[R-pkg-devel] CRAN review

William Dunlap wdun|@p @end|ng |rom t|bco@com
Fri Mar 29 17:42:55 CET 2019 

One can use 'g++ -E' to find the which include file is the culprit.  E.g.,

% g++ -c -E -I`R RHOME`/include -I`R RHOME`/site-library/Rcpp/include -I`R
RHOME`/site-library/RcppEigen/include -Iexternal/LPsolve_src/run_headers
-Iexternal/minimum_ellipsoid -Iinclude -Iinclude/volume
-Iinclude/generators -Iinclude/samplers -Iinclude/annealing
-Iinclude/convex_bodies -std=gnu++11 rotating.cpp | egrep '\<rand\>|^#
*[0-9]+' | grep -C 1 '\<rand\>'
# 315 "/usr/include/stdlib.h" 2 3 4
extern int rand (void) throw ();
# 1 "/usr/include/alloca.h" 1 3 4
--
# 114 "/usr/include/c++/4.8.2/cstdlib" 3
  using ::rand;
# 196 "/usr/include/c++/4.8.2/cstdlib" 3
--
# 5185 "/usr/include/c++/4.8.2/bits/stl_algo.h" 3
     + std::rand() % ((__i - __first) + 1);
# 5218 "/usr/include/c++/4.8.2/bits/stl_algo.h" 3
--
# 455
"/home/R/R-3.5.2/lib64/R/site-library/RcppEigen/include/Eigen/src/Core/MathFunctions.h"
    return x + (y-x) * Scalar(std::rand()) / Scalar(2147483647);
      offset = (std::size_t(std::rand()) * multiplier) / divisor;
    return Scalar((std::rand() >> shift) - offset);
# 689
"/home/R/R-3.5.2/lib64/R/site-library/RcppEigen/include/Eigen/src/Core/MathFunctions.h"
--
# 295
"/home/R/R-3.5.2/lib64/R/site-library/RcppEigen/include/Eigen/src/Core/arch/CUDA/Half.h"
    return x + (y-x) * half(float(std::rand()) / float(2147483647));
# 412 "/home/R/R-3.5.2/lib64/R/site-library/RcppEigen/include/Eigen/Core" 2

Bill Dunlap
TIBCO Software
wdunlap tibco.com


On Fri, Mar 29, 2019 at 9:37 AM William Dunlap <wdunlap using tibco.com> wrote:

> 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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