[R-pkg-devel] CRAN review

William Dunlap wdun|@p @end|ng |rom t|bco@com
Fri Mar 29 17:37:25 CET 2019 

Oops, RcppEigen does contain compiled code, but its header files include
much more code that doesn't get checked because it is not used in
RcppEigen.so.

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Fri, Mar 29, 2019 at 9:35 AM William Dunlap <wdunlap using tibco.com> wrote:

> 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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