[R-pkg-devel] CRAN review

William Dunlap wdun|@p @end|ng |rom t|bco@com
Fri Mar 29 17:05:03 CET 2019 

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
>>
>

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