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