[Rd] can't build from source: error: template with C linkage
Martyn Plummer
plummerm at iarc.fr
Fri Aug 19 16:51:40 CEST 2016
This looks like the result of including a C++ system header inside an
extern "C" block. There is no evidence of this happening in the current
version 2.22.1. However, it did happen in the previous version 2.22 via
the chain of inclusions:
MCMCglmmcc.h -> cs.h -> R.h -> various C++ system headers
See Writing R Extensions P 108.
I would check that the people reporting this bug are using the latest
version. If not then you have already fixed this.
Martyn
On Fri, 2016-08-19 at 06:25 -0500, Dirk Eddelbuettel wrote:
> Jarrod,
>
> On 19 August 2016 at 04:43, Jarrod Hadfield wrote:
> >
> > 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: error: template
> > with C linkage
> > template<typename _Tp>
> >
> > I see a bug report has been filed for the CRAN package tgp that was
> > experiencing similar problems, but it is not clear whether it has
> > been resolved.
> >
> > Any help would be greatly appreciated.
>
> I am on Ubuntu 16.04 with gcc/g++ 5.4.0 and I _cannot_ reproduce
> this.
>
> Your package installs fine [1].
>
> Dirk
>
>
> [1] For some definition of 'fine' which overlooks pages of compiler
> _warnings_.
> Still no errors. A log is below. Note that I a) had to turn off '-
> Wall
> -pedantic' which I normally use, and add two explicit 'do not warn'
> switches. The rest is stock Ubuntu behaviour.
>
> edd at max:/tmp/mcmcglmm$ R_LIBS_USER=/tmp/RcppDepends/lib R 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 -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_addR.c -o cs_addR.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_cbind.c -o cs_cbind.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_chol.c -o cs_chol.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_cholsol.c -o cs_cholsol.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_amd.c -o cs_amd.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_compress.c -o cs_compress.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_cov2cor.c -o cs_cov2cor.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_counts.c -o cs_counts.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_cumsum.c -o cs_cumsum.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_dfs.c -o cs_dfs.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_dcmvnorm.c -o cs_dcmvnorm.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_directsum.c -o cs_directsum.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_directsumupdate.c -o cs_directsumupdate.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_dmvnorm.c -o cs_dmvnorm.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_droptol.c -o cs_droptol.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_dropzeros.c -o cs_dropzeros.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_dmperm.c -o cs_dmperm.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_entry.c -o cs_entry.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_dupl.c -o cs_dupl.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_ereach.c -o cs_ereach.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_etree.c -o cs_etree.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_gaxpy.c -o cs_gaxpy.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_fkeep.c -o cs_fkeep.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_happly.c -o cs_happly.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_house.c -o cs_house.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_invR.c -o cs_invR.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_inv.c -o cs_inv.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_ipvec.c -o cs_ipvec.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerA.c -o cs_kroneckerA.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerAupdate.c -o cs_kroneckerAupdate.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerDA.c -o cs_kroneckerDA.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerDI.c -o cs_kroneckerDI.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerIadd.c -o cs_kroneckerIadd.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerI.c -o cs_kroneckerI.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerIupdate.c -o cs_kroneckerIupdate.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerSI.c -o cs_kroneckerSI.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_kroneckerSIupdate.c -o cs_kroneckerSIupdate.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_leaf.c -o cs_leaf.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_load.c -o cs_load.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_lsolve.c -o cs_lsolve.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_ltsolve.c -o cs_ltsolve.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_lu.c -o cs_lu.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_lusol.c -o cs_lusol.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_malloc.c -o cs_malloc.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_multiply.c -o cs_multiply.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_maxtrans.c -o cs_maxtrans.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_norm.c -o cs_norm.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_omegaupdate.c -o cs_omegaupdate.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_omega.c -o cs_omega.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_permute.c -o cs_permute.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_pinv.c -o cs_pinv.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_post.c -o cs_post.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_print.c -o cs_print.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_pvec.c -o cs_pvec.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_qrsol.c -o cs_qrsol.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_qr.c -o cs_qr.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rCinvwishart.c -o cs_rCinvwishart.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rAnte.c -o cs_rAnte.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rR.c -o cs_rR.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rRsubinvwishart.c -o cs_rRsubinvwishart.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_randperm.c -o cs_randperm.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rSinvwishart.c -o cs_rSinvwishart.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_reach.c -o cs_reach.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rinvwishart.c -o cs_rinvwishart.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_rwishart.c -o cs_rwishart.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_scatter.c -o cs_scatter.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_schol.c -o cs_schol.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_scc.c -o cs_scc.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_sortdv.c -o cs_sortdv.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_schur.c -o cs_schur.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_spsolve.c -o cs_spsolve.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_sqr.c -o cs_sqr.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_symperm.c -o cs_symperm.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_tdfs.c -o cs_tdfs.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_transpose.c -o cs_transpose.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_usolve.c -o cs_usolve.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_updown.c -o cs_updown.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_util.c -o cs_util.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c cs_utsolve.c -o cs_utsolve.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c dcutpoints.c -o dcutpoints.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c dcmvnormR.cc -o
> dcmvnormR.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c pcmvnorm.c -o pcmvnorm.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c inverseA.cc -o
> inverseA.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c rIW.cc -o rIW.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c rante.cc -o
> rante.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c rtcmvnorm.c -o rtcmvnorm.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c rbv.cc -o rbv.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 -std=gnu99 -Wno-maybe-uninitialized -Wno-unused-but-set-
> variable -c rtnorm.c -o rtnorm.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c rtcmvnormR.cc -o
> rtcmvnormR.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c rtnormR.cc -o
> rtnormR.o
> g++ -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 -Wno-unused -O3 -pipe -Wno-
> maybe-uninitialized -Wno-unused-but-set-variable -c MCMCglmm.cc -o
> MCMCglmm.o
> g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o
> MCMCglmm.so MCMCglmm.o cs_add.o cs_addR.o cs_amd.o cs_cbind.o
> cs_chol.o cs_cholsol.o cs_compress.o cs_counts.o cs_cov2cor.o
> cs_cumsum.o cs_dcmvnorm.o cs_dfs.o cs_directsum.o
> cs_directsumupdate.o cs_dmperm.o cs_dmvnorm.o cs_droptol.o
> cs_dropzeros.o cs_dupl.o cs_entry.o cs_ereach.o cs_etree.o cs_fkeep.o
> cs_gaxpy.o cs_happly.o cs_house.o cs_inv.o cs_invR.o cs_ipvec.o
> cs_kroneckerA.o cs_kroneckerAupdate.o cs_kroneckerDA.o
> cs_kroneckerDI.o cs_kroneckerI.o cs_kroneckerIadd.o
> cs_kroneckerIupdate.o cs_kroneckerSI.o cs_kroneckerSIupdate.o
> cs_leaf.o cs_load.o cs_lsolve.o cs_ltsolve.o cs_lu.o cs_lusol.o
> cs_malloc.o cs_maxtrans.o cs_multiply.o cs_norm.o cs_omega.o
> cs_omegaupdate.o cs_permute.o cs_pinv.o cs_post.o cs_print.o
> cs_pvec.o cs_qr.o cs_qrsol.o cs_rAnte.o cs_rCinvwishart.o cs_rR.o
> cs_rRsubinvwishart.o cs_rSinvwishart.o cs_randperm.o cs_reach.o
> cs_rinvwishart.o cs_rwishart.o cs_scatter.o cs_scc.o cs_schol.o
> cs_schur.o cs_sortdv.o cs_spsolve.o cs_sqr.o cs_symperm.o cs_tdfs.o
> cs_transpose.o cs_updown.o cs_usolve.o cs_util.o cs_utsolve.o
> dcmvnormR.o dcutpoints.o inverseA.o pcmvnorm.o rIW.o rante.o rbv.o
> rtcmvnorm.o rtcmvnormR.o rtnorm.o rtnormR.o -L/usr/lib/R/lib -lR
> installing to /tmp/RcppDepends/lib/MCMCglmm/libs
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> * DONE (MCMCglmm)
> edd at max:/tmp/mcmcglmm$
>
> --
> http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> ______________________________________________
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