R SIG Debian - Nov 2016 - Ubuntu 16.10 Yakkety Yak uses GCC 6 but -std=c++98 is missing

On 12 November 2016 at 07:59, Dirk Eddelbuettel wrote:
| 
| On 12 November 2016 at 14:23, Kirill M?ller wrote:
| | Thanks. I have now CXX = g++ -std=c++98 in my /etc/R/Makeconf, it's 
| | picked up properly. I can only assume that the last -std= option wins if 
| | more than one are given on the same command line [1].
| 
| Good to know it works.
| 
| I am still a little puzzled why it was needed when it doesn't seem to be
| needed on the Debian side.

I just upgraded an old (unused, underpowered) box to 16.10 as a first
test. No issues so far, and basic cppFunction("...") tests with Rcpp
work.

Could you get us a minimal reproducible example of what broke without the
explicit -std=c++98 ?

Dirk


-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On 12.11.2016 18:38, Dirk Eddelbuettel wrote:
> On 12 November 2016 at 07:59, Dirk Eddelbuettel wrote:
> |
> | On 12 November 2016 at 14:23, Kirill M?ller wrote:
> | | Thanks. I have now CXX = g++ -std=c++98 in my /etc/R/Makeconf, it's
> | | picked up properly. I can only assume that the last -std= option wins
if
> | | more than one are given on the same command line [1].
> |
> | Good to know it works.
> |
> | I am still a little puzzled why it was needed when it doesn't seem to
be
> | needed on the Debian side.
>
> I just upgraded an old (unused, underpowered) box to 16.10 as a first
> test. No issues so far, and basic cppFunction("...") tests with
Rcpp work.
>
> Could you get us a minimal reproducible example of what broke without the
> explicit -std=c++98 ?
>
When I posted, there was only "xenial", not "yakkety", on
CRAN. This has
changed now (thanks a lot!). When I try to upgrade, I'm presented with 
the following diff of /etc/R/Makeconf (excerpt), which looks *very* 
strange to me.

-# configure  '--prefix=/usr' '--with-cairo'
'--with-jpeglib'
'--with-readline' '--with-tcltk' '--with-system-bzlib' 
'--with-system-pcre' '--with-system-zlib'
'--mandir=/usr/share/man'
'--infodir=/usr/share/info' '--datadir=/usr/share/R/share' 
'--includedir=/usr/share/R/include' '--with-blas'
'--with-lapack'
'--enable-R-profiling' '--enable-R-shlib'
'--enable-memory-profiling'
'--without-recommended-packages' '--build'
'x86_64-linux-gnu'
'build_alias=x86_64-linux-gnu' 'R_PRINTCMD=/usr/bin/lpr' 
'R_PAPERSIZE=letter' 'R_BROWSER=xdg-open' 'LIBnn=lib' 
'JAVA_HOME=/usr/lib/jvm/default-java' 'CC=gcc -std=gnu99'
'CFLAGS=-g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g' 'LDFLAGS=-Wl,-Bsymbolic-functions
-Wl,-z,relro'
'CPPFLAGS=' 'F77=gfortran' 'FFLAGS=-g -O2
-fstack-protector-strong'
'CXX=g++' 'CXXFLAGS=-g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g' 
'FC=gfortran' 'FCFLAGS=-g -O2 -fstack-protector-strong'
+# configure  '--prefix=/usr' '--with-cairo'
'--with-jpeglib'
'--with-readline' '--with-tcltk' '--with-system-bzlib' 
'--with-system-pcre' '--with-system-zlib'
'--mandir=/usr/share/man'
'--infodir=/usr/share/info' '--datadir=/usr/share/R/share' 
'--includedir=/usr/share/R/include' '--with-blas'
'--with-lapack'
'--enable-R-profiling' '--enable-R-shlib'
'--enable-memory-profiling'
'--without-recommended-packages' '--build'
'x86_64-linux-gnu'
'build_alias=x86_64-linux-gnu' 'R_PRINTCMD=/usr/bin/lpr' 
'R_PAPERSIZE=letter' 'R_BROWSER=xdg-open' 'LIBnn=lib' 
'JAVA_HOME=/usr/lib/jvm/default-java' 'CC=gcc -std=gnu99'
'CFLAGS=-g -O2
-fdebug-prefix-map=/build/r-base-qk3a9o/r-base-3.3.2=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g' 'LDFLAGS=-Wl,-Bsymbolic-functions
-Wl,-z,relro'
'CPPFLAGS=' 'F77=gfortran' 'FFLAGS=-g -O2 
-fdebug-prefix-map=/build/r-base-qk3a9o/r-base-3.3.2=. 
-fstack-protector-strong' 'CXX=g++' 'CXXFLAGS=-g -O2 
-fdebug-prefix-map=/build/r-base-qk3a9o/r-base-3.3.2=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g' 'FC=gfortran' 'FCFLAGS=-g -O2 
-fdebug-prefix-map=/build/r-base-qk3a9o/r-base-3.3.2=. 
-fstack-protector-strong'


-CFLAGS = -g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g $(LTO)
+CFLAGS = -g -O2 -fdebug-prefix-map=/build/r-base-qk3a9o/r-base-3.3.2=. 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2 -g $(LTO)

Also, no "-std=c++98" in the maintainer's version.

I noticed this because plogr logging crashed in dplyr (compiled with gcc 
6) right after upgrading to yakkety; I still had a gcc-5 built version 
of Rcpp installed. As soon as I added -std, everything worked as before. 
No minimal example, sorry. Don't we need "-std=c++98" in Makevars 
anyway, even if it's just to avoid users using C++11 constructs and then 
wondering why their packages fail on CRAN?


-Kirill


-Kirill

On 12 November 2016 at 22:54, Kirill M?ller wrote:

[... lots of stuff deleted ...]

| I noticed this because plogr logging crashed in dplyr (compiled with gcc 
| 6) right after upgrading to yakkety; I still had a gcc-5 built version 
| of Rcpp installed. As soon as I added -std, everything worked as before. 
| No minimal example, sorry. Don't we need "-std=c++98" in
Makevars
| anyway, even if it's just to avoid users using C++11 constructs and then 
| wondering why their packages fail on CRAN?

There is still no minimally preproducible example here; just a (pardon me
here) rambling description of a hasty system upgrade.

It is _somewhat common_ to have to recompile C++ shared objects when compiler
major versions change.

So I am unsure if we have actually demonstrated a bug here.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org