[R-pkg-devel] SHLIB_OPENMP_*FLAGS in Makefiles
In checking my R package via devtools::check and devtools::check_built, I received the following NOTE which I am unsure how to fix. My package contains compiled code (via Rcpp). Within my .cpp file I have the following line: #define ARMA_DONT_PRINT_OPENMP_WARNING Is this the issue? checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 linking is by C++ 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 linking is by C++ Thanks. [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] SHLIB_OPENMP_*FLAGS in Makefiles
The NOTE refers to Makevars and Makevars.win. The most logical place to start your investigation would be those two files. Do you have any reason to believe that they are *not* the culprits? Max From: R-package-devel on behalf of Jarrett Phillips Sent: April 15, 2019 11:21 AM To: r-package-devel@r-project.org Subject: [R-pkg-devel] SHLIB_OPENMP_*FLAGS in Makefiles In checking my R package via devtools::check and devtools::check_built, I received the following NOTE which I am unsure how to fix. My package contains compiled code (via Rcpp). Within my .cpp file I have the following line: #define ARMA_DONT_PRINT_OPENMP_WARNING Is this the issue? checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 linking is by C++ 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 linking is by C++ Thanks. [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] SHLIB_OPENMP_*FLAGS in Makefiles
On 15 April 2019 at 11:21, Jarrett Phillips wrote: | In checking my R package via devtools::check and devtools::check_built, I | received the following NOTE which I am unsure how to fix. My package | contains compiled code (via Rcpp). Within my .cpp file I have the following | line: | | #define ARMA_DONT_PRINT_OPENMP_WARNING | | Is this the issue? No. | checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... 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 | linking is by C++ | 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 | linking is by C++ R is now quite explicit about something is used to not complain about: a mix of C and CXX flags used in the two listed files (as Maxime pointed out). This is quite possibly due to the skeleton version of these files included in older versions of RcppArmadillo. We of course switched to a corrected one once these warnings appeared, but we cannot fix the packages already out there. "Better" versions are at https://github.com/RcppCore/RcppArmadillo/blob/master/inst/skeleton/Makevars https://github.com/RcppCore/RcppArmadillo/blob/master/inst/skeleton/Makevars.win and in essence you just need these two updated lines: PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) and we also recommend including CXX_STD = CXX11 as the files do. Hope this helps, Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories
Hi,
I am trying to put the r package on the CRAN. But one of the package
dependencies is not from CRAN. I can use the following can install in local.
if (!require("rPeaks")) {
devtools::install_github("jrminter/rPeaks")
}
I followed the suggestions based on
https://stackoverflow.com/questions/29419776/r-package-dependencies-not-installed-from-additional-repositories
.
But it didn't work out for me. OR maybe I didn't set up it right.
My GitHub repository is https://github.com/tankwin08/waveformlidar.
My DESCRIPTION:
Suggests:
knitr,
rPeaks
Additional_repositories: https://github.com/jrminter/rPeaks/
I am not sure I need to add an additional step to change anything. The R
function needs to use the rPeaks is waveformlidar
/R
/deconvolution.R
Any suggestion of how to set up the additional_repositories are appreciated.
--
Best regards
Tan Zhou
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories
On 15.04.19 18:50, Tan Zhou wrote: > I followed the suggestions based on > https://stackoverflow.com/questions/29419776/r-package-dependencies-not-installed-from-additional-repositories > . > But it didn't work out for me. OR maybe I didn't set up it right. > > My GitHub repository is https://github.com/tankwin08/waveformlidar. > > My DESCRIPTION: > Suggests: > knitr, > rPeaks > Additional_repositories: https://github.com/jrminter/rPeaks/ The 'Additional_repositories' field is meant for additional CRAN-like repositories, not for a git(hub) repository. A simple way to create such a CRAN-like repository is given by the drat package, as mentioned in the referenced SO answer. I am using that for the swephR package: ... Suggests: testthat, swephRdata, knitr, rmarkdown Encoding: UTF-8 URL: https://github.com/rstub/swephR/, http://www.astro.com/swisseph/ BugReports: https://github.com/rstub/swephR/issues/ Additional_repositories: https://rstub.github.io/drat ... So while the 'swephRdata' can be found at https://github.com/rstub/swephRdata/, the 'Additional_repositories' field points to my drat repository. In your case, you could either ask the rPeaks author to create a drat repo or do that yourself (possibly with the author's consent). Greetings Ralf -- Ralf Stubner Senior Software Engineer / Trainer daqana GmbH Dortustraße 48 14467 Potsdam T: +49 331 23 61 93 11 F: +49 331 23 61 93 90 M: +49 162 20 91 196 Mail: ralf.stub...@daqana.com Sitz: Potsdam Register: AG Potsdam HRB 27966 Ust.-IdNr.: DE300072622 Geschäftsführer: Dr.-Ing. Stefan Knirsch, Prof. Dr. Dr. Karl-Kuno Kunze signature.asc Description: OpenPGP digital signature __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories
On 15.04.2019 18:50, Tan Zhou wrote:
Hi,
I am trying to put the r package on the CRAN. But one of the package
dependencies is not from CRAN. I can use the following can install in local.
if (!require("rPeaks")) {
devtools::install_github("jrminter/rPeaks")
}
You must not do that as it would install without explicit user permission.
Best,
Uwe Ligges
I followed the suggestions based on
https://stackoverflow.com/questions/29419776/r-package-dependencies-not-installed-from-additional-repositories
.
But it didn't work out for me. OR maybe I didn't set up it right.
My GitHub repository is https://github.com/tankwin08/waveformlidar.
My DESCRIPTION:
Suggests:
knitr,
rPeaks
Additional_repositories: https://github.com/jrminter/rPeaks/
I am not sure I need to add an additional step to change anything. The R
function needs to use the rPeaks is waveformlidar
/R
/deconvolution.R
Any suggestion of how to set up the additional_repositories are appreciated.
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Package suggested but not available for checking: 'rPeaks'; Additional_repositories
Thank you very much for your suggestions and explanation, Ralf. They are
very helpful.
I got permission from the author and use *drat::addRepo("jrminter").*
*When I try to test if this package can be installed with install.package*
*install.packages("rPeaks", repos = "https://jrminter.github.io/drat/
: cannot open URL
'https://tankwin08.github.io/drat/src/contrib/PACKAGES
'Warning in
install.packages : unable to access index for repository
https://jrminter.github.io/drat/src/contrib
: cannot open URL
'https://jrminter.github.io/drat/src/contrib/PACKAGES
'Installing package
into ‘C:/Users/tank/Documents/R/win-library/3.4’(as ‘lib’ is
unspecified)Warning in install.packages : unable to access index for
repository https://jrminter.github.io/drat/src/contrib
: cannot open URL
'https://jrminter.github.io/drat/src/contrib/PACKAGES
'Warning in
install.packages : package ‘rPeaks’ is not available (for R version 3.4.3)*
*Do you have any suggestion? *
Best
Tan
On Mon, Apr 15, 2019 at 12:16 PM Ralf Stubner
wrote:
> On 15.04.19 18:50, Tan Zhou wrote:
> > I followed the suggestions based on
> >
> https://stackoverflow.com/questions/29419776/r-package-dependencies-not-installed-from-additional-repositories
> > .
> > But it didn't work out for me. OR maybe I didn't set up it right.
> >
> > My GitHub repository is https://github.com/tankwin08/waveformlidar.
> >
> > My DESCRIPTION:
> > Suggests:
> > knitr,
> > rPeaks
> > Additional_repositories: https://github.com/jrminter/rPeaks/
>
> The 'Additional_repositories' field is meant for additional CRAN-like
> repositories, not for a git(hub) repository. A simple way to create such
> a CRAN-like repository is given by the drat package, as mentioned in the
> referenced SO answer. I am using that for the swephR package:
>
> ...
> Suggests:
> testthat,
> swephRdata,
> knitr,
> rmarkdown
> Encoding: UTF-8
> URL: https://github.com/rstub/swephR/, http://www.astro.com/swisseph/
> BugReports: https://github.com/rstub/swephR/issues/
> Additional_repositories: https://rstub.github.io/drat
> ...
>
>
> So while the 'swephRdata' can be found at
> https://github.com/rstub/swephRdata/, the 'Additional_repositories'
> field points to my drat repository.
>
> In your case, you could either ask the rPeaks author to create a drat
> repo or do that yourself (possibly with the author's consent).
>
> Greetings
> Ralf
>
> --
> Ralf Stubner
> Senior Software Engineer / Trainer
>
> daqana GmbH
> Dortustraße 48
> 14467 Potsdam
>
> T: +49 331 23 61 93 11
> F: +49 331 23 61 93 90
> M: +49 162 20 91 196
> Mail: ralf.stub...@daqana.com
>
> Sitz: Potsdam
> Register: AG Potsdam HRB 27966
> Ust.-IdNr.: DE300072622
> Geschäftsführer: Dr.-Ing. Stefan Knirsch, Prof. Dr. Dr. Karl-Kuno Kunze
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
--
Best regards
Tan Zhou
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
