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.turg...@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-boun...@r-project.org> on behalf > of William Dunlap <wdun...@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 <wdun...@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 < > fisi...@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 <fisi...@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, <lig...@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.fisikopou...@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.bengts...@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 > >> > <fisi...@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.c...@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@r-project.org> wrote: > >> > > > > >> > > > > > >> > > > > > >> > > > > > >> > > > > ---------- Forwarded message ---------- > >> > > > > From: "Maëlle SALMON" <maelle.sal...@yahoo.se> > >> > > > > To: Duncan Murdoch <murdoch.dun...@gmail.com>, Henrik > Bengtsson < > >> > > > > henrik.bengts...@gmail.com> > >> > > > > Cc: r-package-devel@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@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.bengts...@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.dun...@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@r-project.org mailing list > >> > > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > > > > >> > > > > ______________________________________________ > >> > > > > R-package-devel@r-project.org mailing list > >> > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > > > [[alternative HTML version deleted]] > >> > > > > > >> > > > > ______________________________________________ > >> > > > > R-package-devel@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@r-project.org> > >> > > > > To: Duncan Murdoch <murdoch.dun...@gmail.com>, Henrik > Bengtsson < > >> > > > > henrik.bengts...@gmail.com> > >> > > > > Cc: r-package-devel@r-project.org > >> > > > > Bcc: > >> > > > > Date: Wed, 13 Mar 2019 07:56:45 +0000 (UTC) > >> > > > > Subject: Re: [R-pkg-devel] CRAN review > >> > > > > ______________________________________________ > >> > > > > R-package-devel@r-project.org mailing list > >> > > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > > > > >> > > > > >> > > > [[alternative HTML version deleted]] > >> > > > > >> > > > ______________________________________________ > >> > > > R-package-devel@r-project.org mailing list > >> > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > > >> > > ______________________________________________ > >> > > R-package-devel@r-project.org mailing list > >> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > >> ______________________________________________ > >> R-package-devel@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-package-devel > >> > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
