[R-pkg-devel] CRAN review

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 at 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 at r-project.org> on
behalf of William Dunlap <wdunlap at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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, ????? ?????? <tolis.chal at gmail.com>

wrote:

Of course we will resubmit. Thank you all for the info.

Chalkis Apostolos

On Wed, 13 Mar 2019 at 10:05, Ma?lle SALMON via R-package-devel <
r-package-devel at r-project.org> wrote:

---------- Forwarded message ----------
From: "Ma?lle SALMON" <maelle.salmon at yahoo.se>
To: Duncan Murdoch <murdoch.duncan at gmail.com>, Henrik

Bengtsson <

henrik.bengtsson at gmail.com>
Cc: r-package-devel at 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, Ma?lle SALMON via
R-package-devel <r-package-devel at 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.
Ma?lle.

    Den tisdag 12 mars 2019 21:37:12 CET, Henrik Bengtsson <
henrik.bengtsson at 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 at gmail.com>

wrote:

On 12/03/2019 2:57 p.m., ????? ?????? 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 at r-project.org>

To: Duncan Murdoch <murdoch.duncan at gmail.com>, Henrik

Bengtsson <

henrik.bengtsson at gmail.com>
Cc: r-package-devel at r-project.org
Bcc:
Date: Wed, 13 Mar 2019 07:56:45 +0000 (UTC)
Subject: Re: [R-pkg-devel] CRAN review

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