Re: [R-pkg-devel] R, BLAS, and FCLEN
On 2019-08-31 21:26, Duncan Murdoch wrote: On 31/08/2019 12:47 p.m., Göran Broström wrote: I'm having difficulties updating my package eha: When I run standard checks 'at home' everything is fine, but 'CRAN-submissions' reports (among other things): geomsup.f:324:9: warning: type of ‘dgemv’ does not match original declaration [-Wlto-type-mismatch] 324 | & one, score, ione) | ^ /home/tmp/R-d-gcc-LTO/include/R_ext/BLAS.h:107:1: note: type mismatch in parameter 12 107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n, | ^ This is odd since the LAPACK subroutine dgemv takes only 11 parameters. However, in include/R_ext/BLAS.h we have F77_NAME(dgemv)(const char *trans, const int *m, const int *n, const double *alpha, const double *a, const int *lda, const double *x, const int *incx, const double *beta, double *y, const int *incy FCLEN); with a 12th parameter FCLEN?? How am I supposed to fix this, and what the ... is FCLEN? googling leads to nothing useful (for me). It seems as if R is redefining some standard LAPACK routines. Also a note I do not understand (in this context): note: type ‘void’ should match type ‘long int’ Any help is much appreciated. Sounds likely to be related to this item from R-devel NEWS: http://developer.r-project.org/blosxom.cgi/R-devel/2019/08/29#n2019-08-29 " Header ‘Rconfig.h’ contains the value of ‘FC_LEN_T’ deduced at installation which is used by the prototypes in headers ‘R_ext/BLAS.h’ and ‘R_ext/Lapack.h’ but to avoid extensive breakage this is only exposed when ‘USE_FC_LEN_T’ is defined. If a package's C/C++ calls to BLAS/LAPACK allow for the ‘hidden’ arguments used by most Fortran compilers to pass the lengths of Fortran character arguments, define ‘USE_FC_LEN_T’ and include ‘Rconfig.h’ (possibly _via_ ‘R.h’) before including ‘R_ext/BLAS.h’ or ‘R_ext/Lapack.h’." Thanks Duncan, but my call to dgemv is from a FORTRAN subroutine, no C is involved. It is called by .Fortran in R code. I am confused (not for the first time). Göran Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] URL of a frame (or a vignette)?
Hello: How can I get a URL for a frame? Specifically, I want a URL that I can cite for the "bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R" vignette in the bssm package on CRAN. If the package is installed, it's available there as "bssm.pdf". However, I want to include it in an RMarkdown vignette I'm writing, and I'd rather not force the reader to be on a computer with the package installed -- and force myself to figure out a way to find it in that case, if that can even be done. Thanks, Spencer Graves __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
Wouldn't you just refer to [1] or one of the links mentioned there? [1] https://cran.r-project.org/package=bssm On September 1, 2019 7:22:43 AM PDT, Spencer Graves wrote: >Hello: > > > How can I get a URL for a frame? > > > Specifically, I want a URL that I can cite for the "bssm: >Bayesian Inference of Non-linear and >Non-Gaussian State Space Models in R" vignette in the bssm package on >CRAN. If the package is installed, it's available there as >"bssm.pdf". >However, I want to include it in an RMarkdown vignette I'm writing, and > >I'd rather not force the reader to be on a computer with the package >installed -- and force myself to figure out a way to find it in that >case, if that can even be done. > > > Thanks, > Spencer Graves > >__ >R-package-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
Hi, Jeff: That's what I needed. I clicked on the vignette I wanted and got the following: https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf Thanks, Spencer Graves On 2019-09-01 09:37, Jeff Newmiller wrote: Wouldn't you just refer to [1] or one of the links mentioned there? [1] https://cran.r-project.org/package=bssm On September 1, 2019 7:22:43 AM PDT, Spencer Graves wrote: Hello: How can I get a URL for a frame? Specifically, I want a URL that I can cite for the "bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R" vignette in the bssm package on CRAN. If the package is installed, it's available there as "bssm.pdf". However, I want to include it in an RMarkdown vignette I'm writing, and I'd rather not force the reader to be on a computer with the package installed -- and force myself to figure out a way to find it in that case, if that can even be done. Thanks, Spencer Graves __ 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
Re: [R-pkg-devel] URL of a frame (or a vignette)?
It may be better to use the canonical url, https://cran.r-project.org/package=bssm, as in: https://cran.r-project.org/package=bssm/bssm.pdf By the way, the vignettes for an installed package can be found by vignette(package="bssm") or help(package="bssm", help_type = "html") The latter has the advantage that it present links in a browser even if by default the help is presented in text mode. Georgi Boshnakov -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Spencer Graves Sent: 01 September 2019 15:42 To: Jeff Newmiller; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? Hi, Jeff: That's what I needed. I clicked on the vignette I wanted and got the following: https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf Thanks, Spencer Graves On 2019-09-01 09:37, Jeff Newmiller wrote: > Wouldn't you just refer to [1] or one of the links mentioned there? > > [1] https://cran.r-project.org/package=bssm > > On September 1, 2019 7:22:43 AM PDT, Spencer Graves > wrote: >> Hello: >> >> >> How can I get a URL for a frame? >> >> >> Specifically, I want a URL that I can cite for the "bssm: >> Bayesian Inference of Non-linear and >> Non-Gaussian State Space Models in R" vignette in the bssm package on >> CRAN. If the package is installed, it's available there as >> "bssm.pdf". >> However, I want to include it in an RMarkdown vignette I'm writing, and >> >> I'd rather not force the reader to be on a computer with the package >> installed -- and force myself to figure out a way to find it in that >> case, if that can even be done. >> >> >> Thanks, >> Spencer Graves >> >> __ >> 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
Re: [R-pkg-devel] URL of a frame (or a vignette)?
Correction: https://cran.r-project.org/package=bssm/vignettes/bssm.pdf -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Georgi Boshnakov Sent: 01 September 2019 15:57 To: Spencer Graves; Jeff Newmiller; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? It may be better to use the canonical url, https://cran.r-project.org/package=bssm, as in: https://cran.r-project.org/package=bssm/bssm.pdf By the way, the vignettes for an installed package can be found by vignette(package="bssm") or help(package="bssm", help_type = "html") The latter has the advantage that it present links in a browser even if by default the help is presented in text mode. Georgi Boshnakov -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Spencer Graves Sent: 01 September 2019 15:42 To: Jeff Newmiller; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? Hi, Jeff: That's what I needed. I clicked on the vignette I wanted and got the following: https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf Thanks, Spencer Graves On 2019-09-01 09:37, Jeff Newmiller wrote: > Wouldn't you just refer to [1] or one of the links mentioned there? > > [1] https://cran.r-project.org/package=bssm > > On September 1, 2019 7:22:43 AM PDT, Spencer Graves > wrote: >> Hello: >> >> >> How can I get a URL for a frame? >> >> >> Specifically, I want a URL that I can cite for the "bssm: >> Bayesian Inference of Non-linear and >> Non-Gaussian State Space Models in R" vignette in the bssm package on >> CRAN. If the package is installed, it's available there as >> "bssm.pdf". >> However, I want to include it in an RMarkdown vignette I'm writing, and >> >> I'd rather not force the reader to be on a computer with the package >> installed -- and force myself to figure out a way to find it in that >> case, if that can even be done. >> >> >> Thanks, >> Spencer Graves >> >> __ >> 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
I am not going to claim definitive knowledge, but my understanding of CRAN is that only the package URL that I copied from the page itself will remain if the package is archived. Thus, unless the package vignette has a non-CRAN permanent URL (e.g. arXiv) it may be safer in the long run to link through the main package URL. On September 1, 2019 8:13:22 AM PDT, Georgi Boshnakov wrote: >Correction: > >https://cran.r-project.org/package=bssm/vignettes/bssm.pdf > > >-Original Message- >From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On >Behalf Of Georgi Boshnakov >Sent: 01 September 2019 15:57 >To: Spencer Graves; Jeff Newmiller; r-package-devel@r-project.org >Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? > >It may be better to use the canonical url, >https://cran.r-project.org/package=bssm, as in: > >https://cran.r-project.org/package=bssm/bssm.pdf > >By the way, the vignettes for an installed package can be found by > >vignette(package="bssm") > >or > >help(package="bssm", help_type = "html") > >The latter has the advantage that it present links in a browser even if >by default the help is presented in text mode. > > >Georgi Boshnakov > > > >-Original Message- >From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On >Behalf Of Spencer Graves >Sent: 01 September 2019 15:42 >To: Jeff Newmiller; r-package-devel@r-project.org >Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? > >Hi, Jeff: > > > That's what I needed. I clicked on the vignette I wanted and got > >the following: > > >https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf > > > Thanks, > Spencer Graves > > >On 2019-09-01 09:37, Jeff Newmiller wrote: >> Wouldn't you just refer to [1] or one of the links mentioned there? >> >> [1] https://cran.r-project.org/package=bssm >> >> On September 1, 2019 7:22:43 AM PDT, Spencer Graves > wrote: >>> Hello: >>> >>> >>> How can I get a URL for a frame? >>> >>> >>> Specifically, I want a URL that I can cite for the "bssm: >>> Bayesian Inference of Non-linear and >>> Non-Gaussian State Space Models in R" vignette in the bssm package >on >>> CRAN. If the package is installed, it's available there as >>> "bssm.pdf". >>> However, I want to include it in an RMarkdown vignette I'm writing, >and >>> >>> I'd rather not force the reader to be on a computer with the package >>> installed -- and force myself to figure out a way to find it in that >>> case, if that can even be done. >>> >>> >>> Thanks, >>> Spencer Graves >>> >>> __ >>> 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 -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
What's the difference between https://cran.r-project.org/package=bssm/vignettes/bssm.pdf and https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf When I tried the former, it automatically changed to the latter. Is the former considered to be more stable? Thanks, Spencer On 2019-09-01 10:13, Georgi Boshnakov wrote: Correction: https://cran.r-project.org/package=bssm/vignettes/bssm.pdf -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Georgi Boshnakov Sent: 01 September 2019 15:57 To: Spencer Graves; Jeff Newmiller; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? It may be better to use the canonical url, https://cran.r-project.org/package=bssm, as in: https://cran.r-project.org/package=bssm/bssm.pdf By the way, the vignettes for an installed package can be found by vignette(package="bssm") or help(package="bssm", help_type = "html") The latter has the advantage that it present links in a browser even if by default the help is presented in text mode. Georgi Boshnakov -Original Message- From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On Behalf Of Spencer Graves Sent: 01 September 2019 15:42 To: Jeff Newmiller; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? Hi, Jeff: That's what I needed. I clicked on the vignette I wanted and got the following: https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf Thanks, Spencer Graves On 2019-09-01 09:37, Jeff Newmiller wrote: Wouldn't you just refer to [1] or one of the links mentioned there? [1] https://cran.r-project.org/package=bssm On September 1, 2019 7:22:43 AM PDT, Spencer Graves wrote: Hello: How can I get a URL for a frame? Specifically, I want a URL that I can cite for the "bssm: Bayesian Inference of Non-linear and Non-Gaussian State Space Models in R" vignette in the bssm package on CRAN. If the package is installed, it's available there as "bssm.pdf". However, I want to include it in an RMarkdown vignette I'm writing, and I'd rather not force the reader to be on a computer with the package installed -- and force myself to figure out a way to find it in that case, if that can even be done. Thanks, Spencer Graves __ 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
The link https://cran.r-project.org/package=bssm is stable (and given at the bottom of the CRAN page. Jeff is right that adding vignettes/bssm.pdf to it is not guaranteed in any way. GB -Original Message- From: Spencer Graves [mailto:spencer.gra...@effectivedefense.org] Sent: 01 September 2019 16:33 To: Georgi Boshnakov; Jeff Newmiller; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? What's the difference between https://cran.r-project.org/package=bssm/vignettes/bssm.pdf and https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf When I tried the former, it automatically changed to the latter. Is the former considered to be more stable? Thanks, Spencer On 2019-09-01 10:13, Georgi Boshnakov wrote: > Correction: > > https://cran.r-project.org/package=bssm/vignettes/bssm.pdf > > > -Original Message- > From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On > Behalf Of Georgi Boshnakov > Sent: 01 September 2019 15:57 > To: Spencer Graves; Jeff Newmiller; r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? > > It may be better to use the canonical url, > https://cran.r-project.org/package=bssm, as in: > > https://cran.r-project.org/package=bssm/bssm.pdf > > By the way, the vignettes for an installed package can be found by > > vignette(package="bssm") > > or > > help(package="bssm", help_type = "html") > > The latter has the advantage that it present links in a browser even if by > default the help is presented in text mode. > > > Georgi Boshnakov > > > > -Original Message- > From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On > Behalf Of Spencer Graves > Sent: 01 September 2019 15:42 > To: Jeff Newmiller; r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? > > Hi, Jeff: > > > That's what I needed. I clicked on the vignette I wanted and got > the following: > > > https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf > > > Thanks, > Spencer Graves > > > On 2019-09-01 09:37, Jeff Newmiller wrote: >> Wouldn't you just refer to [1] or one of the links mentioned there? >> >> [1] https://cran.r-project.org/package=bssm >> >> On September 1, 2019 7:22:43 AM PDT, Spencer Graves >> wrote: >>> Hello: >>> >>> >>> How can I get a URL for a frame? >>> >>> >>> Specifically, I want a URL that I can cite for the "bssm: >>> Bayesian Inference of Non-linear and >>> Non-Gaussian State Space Models in R" vignette in the bssm package on >>> CRAN. If the package is installed, it's available there as >>> "bssm.pdf". >>> However, I want to include it in an RMarkdown vignette I'm writing, and >>> >>> I'd rather not force the reader to be on a computer with the package >>> installed -- and force myself to figure out a way to find it in that >>> case, if that can even be done. >>> >>> >>> Thanks, >>> Spencer Graves >>> >>> __ >>> 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 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
On 01/09/2019 11:33 a.m., Spencer Graves wrote: What's the difference between https://cran.r-project.org/package=bssm/vignettes/bssm.pdf and https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf When I tried the former, it automatically changed to the latter. Is the former considered to be more stable? CRAN puts this on every package page: "Please use the canonical form https://CRAN.R-project.org/package= to link to this page." I think one of the checks will complain if it notices you give the link in a different form. I forget which URLs it checks. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
I don't know if [1] implies vignette persistence after archiving, but it might. I think it just has to fall back to a warning with an archive link to qualify. (Quite a slick trick if so because there can potentially be a parade of different package vignettes over time.) [1] https://stat.ethz.ch/pipermail/r-package-devel/2016q3/001100.html On September 1, 2019 8:49:52 AM PDT, Duncan Murdoch wrote: >On 01/09/2019 11:33 a.m., Spencer Graves wrote: >> What's the difference between >> >> >> https://cran.r-project.org/package=bssm/vignettes/bssm.pdf >> >> >> and >> >> >> https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf >> >> >> When I tried the former, it automatically changed to the >latter. >> Is the former considered to be more stable? > >CRAN puts this on every package page: > >"Please use the canonical form https://CRAN.R-project.org/package= >to link to this page." > >I think one of the checks will complain if it notices you give the link > >in a different form. I forget which URLs it checks. > >Duncan Murdoch -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] URL of a frame (or a vignette)?
I just learned that finding the package on "rdocumentation.org", then clicking on the vignette I want at the end of the page, "bssm.Rmd", gave me a URL that is portable, at least for the moment: https://www.rdocumentation.org/packages/bssm/versions/0.1.7/vignettes/bssm.Rmd This seems less likely to be trapped by CRAN checks unless it actually stops working ;-) Thanks to all who replied to my question. Spencer On 2019-09-01 10:49, Duncan Murdoch wrote: On 01/09/2019 11:33 a.m., Spencer Graves wrote: What's the difference between https://cran.r-project.org/package=bssm/vignettes/bssm.pdf and https://cran.r-project.org/web/packages/bssm/vignettes/bssm.pdf When I tried the former, it automatically changed to the latter. Is the former considered to be more stable? CRAN puts this on every package page: "Please use the canonical form https://CRAN.R-project.org/package= to link to this page." I think one of the checks will complain if it notices you give the link in a different form. I forget which URLs it checks. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R, BLAS, and FCLEN
On 2019-08-31 18:47, Göran Broström wrote: I'm having difficulties updating my package eha: When I run standard checks 'at home' everything is fine, but 'CRAN-submissions' reports (among other things): geomsup.f:324:9: warning: type of ‘dgemv’ does not match original declaration [-Wlto-type-mismatch] 324 | & one, score, ione) | ^ /home/tmp/R-d-gcc-LTO/include/R_ext/BLAS.h:107:1: note: type mismatch in parameter 12 107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n, | ^ This is odd since the LAPACK subroutine dgemv takes only 11 parameters. However, in include/R_ext/BLAS.h we have F77_NAME(dgemv)(const char *trans, const int *m, const int *n, const double *alpha, const double *a, const int *lda, const double *x, const int *incx, const double *beta, double *y, const int *incy FCLEN); with a 12th parameter FCLEN?? How am I supposed to fix this, and what the ... is FCLEN? googling leads to nothing useful (for me). It seems as if R is redefining some standard LAPACK routines. Also a note I do not understand (in this context): note: type ‘void’ should match type ‘long int’ Any help is much appreciated. Best, Göran PS. How can I trigger these Warnings 'at home'? See https://www.stats.ox.ac.uk/pub/bdr/LTO/README.txt (thanks to Uwe Ligges). Another relevant document seems to be (2019-05-15): https://developer.r-project.org/Blog/public/2019/05/15/gfortran-issues-with-lapack/index.html First sentence: "Recent version of the GNU Fortran compiler (7, 8, 9) include optimizations that break interoperability between C and Fortran code with BLAS/LAPACK." And later: "For the time being, everyone should use -fno-optimize-sibling-calls with GFortran version 7 and newer." G, __ 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
