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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:

...ckage ?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 -Wall -pipe -pedant...

...? * 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 -Wall -pipe -pedantic -std=gnu99 -O3 -pipe -s...

Please note that building R on Windows is documented in "R Installation and Administration", including links to external software. Particularly there is a link to texinfo which is part of Rtools. The documentation is maintained and it is a sufficient source of information for building R on Windows. https://cran.r-project.org/doc/manuals/r-release/R-admin.html

...g-from-source After I have done "make all && make recommended", "make bitmapdll" returns the following: E:\sandbox\R-2.13.r55221\src\gnuwin32>make bitmapdll make[1]: Entering directory `/cygdrive/e/sandbox/R-2.13.r55221/src/gnuwin32/bitmap' make CC='gcc -std=gnu99' AR='ar' AR_RC='ar rcs' \ CFLAGS="-O3 -I../../../extra/zlib -DPNG_NO_MMX_CODE" \ RANLIB=ranlib ZLIBLIB=../../../extra/zlib -C libpng \ -f scripts/makefile.gcc prefix=foo libpng.a gcc -std=gnu99 -c -O3 -I../../../extra/zlib -DPNG_NO_MMX_CODE -I../zlib png.c gcc -s...

...blkcnt_t... yes checking for type of socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for gcc option to accept ISO C99... -std=gnu99 checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99 checking for inline... inline checking for int... yes checking size of int... 4 checking for long... yes checking size of long... 4 checking for long long... yes checking size of long long... 8 checking for double......

...preferences.d from preferences.c making psignal.d from psignal.c making rhome.d from rhome.c making rui.d from rui.c making run.d from run.c making shext.d from shext.c making sys-win32.d from sys-win32.c making system.d from system.c making dos_glob.d from dos_glob.c gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c console.c -o console.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c dataentry.c -o dataentry.o gcc -O3 -Wall -pedantic -std=gnu99 -I../include -I. -DHAVE_CONFIG_H -DR_DLL_BUILD -c dynload.c -o dynload.o g...

...ipe -g -c idptip.f -o idptip.o gfortran -fpic -O3 -pipe -g -c idptli.f -o idptli.o gfortran -fpic -O3 -pipe -g -c idsfft.f -o idsfft.o gfortran -fpic -O3 -pipe -g -c idtang.f -o idtang.o gfortran -fpic -O3 -pipe -g -c idxchg.f -o idxchg.o gcc -I/usr/share/R/include -fpic -std=gnu99 -O3 -pipe -g -c init.c -o init.o gfortran -fpic -O3 -pipe -g -c tripack.f -o tripack.o gfortran -fpic -O3 -pipe -g -c ttidbs.f -o ttidbs.o gcc -shared -o akima.so akima.new.o akima433.o akima697.o idbvip.o idcldp.o idgrid.o idlctn.o idpdrv.o idptip.o idptli.o idsfft.o idtang.o idxchg.o ini...

...v but still no luck. Anyone know how to solve this? $ R CMD INSTALL RSQLite_0.11.1.tar.gz * installing to library ‘/home/ubuntu/R/i686-pc-linux-gnu-library/2.14’ * installing *source* package ‘RSQLite’ ... ** package ‘RSQLite’ successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... 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 whethe...

..._tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this function gcc -m64 -std=gnu99 -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 cs_add.c -o cs_add.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FOR...

..._tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this function gcc -m64 -std=gnu99 -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 cs_add.c -o cs_add.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FOR...

...star_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?dev? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?astar_tmp? may be used uninitialized in this function MCMCglmm.cc:225: warning: ?Worig? may be used uninitialized in this function gcc -m64 -std=gnu99 -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 cs_add.c -o cs_add.o gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURC...

...-3.tar.gz RJDBC_0.2-0.tar.gz Rserve_0.6-8.tar.gz [root at localhost Package]# R CMD INSTALL rJava_0.9-3.tar.gz * installing to library ?/usr/local/lib64/R/library? * installing *source* package ?rJava? ... ** package ?rJava? successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... 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 wheth...

...socket length... socklen_t * checking for stack_t... yes checking for intptr_t... yes checking for uintptr_t... yes checking whether byte ordering is bigendian... (cached) no checking for an ANSI C-conforming const... yes checking for x86_64-alpine-linux-uclibc-gcc option to accept ISO C99... -std=gnu99 checking for x86_64-alpine-linux-uclibc-gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99 checking for inline... inline checking size of int... (cached) 4 checking size of long... (cached) 8 checking size of long long... (cached) 8 checking size of double... 8 checking size of l...

...RL 'http://cran.cnr.Berkeley.edu/src/contrib/rgl_0.84.tar.gz' Content type 'application/x-gzip' length 1670659 bytes (1.6 Mb) opened URL ================================================== downloaded 1.6 Mb * Installing *source* package 'rgl' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... 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 whethe...

...get install r-base r-base-core r-base-dev, and then began to update.packages() > update.packages(lib.loc="/usr/local/lib/R/site-library") > update.packages(lib.loc="/usr/lib/R/library") but I get: .... * Installing *source* package 'mgcv' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c gcv.c -o gcv.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c gdi.c -o gdi.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c init.c -o init.o gcc -std=gnu99 -I/usr/share/R/include -fpic -g -O2 -c magic.c -o magic.o gcc -st...

Any ideas? I certainly have X11, I have tried copying it into other directories. At present it is in /etc/X11. This is my error message. /home/user> R CMD INSTALL -l [/usr/local/R/site-library] rgl_0.81.orig.tar.gz * Installing *source* package 'rgl' ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... 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 whethe...

...39; Content type ''application/x-gzip'' length 537153 bytes (524 Kb) URL abierta ================================================== downloaded 524 Kb * installing *source* package ‘rJava’ ... ** package ‘rJava’ successfully unpacked and MD5 sums checked checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... 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 whethe...

...tent type 'application/x-gzip' length 537153 bytes (524 Kb) opened URL ================================================== downloaded 524 Kb * installing *source* package 'rJava' ... ** package 'rJava' successfully unpacked and MD5 sums checked checking for gcc... gcc46 -std=gnu99 checking for C compiler default output file name... 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 whethe...

...66 Kb) opened URL ================================================== 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...