[R-pkg-devel] CRAN review

William Dunlap wdun|@p @end|ng |rom t|bco@com
Fri Mar 29 17:35:32 CET 2019 

The check only looks at compiled code.  BH contains only headers, no
compiled code.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Fri, Mar 29, 2019 at 9:27 AM Maxime Turgeon <
maxime.turgeon using mail.mcgill.ca> wrote:

> Hi Bill,
>
> Maybe I'm missing something, but if RcppEigen were the cause of the NOTE,
> wouldn't RcppEigen also get the same NOTE? However, it does not:
> https://cran.r-project.org/web/checks/check_results_RcppEigen.html
>
> And for what it's worth, neither does BH:
> https://cran.r-project.org/web/checks/check_results_BH.html
>
> Max
> ------------------------------
> *From:* R-package-devel <r-package-devel-bounces using r-project.org> on behalf
> of William Dunlap <wdunlap using tibco.com>
> *Sent:* March 29, 2019 12:05 PM
> *To:* Vissarion Fisikopoulos
> *Cc:* R Package Development
> *Subject:* Re: [R-pkg-devel] CRAN review
>
> It looks like it is not boost but RcppEigen that has the call to
> std::rand() that volesti/src/rotating.cpp contains.
>
> RcppEigen/include/Eigen/src/Core/MathFunctions.h:
>   static inline Scalar run(const Scalar& x, const Scalar& y)
>   {
>     return x + (y-x) * Scalar(std::rand()) / Scalar(RAND_MAX);
>   }
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Fri, Mar 29, 2019 at 8:43 AM William Dunlap <wdunlap using tibco.com> wrote:
>
> > > Library lpSolveAPI uses rand() and srand() in lp_utils.c. We replace
> > > both functions with GetRNGstate(); PutRNGstate(); unif_rand(); from
> > > R’s internal random number generation routines as it is proposed in
> > > `Writing R Extensions`. Moreover if you run in folder `/src`:
> > > $ grep -r 'rand()'
> > > You just get:
> > > `utils.c:  range *= (LPSREAL) unif_rand();`
> > > which is our replacement. If you replace `rand()` with `srand` in grep
> > > search you get a null result.
> > > This NOTE appears because of our functions in `/src/include/samplers`
> > > where word `rand` appears a lot of times, for example
> > > `rand_point_generator()`.
> >
> > I don't think the note about using 'rand' comes from looking at strings
> > in the source code.  It is probably looking at undefined symbols in the
> > symbol table of the compiled and linked code with something like the
> > following
> >
> > % find volesti -iname "*o" | xargs nm -A -g --demangle | grep ' U ' |
> grep
> > rand
> > volesti/src/lp_solve/lp_rlp.o:                 U storevarandweight
> > volesti/src/lp_solve/lp_price.o:                 U rand_uniform
> > volesti/src/lp_solve/lp_utils.o:                 U unif_rand
> > volesti/src/lp_solve/lp_lib.o:                 U rand_uniform
> > volesti/src/rotating.o:                 U rand
> > volesti/src/volesti.so:                 U rand@@GLIBC_2.2.5
> > volesti/src/volesti.so:                 U unif_rand
> >
> > You will have to poke through the boost headers or docs to see how to
> avoid
> > using rand in volesti/src/rotating.cpp.
> >
> > Bill Dunlap
> > TIBCO Software
> > wdunlap tibco.com
> >
> >
> > On Fri, Mar 29, 2019 at 2:12 AM Vissarion Fisikopoulos <
> fisikop using gmail.com>
> > wrote:
> >
> >> Dear all,
> >>
> >> @Henrik: thanks a lot for your reply.
> >>
> >> I did one more submission (the third) and I am posting below my answer
> >> to the automatic cran email with 2 NOTES.
> >>
> >> Looking forward to your feedback.
> >>
> >> Best regards,
> >> Vissarion.
> >>
> >> On Fri, 29 Mar 2019 at 11:04, Vissarion Fisikopoulos <fisikop using gmail.com
> >
> >> wrote:
> >> >
> >> > Dear all,
> >> >
> >> > We got the results from the automated check for our package. There are
> >> > two NOTEs in both checks in Windows and Debian. We are sure that the
> >> > rejections are false positive, so with this e-mail we try to explain
> >> > why. Please find our explanations below.
> >> >
> >> > On Thu, 28 Mar 2019 at 16:40, <ligges using statistik.tu-dortmund.de>
> wrote:
> >> > >
> >> > > Dear maintainer,
> >> > >
> >> > > package volesti_0.0.0.tar.gz does not pass the incoming checks
> >> automatically, please see the following pre-tests:
> >> > > Windows: <
> >>
> https://win-builder.r-project.org/incoming_pretest/volesti_0.0.0_20190328_151546/Windows/00check.log
> >> >
> >> > > Status: 2 NOTEs
> >> > > Debian: <
> >>
> https://win-builder.r-project.org/incoming_pretest/volesti_0.0.0_20190328_151546/Debian/00check.log
> >> >
> >> > > Status: 2 NOTEs
> >> > >
> >> > >
> >> > >
> >> > > Please fix all problems and resubmit a fixed version via the
> webform.
> >> > > If you are not sure how to fix the problems shown, please ask for
> >> help on the R-package-devel mailing list:
> >> > > <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
> >> > > If you are fairly certain the rejection is a false positive, please
> >> reply-all to this message and explain.
> >> > >
> >> > > More details are given in the directory:
> >> > > <
> >>
> https://win-builder.r-project.org/incoming_pretest/volesti_0.0.0_20190328_151546/
> >> >
> >> > > The files will be removed after roughly 7 days.
> >> > >
> >> > > No strong reverse dependencies to be checked.
> >> > >
> >> > > Best regards,
> >> > > CRAN teams' auto-check service
> >> > > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
> >> > > Check: CRAN incoming feasibility, Result: NOTE
> >> > >   Maintainer: 'Vissarion Fisikopoulos <
> >> vissarion.fisikopoulos using gmail.com>'
> >> > >
> >> > >   New submission
> >> > >
> >> > >   Possibly mis-spelled words in DESCRIPTION:
> >> > >     Minkowski (9:17)
> >> > >     Polytopes (4:49)
> >> > >     Volesti (7:71)
> >> > >     polytopes (8:39, 10:83)
> >> > >     volesti (7:50)
> >> > >     zonotopes (9:44)
> >> > These words, except of 'volesti' (which is the name of our package),
> >> > describe geometrical concepts.
> >> >
> >> > > Flavor: r-devel-windows-ix86+x86_64
> >> > > Check: compiled code, Result: NOTE
> >> > >   File 'volesti/libs/i386/volesti.dll':
> >> > >     Found 'rand', possibly from 'rand' (C)
> >> > >       Object: 'rotating.o'
> >> > >   File 'volesti/libs/x64/volesti.dll':
> >> > >     Found 'rand', possibly from 'rand' (C)
> >> > >       Object: 'rotating.o'
> >> > >
> >> > >   Compiled code should not call entry points which might terminate R
> >> nor
> >> > >   write to stdout/stderr instead of to the console, nor use Fortran
> >> I/O
> >> > >   nor system RNGs.
> >> > >
> >> > >   See 'Writing portable packages' in the 'Writing R Extensions'
> >> manual.
> >> > >
> >> > > Flavor: r-devel-linux-x86_64-debian-gcc
> >> > > Check: compiled code, Result: NOTE
> >> > >   File 'volesti/libs/volesti.so':
> >> > >     Found 'rand', possibly from 'rand' (C)
> >> > >       Object: 'rotating.o'
> >> > >
> >> > >   Compiled code should not call entry points which might terminate R
> >> nor
> >> > >   write to stdout/stderr instead of to the console, nor use Fortran
> >> I/O
> >> > >   nor system RNGs.
> >> >
> >> > Library lpSolveAPI uses rand() and srand() in lp_utils.c. We replace
> >> > both functions with GetRNGstate(); PutRNGstate(); unif_rand(); from
> >> > R’s internal random number generation routines as it is proposed in
> >> > `Writing R Extensions`. Moreover if you run in folder `/src`:
> >> > $ grep -r 'rand()'
> >> > You just get:
> >> > `utils.c:  range *= (LPSREAL) unif_rand();`
> >> > which is our replacement. If you replace `rand()` with `srand` in grep
> >> > search you get a null result.
> >> > This NOTE appears because of our functions in `/src/include/samplers`
> >> > where word `rand` appears a lot of times, for example
> >> > `rand_point_generator()`.
> >> >
> >> > Best regards,
> >> > Vissarion Fisikopoulos
> >>
> >> On Fri, 22 Mar 2019 at 22:03, Henrik Bengtsson
> >> <henrik.bengtsson using gmail.com> wrote:
> >> >
> >> > Not a CRAN maintainer, but from my experience, it sounds like you're
> >> > hitting some very unusual hiccup here - that's unfortunate.  I just
> >> > had a look around at ftp://cran.r-project.org/incoming/ and your
> >> > package is not there anymore. Just a wild guess but I wonder if your
> >> > email reply back to CRAN ends up in their spam folders?
> >> >
> >> > BTW, what are the two NOTEs you're getting?  Maybe they're avoidable.
> >> > Since packages with all OKs can go straight through the CRAN incoming
> >> > checks and be published automatically (at least if the package is
> >> > already on CRAN), I try to walk an extra mile just avoid NOTEs in my
> >> > packages even if I know they're false positives.
> >> >
> >> > My $.02
> >> >
> >> > /Henrik
> >> >
> >> > On Fri, Mar 22, 2019 at 6:28 AM Vissarion Fisikopoulos
> >> > <fisikop using gmail.com> wrote:
> >> > >
> >> > > Hello,
> >> > >
> >> > > we have resubmitted the package 'volesti'. I got the email and
> >> > > confirmed submission. Later I got the confirmation email starting:
> >> > > "The following package was uploaded to CRAN:..." and then the email
> on
> >> > > automated check complaining about the same 2 notes as in the
> previous
> >> > > submission. I answered (reply to all) explaining why those notes are
> >> > > false positives. Then no news for 9 days. Could you please update us
> >> > > on this.
> >> > >
> >> > > Best regards,
> >> > > Vissarion
> >> > >
> >> > >
> >> > > On Wed, 13 Mar 2019 at 10:15, Τόλης Χαλκής <tolis.chal using gmail.com>
> >> wrote:
> >> > > >
> >> > > > Of course we will resubmit. Thank you all for the info.
> >> > > >
> >> > > > Chalkis Apostolos
> >> > > >
> >> > > > On Wed, 13 Mar 2019 at 10:05, Maëlle SALMON via R-package-devel <
> >> > > > r-package-devel using r-project.org> wrote:
> >> > > >
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > > ---------- Forwarded message ----------
> >> > > > > From: "Maëlle SALMON" <maelle.salmon using yahoo.se>
> >> > > > > To: Duncan Murdoch <murdoch.duncan using gmail.com>, Henrik
> Bengtsson <
> >> > > > > henrik.bengtsson using gmail.com>
> >> > > > > Cc: r-package-devel using r-project.org
> >> > > > > Bcc:
> >> > > > > Date: Wed, 13 Mar 2019 07:56:45 +0000 (UTC)
> >> > > > > Subject: Re: [R-pkg-devel] CRAN review
> >> > > > >  Sorry, the link was removed (by my copy-pasting it wrongly):
> >> > > > > https://itsalocke.com/cransays/articles/dashboard
> >> > > > >
> >> > > > >     Den onsdag 13 mars 2019 08:54:00 CET, Maëlle SALMON via
> >> > > > > R-package-devel <r-package-devel using r-project.org> skrev:
> >> > > > >
> >> > > > >   We at Locke Data have made an hourly updated dashboard based
> on
> >> the FTP
> >> > > > > server
> >> > > > > CRAN incoming dashboard • cransays
> >> > > > >
> >> > > > > |
> >> > > > > |
> >> > > > > |  |
> >> > > > > CRAN incoming dashboard • cransays
> >> > > > >
> >> > > > >
> >> > > > >  |
> >> > > > >
> >> > > > >  |
> >> > > > >
> >> > > > >  |
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > > We hope it makes data more accessible whilst reducing load on
> the
> >> FTP
> >> > > > > server.
> >> > > > > Maëlle.
> >> > > > >
> >> > > > >     Den tisdag 12 mars 2019 21:37:12 CET, Henrik Bengtsson <
> >> > > > > henrik.bengtsson using gmail.com> skrev:
> >> > > > >
> >> > > > >  You can also "follow" your package submission on the CRAN FTP
> >> server:
> >> > > > >
> >> > > > >   ftp://cran.r-project.org/incoming/
> >> > > > >
> >> > > > > /Henrik
> >> > > > >
> >> > > > > On Tue, Mar 12, 2019 at 1:26 PM Duncan Murdoch <
> >> murdoch.duncan using gmail.com>
> >> > > > > wrote:
> >> > > > > >
> >> > > > > > On 12/03/2019 2:57 p.m., Τόλης Χαλκής wrote:
> >> > > > > > > Dear all,
> >> > > > > > >
> >> > > > > > > We have submitted a package to CRAN in 25th of February and
> >> we have
> >> > > > > not got
> >> > > > > > > a
> >> > > > > > > positive or a negative answer for the submission since then.
> >> Is this
> >> > > > > > > normal? Is
> >> > > > > > > there any way to get informed for the review process?
> >> > > > > >
> >> > > > > > Did you get the two messages after submission (one to confirm
> >> that you
> >> > > > > > are the maintainer, the second to let you know the review has
> >> started)?
> >> > > > > > They'll both have subject lines like
> >> > > > > >
> >> > > > > > CRAN submission ....
> >> > > > > >
> >> > > > > >
> >> > > > > > The first one will start out saying something like
> >> > > > > > >
> >> > > > > > > Dear Duncan Murdoch
> >> > > > > > > Someone has submitted the package rgl to CRAN.
> >> > > > > > > You are receiving this email to confirm the submission as
> the
> >> > > > > maintainer of
> >> > > > > > > this package.
> >> > > > > >
> >> > > > > > and then ask you to confirm submission.
> >> > > > > >
> >> > > > > > The second one will start like
> >> > > > > >
> >> > > > > > > [This was generated from CRAN.R-project.org/submit.html]
> >> > > > > > >
> >> > > > > > > The following package was uploaded to CRAN:
> >> > > > > > > ===========================================
> >> > > > > > >
> >> > > > > > > Package Information:
> >> > > > > > > Package: rgl
> >> > > > > >
> >> > > > > > A while later you should get a third message about the
> >> automatic checks.
> >> > > > > >
> >> > > > > > Duncan Murdoch
> >> > > > > >
> >> > > > > > ______________________________________________
> >> > > > > > R-package-devel using r-project.org mailing list
> >> > > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> > > > >
> >> > > > > ______________________________________________
> >> > > > > R-package-devel using r-project.org mailing list
> >> > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> > > > >     [[alternative HTML version deleted]]
> >> > > > >
> >> > > > > ______________________________________________
> >> > > > > R-package-devel using r-project.org mailing list
> >> > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> > > > >
> >> > > > >         [[alternative HTML version deleted]]
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > >
> >> > > > > ---------- Forwarded message ----------
> >> > > > > From: "Maëlle SALMON via R-package-devel" <
> >> r-package-devel using r-project.org>
> >> > > > > To: Duncan Murdoch <murdoch.duncan using gmail.com>, Henrik
> Bengtsson <
> >> > > > > henrik.bengtsson using gmail.com>
> >> > > > > Cc: r-package-devel using r-project.org
> >> > > > > Bcc:
> >> > > > > Date: Wed, 13 Mar 2019 07:56:45 +0000 (UTC)
> >> > > > > Subject: Re: [R-pkg-devel] CRAN review
> >> > > > > ______________________________________________
> >> > > > > R-package-devel using r-project.org mailing list
> >> > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> > > > >
> >> > > >
> >> > > >         [[alternative HTML version deleted]]
> >> > > >
> >> > > > ______________________________________________
> >> > > > R-package-devel using r-project.org mailing list
> >> > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >> > >
> >> > > ______________________________________________
> >> > > R-package-devel using r-project.org mailing list
> >> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >> ______________________________________________
> >> R-package-devel using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >>
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-package-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>

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