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[R-pkg-devel] CRAN note: src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS

4 messages · Georgi Boshnakov, Dirk Eddelbuettel, Balamuta, James Joseph

Original
Georgi Boshnakov
# 
Hi,

Recently the results page of my package on CRAN at
https://cran.r-project.org/web/checks/check_results_sarima.html,
started to show the NOTE below for some systems.
I am using Rcpp/RcppArmadillo without any manual interventions on my side. 

Is it reasonable to expect that the NOTE will disappear if I rebuild the package with an up-to-date version of  Rcpp
and maybe rerunning RcppAttributes().?

Georgi Boshnakov

==================================

Check: use of SHLIB_OPENMP_*FLAGS in Makefiles 
Result: NOTE 
???? src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
???? src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
???? src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
???? src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
????Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
????Extensions'. The macros for different languages may differ so the
????matching macro must be used in PKG_CXXFLAGS (etc) and match that used
????in PKG_LIBS (except for F77: see the manual).

====================================
Dirk Eddelbuettel
#
On 20 August 2018 at 22:14, Georgi Boshnakov wrote:
| Hi,
| 
| Recently the results page of my package on CRAN at
| https://cran.r-project.org/web/checks/check_results_sarima.html,
| started to show the NOTE below for some systems.
| I am using Rcpp/RcppArmadillo without any manual interventions on my side. 
| 
| Is it reasonable to expect that the NOTE will disappear if I rebuild the package with an up-to-date version of  Rcpp
| and maybe rerunning RcppAttributes().?

No you have to edit src/Makevars{,win} yourself.

| ==================================
| 
| Check: use of SHLIB_OPENMP_*FLAGS in Makefiles 
| Result: NOTE 
| ???? src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
| ???? src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
| ???? src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
| ???? src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS

Basically just use SHLIB_OPENMP_CXXFLAGS in PKG_LIBS as well. As the
paragraph quoted below suggests.

Our initial example in RcppArmadillo was sloppy was mix *_CFLAGS and
*_CXXFLAGS use, and that is no longer liked at the CRAN side.

Dirk

| ????Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
| ????Extensions'. The macros for different languages may differ so the
| ????matching macro must be used in PKG_CXXFLAGS (etc) and match that used
| ????in PKG_LIBS (except for F77: see the manual).
| 
| ====================================
| 
| ______________________________________________
| R-package-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-package-devel
Balamuta, James Joseph
# 
In short, the default Makevars{.win} file should be updated with:

CXX_STD = CXX11
PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) 
PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

c.f. https://github.com/RcppCore/RcppArmadillo/blob/58b11c738d31b9e8d9fa6b39e2290b2ac08aefc4/inst/skeleton/Makevars#L11-L14

Sincerely,

JJB

?On 8/20/18, 5:40 PM, "R-package-devel on behalf of Dirk Eddelbuettel" <r-package-devel-bounces at r-project.org on behalf of edd at debian.org> wrote:
On 20 August 2018 at 22:14, Georgi Boshnakov wrote:
| Hi,
    | 
    | Recently the results page of my package on CRAN at
    | https://cran.r-project.org/web/checks/check_results_sarima.html,
    | started to show the NOTE below for some systems.
    | I am using Rcpp/RcppArmadillo without any manual interventions on my side. 
    | 
    | Is it reasonable to expect that the NOTE will disappear if I rebuild the package with an up-to-date version of  Rcpp
    | and maybe rerunning RcppAttributes().?
    
    No you have to edit src/Makevars{,win} yourself.
    
    | ==================================
    | 
    | Check: use of SHLIB_OPENMP_*FLAGS in Makefiles 
    | Result: NOTE 
    |      src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
    |      src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
    |      src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
    |      src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
    
    Basically just use SHLIB_OPENMP_CXXFLAGS in PKG_LIBS as well. As the
    paragraph quoted below suggests.
    
    Our initial example in RcppArmadillo was sloppy was mix *_CFLAGS and
    *_CXXFLAGS use, and that is no longer liked at the CRAN side.
    
    Dirk
    
    |     Use of these macros is discussed in sect 1.2.1.1 of 'Writing R
    |     Extensions'. The macros for different languages may differ so the
    |     matching macro must be used in PKG_CXXFLAGS (etc) and match that used
    |     in PKG_LIBS (except for F77: see the manual).
    | 
    | ====================================
    | 
    | ______________________________________________
    | R-package-devel at r-project.org mailing list
    | https://stat.ethz.ch/mailman/listinfo/r-package-devel
    
    -- 
    http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
    
    ______________________________________________
    R-package-devel at r-project.org mailing list
    https://stat.ethz.ch/mailman/listinfo/r-package-devel
Georgi Boshnakov
# 
Dirk and James,

Many thanks for the detailed advice.

Georgi