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 at 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 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
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 ' |
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
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 <
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 <
Dear all,
We got the results from the automated check for our package. There
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>
Dear maintainer,
package volesti_0.0.0.tar.gz does not pass the incoming checks
automatically, please see the following pre-tests:
Status: 2 NOTEs
Debian: <
Status: 2 NOTEs
Please fix all problems and resubmit a fixed version via the
If you are not sure how to fix the problems shown, please ask for
help on the R-package-devel mailing list:
reply-all to this message and explain.
More details are given in the directory:
<
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
write to stdout/stderr instead of to the console, nor use
nor system RNGs.
See 'Writing portable packages' in the 'Writing R Extensions'
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
write to stdout/stderr instead of to the console, nor use
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
search you get a null result.
This NOTE appears because of our functions in
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
Since packages with all OKs can go straight through the CRAN
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
automated check complaining about the same 2 notes as in the
submission. I answered (reply to all) explaining why those notes
false positives. Then no news for 9 days. Could you please update
on this.
Best regards,
Vissarion
On Wed, 13 Mar 2019 at 10:15, ????? ?????? <tolis.chal at gmail.com>
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
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
server
CRAN incoming dashboard ? cransays
|
|
| |
CRAN incoming dashboard ? cransays
|
|
|
We hope it makes data more accessible whilst reducing load on
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
ftp://cran.r-project.org/incoming/
/Henrik
On Tue, Mar 12, 2019 at 1:26 PM Duncan Murdoch <
murdoch.duncan at gmail.com>
On 12/03/2019 2:57 p.m., ????? ?????? wrote:
Dear all,
We have submitted a package to CRAN in 25th of February
a
positive or a negative answer for the submission since
normal? Is
there any way to get informed for the review process?
Did you get the two messages after submission (one to
are the maintainer, the second to let you know the review
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
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