Re: [R-pkg-devel] compilation flags WARNING
On 5 July 2018 at 22:19, Göran Broström wrote: | Thanks Heather and Iñaki: I understand. | | I have an old Makevars file in the src directory of the package. I | guess I can set the flags there? No, because those get scanned by R CMD check and friends. For the one you do not want, Heather's suggestion was spot. Supply a new (cleaner) system-wide default. Those values are not checked. I sometimes do the opposite and add (what would be "non-portable") options in ~/.R/Makevars to make very noisy builds quieter etc. | Now it only contains | | # PKG_CFLAGS = -Wall | # PKG_FFLAGS = -Wall -fbounds-check | PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) As we said no issues as nothing not allowed by R here. 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
Re: [R-pkg-devel] compilation flags WARNING
I would suggest not to set the CFLAGS in the package itself - at least not exclusively. R-admin 6.3.3 (the section I linked before) recommends "to enable a reasonable amount of diagnostic messaging (“warnings”) when compiling, such as e.g. -Wall -pedantic for tools from GCC", while R-exts 1.2.1 says"When writing a Makevars file for a package you intend to distribute, take care to ensure that it is not specific to your compiler: flags such as -O2 -Wall -pedantic (and all other -W flags: for the Oracle compilers these are used to pass arguments to compiler phases) are all specific to GCC." Since these are contradictory, you can't satisfy both via PKG_CFLAGS alone. That is why I suggest to use the Makevars.site file to set pedantic flags for local use that are not distributed with the package (if you don't want to set them at a site-wide level R-admin 6.3.3 gives alternatives for setting at user-level). Heather On Thu, Jul 5, 2018, at 9:19 PM, Göran Broström wrote: > Thanks Heather and Iñaki: I understand. > > I have an old Makevars file in the src directory of the package. I > guess I can set the flags there? Now it only contains > > # PKG_CFLAGS = -Wall > # PKG_FFLAGS = -Wall -fbounds-check > PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) > > Göran > > On 2018-07-05 17:43, Heather Turner wrote: > > > > > > On Thu, Jul 5, 2018, at 3:39 PM, Iñaki Úcar wrote: > >> El jue., 5 jul. 2018 a las 16:11, Göran Broström > >> () escribió: > >>> > >>> I am preparing a CRAN release of eha (a trivial change due to a change > >>> in the survival package), but when checking the build I get: > >>> > >>> goran@M6800:~/R$ R CMD check --as-cran eha_2.5.2.tar.gz > >>> ... > >>> * checking compilation flags used ... WARNING > >>> Compilation used the following non-portable flag(s): > >>> ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ > >>> ... > >> > >> AFAIK, these are new checks. I get similar warnings on Fedora for > >> different flags. > >> > >>> I have never seen this before and I haven't (to my knowledge) set any > >>> compilation flags. It is my first build and check on a newly upgraded > >>> ubuntu 18.04 (no issues on 17.10). Should I perhaps ask on r-sig-debian, > >>> or is that observation irrelevant? > >> > >> Again AFAIK (there are package maintainers for several distros here > >> that can correct me if I'm wrong), each distro defines some policies > >> regarding compilation flags that are applied to all packages by > >> default. So these warnings can be safely ignored locally (or you may > >> override them), because those flags won't be defined on CRAN. > >> > > Yes, by default the compilation flags are those set when R was installed. > > You can see the current flags via > > > > R CMD config CFLAGS > > > > which in your case should include ‘-Wdate-time’ etc. > > > > As Iñaki says you can safely ignore the warning, but if you prefer to not > > to have any warnings you can solve this by creating a Makevars.site file > > with CFLAGS excluding the non-portable ones, e.g. > > > > CFLAGS=-Wall -g O0 -fPIC > > > > This should be saved in the /etc directory of R.home(), e.g. /usr/lib/R/etc. > > > > See > > https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Customizing-package-compilation > > for more information. > > > > Heather > > > >> Iñaki > >> > >>> > >>> Göran Broström > >> > >> __ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] compilation flags WARNING
El jue., 5 jul. 2018 a las 22:23, Göran Broström () escribió: > > Thanks Heather and Iñaki: I understand. > > I have an old Makevars file in the src directory of the package. I > guess I can set the flags there? Now it only contains > > # PKG_CFLAGS = -Wall > # PKG_FFLAGS = -Wall -fbounds-check > PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) IMHO it's better to do it outside the package. The best way, without changing the system settings, is to place a Makevars under ~/.R/ Iñaki > > Göran > > On 2018-07-05 17:43, Heather Turner wrote: > > > > > > On Thu, Jul 5, 2018, at 3:39 PM, Iñaki Úcar wrote: > >> El jue., 5 jul. 2018 a las 16:11, Göran Broström > >> () escribió: > >>> > >>> I am preparing a CRAN release of eha (a trivial change due to a change > >>> in the survival package), but when checking the build I get: > >>> > >>> goran@M6800:~/R$ R CMD check --as-cran eha_2.5.2.tar.gz > >>> ... > >>> * checking compilation flags used ... WARNING > >>> Compilation used the following non-portable flag(s): > >>> ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ > >>> ... > >> > >> AFAIK, these are new checks. I get similar warnings on Fedora for > >> different flags. > >> > >>> I have never seen this before and I haven't (to my knowledge) set any > >>> compilation flags. It is my first build and check on a newly upgraded > >>> ubuntu 18.04 (no issues on 17.10). Should I perhaps ask on r-sig-debian, > >>> or is that observation irrelevant? > >> > >> Again AFAIK (there are package maintainers for several distros here > >> that can correct me if I'm wrong), each distro defines some policies > >> regarding compilation flags that are applied to all packages by > >> default. So these warnings can be safely ignored locally (or you may > >> override them), because those flags won't be defined on CRAN. > >> > > Yes, by default the compilation flags are those set when R was installed. > > You can see the current flags via > > > > R CMD config CFLAGS > > > > which in your case should include ‘-Wdate-time’ etc. > > > > As Iñaki says you can safely ignore the warning, but if you prefer to not > > to have any warnings you can solve this by creating a Makevars.site file > > with CFLAGS excluding the non-portable ones, e.g. > > > > CFLAGS=-Wall -g O0 -fPIC > > > > This should be saved in the /etc directory of R.home(), e.g. /usr/lib/R/etc. > > > > See > > https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Customizing-package-compilation > > for more information. > > > > Heather > > > >> Iñaki > >> > >>> > >>> Göran Broström > >> > >> __ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Iñaki Úcar http://www.enchufa2.es @Enchufa2 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] compilation flags WARNING
Thanks Heather and Iñaki: I understand. I have an old Makevars file in the src directory of the package. I guess I can set the flags there? Now it only contains # PKG_CFLAGS = -Wall # PKG_FFLAGS = -Wall -fbounds-check PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) Göran On 2018-07-05 17:43, Heather Turner wrote: On Thu, Jul 5, 2018, at 3:39 PM, Iñaki Úcar wrote: El jue., 5 jul. 2018 a las 16:11, Göran Broström () escribió: I am preparing a CRAN release of eha (a trivial change due to a change in the survival package), but when checking the build I get: goran@M6800:~/R$ R CMD check --as-cran eha_2.5.2.tar.gz ... * checking compilation flags used ... WARNING Compilation used the following non-portable flag(s): ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ ... AFAIK, these are new checks. I get similar warnings on Fedora for different flags. I have never seen this before and I haven't (to my knowledge) set any compilation flags. It is my first build and check on a newly upgraded ubuntu 18.04 (no issues on 17.10). Should I perhaps ask on r-sig-debian, or is that observation irrelevant? Again AFAIK (there are package maintainers for several distros here that can correct me if I'm wrong), each distro defines some policies regarding compilation flags that are applied to all packages by default. So these warnings can be safely ignored locally (or you may override them), because those flags won't be defined on CRAN. Yes, by default the compilation flags are those set when R was installed. You can see the current flags via R CMD config CFLAGS which in your case should include ‘-Wdate-time’ etc. As Iñaki says you can safely ignore the warning, but if you prefer to not to have any warnings you can solve this by creating a Makevars.site file with CFLAGS excluding the non-portable ones, e.g. CFLAGS=-Wall -g O0 -fPIC This should be saved in the /etc directory of R.home(), e.g. /usr/lib/R/etc. See https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Customizing-package-compilation for more information. Heather Iñaki Göran Broström __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] compilation flags WARNING
On Thu, Jul 5, 2018, at 3:39 PM, Iñaki Úcar wrote: > El jue., 5 jul. 2018 a las 16:11, Göran Broström > () escribió: > > > > I am preparing a CRAN release of eha (a trivial change due to a change > > in the survival package), but when checking the build I get: > > > > goran@M6800:~/R$ R CMD check --as-cran eha_2.5.2.tar.gz > > ... > > * checking compilation flags used ... WARNING > > Compilation used the following non-portable flag(s): > >‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ > > ... > > AFAIK, these are new checks. I get similar warnings on Fedora for > different flags. > > > I have never seen this before and I haven't (to my knowledge) set any > > compilation flags. It is my first build and check on a newly upgraded > > ubuntu 18.04 (no issues on 17.10). Should I perhaps ask on r-sig-debian, > > or is that observation irrelevant? > > Again AFAIK (there are package maintainers for several distros here > that can correct me if I'm wrong), each distro defines some policies > regarding compilation flags that are applied to all packages by > default. So these warnings can be safely ignored locally (or you may > override them), because those flags won't be defined on CRAN. > Yes, by default the compilation flags are those set when R was installed. You can see the current flags via R CMD config CFLAGS which in your case should include ‘-Wdate-time’ etc. As Iñaki says you can safely ignore the warning, but if you prefer to not to have any warnings you can solve this by creating a Makevars.site file with CFLAGS excluding the non-portable ones, e.g. CFLAGS=-Wall -g O0 -fPIC This should be saved in the /etc directory of R.home(), e.g. /usr/lib/R/etc. See https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Customizing-package-compilation for more information. Heather > Iñaki > > > > > Göran Broström > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] compilation flags WARNING
El jue., 5 jul. 2018 a las 16:11, Göran Broström () escribió: > > I am preparing a CRAN release of eha (a trivial change due to a change > in the survival package), but when checking the build I get: > > goran@M6800:~/R$ R CMD check --as-cran eha_2.5.2.tar.gz > ... > * checking compilation flags used ... WARNING > Compilation used the following non-portable flag(s): >‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ > ... AFAIK, these are new checks. I get similar warnings on Fedora for different flags. > I have never seen this before and I haven't (to my knowledge) set any > compilation flags. It is my first build and check on a newly upgraded > ubuntu 18.04 (no issues on 17.10). Should I perhaps ask on r-sig-debian, > or is that observation irrelevant? Again AFAIK (there are package maintainers for several distros here that can correct me if I'm wrong), each distro defines some policies regarding compilation flags that are applied to all packages by default. So these warnings can be safely ignored locally (or you may override them), because those flags won't be defined on CRAN. Iñaki > > Göran Broström __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] compilation flags WARNING
I am preparing a CRAN release of eha (a trivial change due to a change in the survival package), but when checking the build I get: goran@M6800:~/R$ R CMD check --as-cran eha_2.5.2.tar.gz ... * checking compilation flags used ... WARNING Compilation used the following non-portable flag(s): ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’ ... I have never seen this before and I haven't (to my knowledge) set any compilation flags. It is my first build and check on a newly upgraded ubuntu 18.04 (no issues on 17.10). Should I perhaps ask on r-sig-debian, or is that observation irrelevant? Göran Broström __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
