Re: [R-pkg-devel] Fix non-ASCII characters in R packages
Thank you for the clarification, Uwe Ligges. best, Rafael Pereira On Mon, Dec 2, 2019 at 4:36 PM Uwe Ligges wrote: > OK, but this note did not lead to a rejection (and the mail we sent did > not even include the Note you apparently cited from the check.log) > > The actual issues are: > > >Found the following (possibly) invalid URLs: > URL: https://cran.r-project.org/web/packages/geobr/index.html >From: README.md > NEWS.md >Status: 200 >Message: OK >CRAN URL not in canonical form > > URL: > https://cran.r-project.org/web/packages/geobr/vignettes/intro_to_geobr.html >From: README.md >Status: 200 >Message: OK >CRAN URL not in canonical form > > The canonical URL of the CRAN page for a package is >https://CRAN.R-project.org/package=pkgname > > > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 > Check: for hidden files and directories, Result: NOTE >Found the following hidden files and directories: > .travis.yml >These were most likely included in error. See section 'Package >structure' in the 'Writing R Extensions' manual. > > > > Best, > Uwe Ligges > > > > > On 02.12.2019 18:46, Rafael Pereira wrote: > > Thanks for the heads up, Ivan. In any case, I’ll change the encoding of > the database. > > > > Uwe, I’m faxing this issue in the geobr package > > > > Rafael H.M. Pereira > > > > > >> On 2 Dec 2019, at 13:39, Uwe Ligges > wrote: > >> > >> > >> > >>> On 02.12.2019 15:29, peter dalgaard wrote: > >>> Dunno if it helps, but the NOTE is about "checking data", which, as > far as I can decipher the code, means that it is looking at datasets in the > data/ directory. So I suspect that looking at *.R files is not going to be > the right thing to do. > >>> -pd > On 2 Dec 2019, at 14:57 , Rafael Pereira > wrote: > > Hi all, > > I am trying to update my R package on CRAN but I am being requested > to fix > this NOTE: > > checking data for non-ASCII characters ... NOTE Note: found 58 marked > Latin-1 strings > >> > >> Have we really asked you to fix these? > >> Which packages is this? > >> > >> Best, > >> Uwe Ligges > >> > >> > >>> > I have used to code below to identify my scripts that have strings > using > non-ASCII characters. The problem is that in most cases these > non-ASCII > characters are used in the documentation of functions, so I cannot > simply > convert their encoding using iconv() for example > > # Find scripts using non-ASCII characters > f <- list.files(pattern = "*.R", recursive = T) > r <- lapply(f, tools::showNonASCIIfile) > > I've tried (1) reopening and (2) resaving those scripts with UTF-8 > encoding, (3) setting UTF-8 as the default encoding of the project, > but > nothing seems to fix this issue. Any suggestions? > > obs. I've posted this question on SO > > https://stackoverflow.com/questions/59139923/fix-non-ascii-characters-in-r-packages > > best, > > Rafael Pereira > > [[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
Re: [R-pkg-devel] Fix non-ASCII characters in R packages
OK, but this note did not lead to a rejection (and the mail we sent did not even include the Note you apparently cited from the check.log) The actual issues are: Found the following (possibly) invalid URLs: URL: https://cran.r-project.org/web/packages/geobr/index.html From: README.md NEWS.md Status: 200 Message: OK CRAN URL not in canonical form URL: https://cran.r-project.org/web/packages/geobr/vignettes/intro_to_geobr.html From: README.md Status: 200 Message: OK CRAN URL not in canonical form The canonical URL of the CRAN page for a package is https://CRAN.R-project.org/package=pkgname Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64 Check: for hidden files and directories, Result: NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. Best, Uwe Ligges On 02.12.2019 18:46, Rafael Pereira wrote: Thanks for the heads up, Ivan. In any case, I’ll change the encoding of the database. Uwe, I’m faxing this issue in the geobr package Rafael H.M. Pereira On 2 Dec 2019, at 13:39, Uwe Ligges wrote: On 02.12.2019 15:29, peter dalgaard wrote: Dunno if it helps, but the NOTE is about "checking data", which, as far as I can decipher the code, means that it is looking at datasets in the data/ directory. So I suspect that looking at *.R files is not going to be the right thing to do. -pd On 2 Dec 2019, at 14:57 , Rafael Pereira wrote: Hi all, I am trying to update my R package on CRAN but I am being requested to fix this NOTE: checking data for non-ASCII characters ... NOTE Note: found 58 marked Latin-1 strings Have we really asked you to fix these? Which packages is this? Best, Uwe Ligges I have used to code below to identify my scripts that have strings using non-ASCII characters. The problem is that in most cases these non-ASCII characters are used in the documentation of functions, so I cannot simply convert their encoding using iconv() for example # Find scripts using non-ASCII characters f <- list.files(pattern = "*.R", recursive = T) r <- lapply(f, tools::showNonASCIIfile) I've tried (1) reopening and (2) resaving those scripts with UTF-8 encoding, (3) setting UTF-8 as the default encoding of the project, but nothing seems to fix this issue. Any suggestions? obs. I've posted this question on SO https://stackoverflow.com/questions/59139923/fix-non-ascii-characters-in-r-packages best, Rafael Pereira [[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
Re: [R-pkg-devel] Fix non-ASCII characters in R packages
Thanks for the heads up, Ivan. In any case, I’ll change the encoding of the database. Uwe, I’m faxing this issue in the geobr package Rafael H.M. Pereira > On 2 Dec 2019, at 13:39, Uwe Ligges wrote: > > > >> On 02.12.2019 15:29, peter dalgaard wrote: >> Dunno if it helps, but the NOTE is about "checking data", which, as far as I >> can decipher the code, means that it is looking at datasets in the data/ >> directory. So I suspect that looking at *.R files is not going to be the >> right thing to do. >> -pd >>> On 2 Dec 2019, at 14:57 , Rafael Pereira wrote: >>> >>> Hi all, >>> >>> I am trying to update my R package on CRAN but I am being requested to fix >>> this NOTE: >>> >>> checking data for non-ASCII characters ... NOTE Note: found 58 marked >>> Latin-1 strings > > Have we really asked you to fix these? > Which packages is this? > > Best, > Uwe Ligges > > >> >>> I have used to code below to identify my scripts that have strings using >>> non-ASCII characters. The problem is that in most cases these non-ASCII >>> characters are used in the documentation of functions, so I cannot simply >>> convert their encoding using iconv() for example >>> >>> # Find scripts using non-ASCII characters >>> f <- list.files(pattern = "*.R", recursive = T) >>> r <- lapply(f, tools::showNonASCIIfile) >>> >>> I've tried (1) reopening and (2) resaving those scripts with UTF-8 >>> encoding, (3) setting UTF-8 as the default encoding of the project, but >>> nothing seems to fix this issue. Any suggestions? >>> >>> obs. I've posted this question on SO >>> https://stackoverflow.com/questions/59139923/fix-non-ascii-characters-in-r-packages >>> >>> best, >>> >>> Rafael Pereira >>> >>>[[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
Re: [R-pkg-devel] Fix non-ASCII characters in R packages
On 02.12.2019 15:29, peter dalgaard wrote: Dunno if it helps, but the NOTE is about "checking data", which, as far as I can decipher the code, means that it is looking at datasets in the data/ directory. So I suspect that looking at *.R files is not going to be the right thing to do. -pd On 2 Dec 2019, at 14:57 , Rafael Pereira wrote: Hi all, I am trying to update my R package on CRAN but I am being requested to fix this NOTE: checking data for non-ASCII characters ... NOTE Note: found 58 marked Latin-1 strings Have we really asked you to fix these? Which packages is this? Best, Uwe Ligges I have used to code below to identify my scripts that have strings using non-ASCII characters. The problem is that in most cases these non-ASCII characters are used in the documentation of functions, so I cannot simply convert their encoding using iconv() for example # Find scripts using non-ASCII characters f <- list.files(pattern = "*.R", recursive = T) r <- lapply(f, tools::showNonASCIIfile) I've tried (1) reopening and (2) resaving those scripts with UTF-8 encoding, (3) setting UTF-8 as the default encoding of the project, but nothing seems to fix this issue. Any suggestions? obs. I've posted this question on SO https://stackoverflow.com/questions/59139923/fix-non-ascii-characters-in-r-packages best, Rafael Pereira [[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
Re: [R-pkg-devel] Compiler warning using C versions of base R integrate function
Thank you, Tomas, that is very helpful. On Thu, Nov 28, 2019 at 4:41 AM Tomas Kalibera wrote: > On 11/21/19 7:25 PM, Devin Incerti wrote: > > Hi, > > > > I'm attempting to submit a very minor update to my package where I > replaced > > a deprecated C++ function with an alternative. However, I'm receiving an > > unrelated warning "*array subscript -1 is outside array bounds of ‘double > > [52]’ [-Warray-bounds] *" on Debian during the CRAN pre-tests. I do not > > receive this warning on my local OS X, Ubuntu 16.04 (on Travis-CI), with > > Win-builder, or with R-hub builder. I also did not receive this warning > on > > previous submissions to CRAN, but it does now show up on the most recent > CRAN > > checks > > < > http://s.bl-1.com/h/cH9zB21r?url=https://cran.r-project.org/web/checks/check_results_hesim.html > > > > . > > > > The warning is related to the header file integrate.h > > < > http://s.bl-1.com/h/cH9zB6Qt?url=https://github.com/hesim-dev/hesim/blob/master/inst/include/hesim/Rbase/integrate.h > >, > > which is just integrate.c > > < > http://s.bl-1.com/h/cH9zBCpw?url=https://github.com/wch/r-source/blob/5a156a0865362bb8381dcd69ac335f5174a4f60c/src/appl/integrate.c > > > > from > > R source with function pointers replaced by C++ functors. These > integration > > functions are needed so that the package can integrate at the C++ level. > > > > I don't know how to avoid this warning. Is it perhaps related to the > > particular version of GCC used during the CRAN checks. Any thoughts or > > suggestions would be much appreciated. > > > > Thank you! > > The warning is generated by GCC when inlining the function rdqelg(), I > can reproduce it with the integrate.c we have in R, but only if I add > "inline" to rdqelg() definition (GCC 6 and newer - on Ubuntu but that > should not matter). The inliner knows the callsite, so it knows that > what is being passed is an array (and not an arbitrary pointer), and > hence it emits the warning. It is not smart enough to know that the > first element of the new "array" will (unless there is a bug) never be > used. When not inlining and the function is compiled independently from > its callsites, it assumes it is a pointer, and hence there is no warning. > > The code is automatically converted from Fortran, maybe these pointer > decrements in function prologues are to adjust to Fortran 1-based array > indexing. If you must use this modified copy of integrate.c from R, > perhaps a quick hack to get rid of the warning would be to avoid the > "inline" keywords in declarations of functions like rdqelg(). In a > perfect world, the code would be rewritten to more idiomatic C (not just > to avoid these decrements). Or perhaps the Fortran original could be used. > > Tomas > > > () > > > > Devin > > > > [[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
Re: [R-pkg-devel] Fix non-ASCII characters in R packages
On Mon, 2 Dec 2019 10:57:51 -0300
Rafael Pereira wrote:
> checking data for non-ASCII characters ... NOTE Note: found 58 marked
> Latin-1 strings
>
> I have used to code below to identify my scripts that have strings
> using non-ASCII characters.
I don't think it's about non-ASCII in source code; it's about Latin-1
strings in the package data:
git clone https://github.com/ipeaGIT/geobr
cd geobr/data
R
load('grid_state_correspondence_table.RData')
sum(
unlist(
lapply(grid_state_correspondence_table, Encoding)
) == 'latin1'
)
# [1] 58
What I'm not sure of is *how* this NOTE should be fixed. "Writing R
extensions" §1.6.3 provides advice on UTF-8 strings in the R code, not
data; §5.15 only says that strings *could* be marked as Latin-1 or
UTF-8 (but doesn't say what *should* be done); finally,
tools:::.check_package_datasets seems to produce NOTEs about Latin-1,
UTF-8 and strings marked as bytes.
--
Best regards,
Ivan
__
R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] Fix non-ASCII characters in R packages
Dunno if it helps, but the NOTE is about "checking data", which, as far as I can decipher the code, means that it is looking at datasets in the data/ directory. So I suspect that looking at *.R files is not going to be the right thing to do. -pd > On 2 Dec 2019, at 14:57 , Rafael Pereira wrote: > > Hi all, > > I am trying to update my R package on CRAN but I am being requested to fix > this NOTE: > > checking data for non-ASCII characters ... NOTE Note: found 58 marked > Latin-1 strings > > I have used to code below to identify my scripts that have strings using > non-ASCII characters. The problem is that in most cases these non-ASCII > characters are used in the documentation of functions, so I cannot simply > convert their encoding using iconv() for example > > # Find scripts using non-ASCII characters > f <- list.files(pattern = "*.R", recursive = T) > r <- lapply(f, tools::showNonASCIIfile) > > I've tried (1) reopening and (2) resaving those scripts with UTF-8 > encoding, (3) setting UTF-8 as the default encoding of the project, but > nothing seems to fix this issue. Any suggestions? > > obs. I've posted this question on SO > https://stackoverflow.com/questions/59139923/fix-non-ascii-characters-in-r-packages > > best, > > Rafael Pereira > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Fix non-ASCII characters in R packages
Hi all, I am trying to update my R package on CRAN but I am being requested to fix this NOTE: checking data for non-ASCII characters ... NOTE Note: found 58 marked Latin-1 strings I have used to code below to identify my scripts that have strings using non-ASCII characters. The problem is that in most cases these non-ASCII characters are used in the documentation of functions, so I cannot simply convert their encoding using iconv() for example # Find scripts using non-ASCII characters f <- list.files(pattern = "*.R", recursive = T) r <- lapply(f, tools::showNonASCIIfile) I've tried (1) reopening and (2) resaving those scripts with UTF-8 encoding, (3) setting UTF-8 as the default encoding of the project, but nothing seems to fix this issue. Any suggestions? obs. I've posted this question on SO https://stackoverflow.com/questions/59139923/fix-non-ascii-characters-in-r-packages best, Rafael Pereira [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
