[Rd] data.frame could handle long vectors
Dear R-devel,
It seems that data.frame class could be improved to handle long
vectors better. It fails while using `data.frame(.)` and the same
using, I believe, lower overhead, `as.data.frame(list(.)). Please find
reproducible example below, tested on 2019-12-01 r77492.
id1 = sample.int(3e9, replace=TRUE)
v1 = runif(3e9)
df = data.frame(id1=id1, v1=v1)
#Error in if (mirn && nrows[i] > 0L) { :
# missing value where TRUE/FALSE needed
#In addition: Warning message:
#In attributes(.Data) <- c(attributes(.Data), attrib) :
# NAs introduced by coercion to integer range
df = as.data.frame(list(id1=id1, v1=v1))
#Error in if (mirn && nrows[i] > 0L) { :
# missing value where TRUE/FALSE needed
#In addition: Warning message:
#In attributes(.Data) <- c(attributes(.Data), attrib) :
# NAs introduced by coercion to integer range
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Re: [Bioc-devel] Error in Vignette of package
Thanks for that insight, we'll try to solve the issue with BiocStyle. Martin On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay" wrote: I’ve been getting the exact same error for compiling the Rmarkdown vignettes in my own package. Some partial testing before the weekend revealed that in my case the error could be circumvented simply by not using output: BiocStyle::pdf_document but instead output: pdf_document in the yaml header. I’m not quite sure why, but when BiocStyle is used some of the latex code for code highlighting is repeated, leading to the 'already defined' error. I’ve not updated my package since before this error started. BT > Le 30 nov. 2019 à 10:25, Ioannis Vardaxis a écrit : > > Hey, > > I am trying to build my package Vegnette and I get the following error: > > ! LaTeX Error: Command \VerbBar already defined. > Or name \end... illegal, see p.192 of the manual. > > I tried to find what this means with no luck. > > Best, > Ioannis > > > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[R-pkg-devel] check_win_release cannot find tidyr and other common packages?
Hi! I am preparing an R package to be uploaded to CRAN. I have already checked using rhub and every check passed. I have also checked using winbuilder for the release version of R (devtools:check_win_release) and there were no ERRORs or WARNINGs. However, for the devel version (devtools:check_win_devel) I got the following error: checking package dependencies ... ERROR Packages required but not available: 'tidyr', 'googlesheets', 'stringr', 'readtext' Package suggested but not available for checking: 'knitr' VignetteBuilder package required for checking but not installed: 'knitr' See section 'The DESCRIPTION file' in the 'Writing R Extensions' manual. I would really appreciate some help to figure out what's going on. This is the relevant part of my DESCRIPTION file: Imports: XML (>= 3.98), purrr (>= 0.2.4), dplyr (>= 0.7.8), tibble (>= 2.0.0), tidyr (>= 0.7.2), rlang (>= 0.3.0.1), googlesheets (>= 0.3.0), stringr (>= 1.4.0), readxl (>= 1.3.1), readtext (>= 0.7.1), zip (>= 2.0.4), xml2 (>= 1.2.0), rjson (>= 0.2.20), shiny (>= 1.3.2), tools (>= 3.5.3), utils (>= 3.5.3), R.utils (>= 2.9.0) Suggests: knitr (>= 1.9), rmarkdown (>= 1.12), testthat VignetteBuilder: knitr Report from win_builder: https://win-builder.r-project.org/EYkQRkLpS8oa/00check.log Thanks! Alberto [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] how to change from -fsanitize=undefined to -fsanitize=address
Good to know. I will pass it on to Dan. He said a few times that he wasn't an expert on this :). Thanks! Youyi On Sun, Dec 1, 2019 at 6:01 AM Dirk Eddelbuettel wrote: > > On 30 November 2019 at 23:24, Youyi Fong wrote: > | Here is a solution worked out by the wonderful staff from our scientific > | computing support team at the Fred Hutchinson Cancer Research Center. I > | really don't know how Dan did it, but the way he explained to me was that > | he came across this github repository by Dirk: > | https://github.com/rocker-org/r-devel-san-clang. There was the Docker > file > | which built the clang-san image, but he did not find the image itself in > | Docker Hub. So he built it himself and pushed it as > > It lives with all the other Rocker containers here: > > https://hub.docker.com/repository/docker/rocker/r-devel-ubsan-clang > > There is a minor 'san at GitHub, ubsan at Docker' labeling issue but you or > Dan could have asked, and the Docker tag clearly links back to > > https://github.com/rocker-org/r-devel-san-clang > > which is where you started from. Anyway, glad to know it helped! > > Dirk > > -- > http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Bioc-devel] Error in Vignette of package
Not using BiocStyle::pdf_document means you can’t use the helpers/macros.
Try this in a fresh interactive session:
library(BiocStyle)
rmarkdown::render("yourvignette.Rmd")
This should make the helpers/macros available. It won’t fix the issue
for passing R CMD check, but at least it’ll confirm what the issue is and
thus you’ll know to wait for BiocStyle to update.
BT
> Le 1 déc. 2019 à 10:47, Ioannis Vardaxis a écrit :
>
> Thanks for the answer. However replacing it resulted in another error for me:
>
> Quitting from lines 2-41 (MACPET.Rmd)
> Error in doc_date() : could not find function "doc_date"
> Calls: ... inline_exec -> hook_eval -> withVisible -> eval -> eval
> Execution halted
>
> Should I wait until BiocStyle is updated?
>
> Best,
> Ioannis
>
> Fra: Martin Morgan
> Sendt: søndag 1. desember 2019 11:51
> Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis
>
> Kopi: bioc-devel@r-project.org
> Emne: Re: [Bioc-devel] Error in Vignette of package
>
> Thanks for that insight, we'll try to solve the issue with BiocStyle.
>
> Martin
>
> On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay"
> wrote:
>
> I’ve been getting the exact same error for compiling the Rmarkdown
> vignettes in my own package. Some partial testing before the weekend
> revealed that in my case the error could be circumvented simply by not
> using
>
> output: BiocStyle::pdf_document
>
> but instead
>
> output: pdf_document
>
> in the yaml header. I’m not quite sure why, but when BiocStyle is used
> some of the latex code for code highlighting is repeated, leading to the
> 'already defined' error. I’ve not updated my package since before this
> error started.
>
> BT
>
> > Le 30 nov. 2019 à 10:25, Ioannis Vardaxis a écrit :
> >
> > Hey,
> >
> > I am trying to build my package Vegnette and I get the following error:
> >
> > ! LaTeX Error: Command \VerbBar already defined.
> > Or name \end... illegal, see p.192 of the manual.
> >
> > I tried to find what this means with no luck.
> >
> > Best,
> > Ioannis
> >
> >
> >[[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in Vignette of package
Thanks for the answer. However replacing it resulted in another error for me: Quitting from lines 2-41 (MACPET.Rmd) Error in doc_date() : could not find function "doc_date" Calls: ... inline_exec -> hook_eval -> withVisible -> eval -> eval Execution halted Should I wait until BiocStyle is updated? Best, Ioannis Fra: Martin Morgan Sendt: søndag 1. desember 2019 11:51 Til: Benjamin Jean-Marie Tremblay ; Ioannis Vardaxis Kopi: bioc-devel@r-project.org Emne: Re: [Bioc-devel] Error in Vignette of package Thanks for that insight, we'll try to solve the issue with BiocStyle. Martin On 12/1/19, 1:32 AM, "Bioc-devel on behalf of Benjamin Jean-Marie Tremblay" wrote: I’ve been getting the exact same error for compiling the Rmarkdown vignettes in my own package. Some partial testing before the weekend revealed that in my case the error could be circumvented simply by not using output: BiocStyle::pdf_document but instead output: pdf_document in the yaml header. I’m not quite sure why, but when BiocStyle is used some of the latex code for code highlighting is repeated, leading to the 'already defined' error. I’ve not updated my package since before this error started. BT > Le 30 nov. 2019 à 10:25, Ioannis Vardaxis a écrit : > > Hey, > > I am trying to build my package Vegnette and I get the following error: > > ! LaTeX Error: Command \VerbBar already defined. > Or name \end... illegal, see p.192 of the manual. > > I tried to find what this means with no luck. > > Best, > Ioannis > > >[[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [R-pkg-devel] how to change from -fsanitize=undefined to -fsanitize=address
On 30 November 2019 at 23:24, Youyi Fong wrote: | Here is a solution worked out by the wonderful staff from our scientific | computing support team at the Fred Hutchinson Cancer Research Center. I | really don't know how Dan did it, but the way he explained to me was that | he came across this github repository by Dirk: | https://github.com/rocker-org/r-devel-san-clang. There was the Docker file | which built the clang-san image, but he did not find the image itself in | Docker Hub. So he built it himself and pushed it as It lives with all the other Rocker containers here: https://hub.docker.com/repository/docker/rocker/r-devel-ubsan-clang There is a minor 'san at GitHub, ubsan at Docker' labeling issue but you or Dan could have asked, and the Docker tag clearly links back to https://github.com/rocker-org/r-devel-san-clang which is where you started from. Anyway, glad to know it helped! Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error
Where can I find the current tex compiler / pandocs setup on CRAN check systems so I can adjust my CI, to replicate the failure? On Sat, Nov 30, 2019 at 11:45 AM Yoni wrote: > Thank you for the clarification regarding roxygen2, it does look like a > confounding issue. > > I will try to resolve the paths in the tex. > > Thank you for the help. > > On Sat, Nov 30, 2019 at 11:39 AM Iñaki Ucar > wrote: > >> >> >> El sáb., 30 nov. 2019 16:22, Yoni escribió: >> >>> Thank you for the clarification. >>> >>> I am then more confused. >>> >>> The CRAN version of the package (texPreview) has been unchanged since Oct >>> 23, at which point it was passing the checks with no errors. >>> >> >> If your package is sitting on CRAN since then, and in fact I see in your >> DESCRIPTION that you generated the docs with roxygen2 6.1.1, then the >> roxygen2 update has nothing to do with your check error. You run roxygen2; >> CRAN doesn't. >> >> Iñaki >> > > > -- > Yoni > > You do not learn to swim from books and lectures on the theory of buoyancy > (Box 1990) > -- Yoni You do not learn to swim from books and lectures on the theory of buoyancy (Box 1990) [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
