From j.hadfield at ed.ac.uk  Fri Aug 19 16:53:58 2016
From: j.hadfield at ed.ac.uk (Jarrod Hadfield)
Date: Fri, 19 Aug 2016 15:53:58 +0100
Subject: [Rd] can't build from source: error: template with C linkage
In-Reply-To: <1471618252.2630.72.camel@iarc.fr>
References: <90f718c0-1299-6da3-b95c-9152ed565609@ed.ac.uk>
	<22454.60601.117571.733489@max.nulle.part>
	<1471618252.2630.72.camel@iarc.fr>
Message-ID: <4e3db613-50b1-b599-3d23-8423d44c97ce@ed.ac.uk>

Hi Martyn,

Thanks for the help. This is now ringing very vague bells and I will 
check it out.

Cheers,

Jarrod



On 19/08/16 15:51, Martyn Plummer wrote:
> 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
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel


-- 
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[Rd] can't build from source: error: template with C linkage
Jarrod Hadfield