frame-pointer -funroll-loops -finline-functions -Winline -DFLaC__INLINE=__inline__ -g -O2 -c bitbuffer.c mkdir .libs gcc -DPACKAGE=\"flac\" -DVERSION=\"1.0\" -DFLAC__CPU_IA32=1 -DFLAC__ALIGN_MALLOC_DATA=1 -DFLAC__HAS_NASM=1 -DSIZEOF_SHORT=2 -DSIZEOF_INT=4 -DSIZEOF_LONG=4...

...O C89... none needed USE_LOCAL = "" Using local libjson code. Copying files /tmp/RtmpFw9QeX/R.INSTALL4ebf657f/RJSONIO configure: creating ./config.status config.status: creating src/Makevars config.status: creating cleanup ** libs gcc -I/usr/share/R/include -I. -Ilibjson -Ilibjson/Source -DNDEBUG=1 -DJSON_NO_EXCEPTIONS=1 -fpic -std=gnu99 -O3 -pipe -g -c ConvertUTF.c -o ConvertUTF.o g++ -I/usr/share/R/include -I. -Ilibjson -Ilibjson/Source -DNDEBUG=1 -DJSON_NO_EXCEPTIONS=1 -fpic -O3 -pipe -g -c JSONChildren.cpp -o JSONChildren.o g++ -I/usr/share/R/include -I. -Ilibjson -Ilibjson/...

...all in libFLAC make[2]: Entering directory `/opt/flac-0.8/src/libFLAC' /bin/sh ../../libtool --mode=compile gcc -DPACKAGE=\"flac\" -DVERSION=\"0.8\" -I. -I. -I./include -I ../../include -Wall -W -O3 -fomit-frame-pointer -funroll-loops -ffast-math -finline-functions -DNDEBUG -c bitbuffer.c mkdir .libs gcc -DPACKAGE=\"flac\" -DVERSION=\"0.8\" -I. -I. -I./include -I ../../include -Wall -W -O3 -fomit-frame-pointer -funroll-loops -ffast-math -finline-functions -DNDEBUG -Wp,-MD,.deps/bitbuffer.pp -c bitbuffer.c -fPIC -DPIC -o .libs/bitbuffer.lo gcc -...

...own' length 80583 bytes (78 KB) ================================================== downloaded 78 KB installing source package 'markdown' ... ** package 'markdown' successfully unpacked and MD5 sums checked ** libs /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rbase64.c -o Rbase64.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/R/include -DNDEBUG -I/usr/local/include -qpic -g -O2 -qstrict -qfloat=nomaf:fenv -c Rinit.c -o Rinit.o /opt/ibm/xlC/13.1.6/bin/xlc_r -q64 -I/usr/local/lib64/...

...ring directory `/openh323/src' g++ -DP_LINUX=2.6.5-1.358 -ffunction-sections -fdata-sections -D_REENTRANT -Wall -fPIC -DP_USE_PRAGMA -DPHAS_TEMPLATES -I/pwlib/include/ptlib/unix -I/usr/include/pwlib -DPTRACING -I/openh323/include -DHAS_OSS -DPTRACING -I/pwlib/include -fPIC -DP_USE_PRAGMA -Os -DNDEBUG -x c++ -c h225_1.cxx -o /openh323/lib/obj_linux_x86_r/h225_1.o g++ -DP_LINUX=2.6.5-1.358 -ffunction-sections -fdata-sections -D_REENTRANT -Wall -fPIC -DP_USE_PRAGMA -DPHAS_TEMPLATES -I/pwlib/include/ptlib/unix -I/usr/include/pwlib -DPTRACING -I/openh323/include -DHAS_OSS -DPTRACING -I/pwlib/incl...

...======================== downloaded 66 Kb * installing *source* package ‘gee’ ... ** package ‘gee’ successfully unpacked and MD5 sums checked ** libs gfortran -fpic -g -O2 -c dgedi.f -o dgedi.o gfortran -fpic -g -O2 -c dgefa.f -o dgefa.o gcc -std=gnu99 -I/ebio/abt6/jmao/R/R-2.15.0/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ugee.c -o ugee.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o gee.so dgedi.o dgefa.o ugee.o -L/ebio/abt6/jmao/R/R-2.15.0/lib -lRblas -lgfortran -lm -lgfortran -lm installing to /ebio/abt6/jmao/R/Rpacks/gee/libs ** R ** preparing package for lazy loading **...

...r_0.4.3.tar.gz' Content type 'application/x-gzip' length 655997 bytes (640 KB) ================================================== downloaded 640 KB * installing *source* package ?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...

...; CPU: 3cores amd64 OS pure-64bit CBLFS liux compiled from sources (kernel 3.2.1, gcc-4.6.2 R-2.15 When I compiled R the compiler spewed out lines like these:- make[3]: Entering directory `/tmp/RtmpiHdDJy/R.INSTALL472339eeb23a/mgcv/src' gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c gcv.c -o gcv.o gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/include -DNDEBUG - I/usr/local/atlas/include -I/usr/local/numerics/include -fpic -g -O2 -c gdi.c -o gdi.o gcc -m64 -std=gnu99 -I/home/Rman/R-2.15.0/incl...

...#39;application/x-gzip' length 655997 bytes (640 KB) > ================================================== > downloaded 640 KB > > * installing *source* package ?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...

...ed versions of the output from R CMD INSTALL: For caTools: * installing to library ?/scratch3/BMC/co2/lib/R-3.1/x86_64-unknown-linux-gnu? * installing *source* package ?caTools? ... ** package ?caTools? successfully unpacked and MD5 sums checked ** libs icpc -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O3 -fp-model precise -c Gif2R.cpp -o Gif2R.o icpc -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O3 -fp-model precise -c GifTools.cpp -o GifTools.o icc -std=gnu99 -I/apps/R/3.1.3-intel/lib64/R/include -DNDEBUG -I/usr/local/i...

...ONValidator.cpp JSONWorker.cpp JSONWriter.cpp JSON_Base64.cpp internalJSONNode.cpp libjson.cpp configure: creating ./config.status config.status: creating src/Makevars config.status: creating cleanup ** libs gcc -std=gnu99 -I/usr/share/R/include -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -fpic -g -O2 -c ConvertUTF.c -o ConvertUTF.o g++ -I/usr/share/R/include -I. -Ilibjson -Ilibjson/Source -DNEW_JSON_NEW_STREAM -DNDEBUG=1 -DJSON_VALIDATE -DJSON_STREAM=1 -DJSON_LIBRARY=1 -DJSON_ISO_STRICT -fpic -g -O...

...access R as below 1) R 2) install.pacakges('vegan') 3) After choosing mirror, here is the output I get * installing *source* package ‘vegan’ ... ** package ‘vegan’ successfully unpacked and MD5 sums checked ** libs gfortran -g -O2 -pipe -c cepin.f -o cepin.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c data2hill.c -o data2hill.o gfortran -g -O2 -pipe -c decorana.f -o decorana.o gcc -I/usr/lib/R/include -DNDEBUG -g -O2 -pipe -std=gnu99 -c goffactor.c -o goffactor.o gfortran -g -O2 -pipe -c monoMDS.f -o monoMDS.o gcc -I/usr/lib/R/include -DND...