[R-pkg-devel] Compilation used the "non-portable flag"
So - even though I am getting the same note: Compilation used the following non-portable flag(s): from Ubuntu Linux, I should go ahead and submit?
From: G?bor Cs?rdi <csardi.gabor at gmail.com>
Sent: Wednesday, May 15, 2019 9:14:50 AM
To: Goldfeld, Keith
Cc: I?aki Ucar; Dirk Eddelbuettel; r-package-devel at r-project.org
Subject: Re: [R-pkg-devel] Compilation used the "non-portable flag"
Sent: Wednesday, May 15, 2019 9:14:50 AM
To: Goldfeld, Keith
Cc: I?aki Ucar; Dirk Eddelbuettel; r-package-devel at r-project.org
Subject: Re: [R-pkg-devel] Compilation used the "non-portable flag"
You don't need to do anything. Gabor On Wed, May 15, 2019 at 2:13 PM Goldfeld, Keith <Keith.Goldfeld at nyulangone.org> wrote: > > Forgive me for not completely understanding the back and forth. Do I need to do anything on my end, or are these changes that are being made on the server side? > > > - Keith > > ________________________________ > From: R-package-devel <r-package-devel-bounces at r-project.org> on behalf of I?aki Ucar <iucar at fedoraproject.org> > Sent: Wednesday, May 15, 2019 9:01:31 AM > To: Dirk Eddelbuettel > Cc: r-package-devel at r-project.org > Subject: Re: [R-pkg-devel] Compilation used the "non-portable flag" > > On Wed, 15 May 2019 at 13:16, Dirk Eddelbuettel <edd at debian.org> wrote: > > > > > > On 15 May 2019 at 11:49, G?bor Cs?rdi wrote: > > | Thinking about this a bit more, I think this might be a bug in R CMD > > | check, actually. > > | > > | I understand that these flags are not portable, and yes, they should > > | be reported if they are specified in the packages's Makevars* files. > > | But in this case they are coming from the Ubuntu system's Makevars > > | setup, and surely, they do work there. I would even say that it is > > | actually good practice to include them in the system setup. > > | > > | I can probably provide a patch for this. > > > > See discussions on r-sig-debian -- in essence I had the same thouht and this > > has been taken care of now in R 3.6.0-2. We add this to Renviron.site > > > > ## edd May 2019 > > ## > > ## Debian (and its derivatives) impose a set of compiler flags to prevent some known > > ## security issues with compiled code. These flags then become defaults for R as well > > ## (see eg /etc/R/Makeconf) but nevertheless confuse R as warnings get triggers. Users, > > ## on the other hand, are often stumped about these. So with this variable we declare > > ## these options as known for the local checks on the machine this file is on. > > ## > > ## See Section 8 of the R Internals manual for many more options to customize tests. > > _R_CHECK_COMPILATION_FLAGS_KNOWN_='-Wformat -Werror=format-security -Wdate-time' > > > > > > It may eventually move to Renviron now that Kurt kindly fixed an Renviron parser > > buglet with `=` assignments in r-devel > > > > So please add the environment variable now on all Debian and Ubuntu flavours, > > and/or upgrade to 3.6.0-2. > > Fedora adds these flags too, plus -D_GLIBCXX_ASSERTIONS since Fedora 28, see: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_r-2Dpackage-2Ddevel_2018q2_002754.html&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=fPRk5fx5iys38LPukC4wc6PALfhKJF_KlHbdD5hrfGc&m=CfJnEvpTss5ER8w_xXRZMDRvEhrseOVfAIu5aLZrY24&s=LjMY_8I7NS1NWWY4b4ijWmd8QV8E4pmF-TEqbB3dz8I&e= > > This last one is particularly difficult to conceal, because the > resulting code includes calls to abort, for which R complains. > > I?aki > > ______________________________________________ > R-package-devel at r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIFaQ&c=j5oPpO0eBH1iio48DtsedeElZfc04rx3ExJHeIIZuCs&r=fPRk5fx5iys38LPukC4wc6PALfhKJF_KlHbdD5hrfGc&m=CfJnEvpTss5ER8w_xXRZMDRvEhrseOVfAIu5aLZrY24&s=AH5qvmlvudRzUv7tgGCbKEP_Fi0gkNWLKehp-PlnUJ8&e= > > ------------------------------------------------------------ > This email message, including any attachments, is for ...{{dropped:25}}