[R-pkg-devel] a problem with the underscore in a R function document

Yaoyong Li ||y@oyong85 @end|ng |rom gm@||@com
Mon Jun 13 12:57:02 CEST 2022


Dear Martin and Duncan,

Thank you very much indeed for the help. I have adopted both your
suggestions. Using Martin's suggestion has made the Notes concerning the
underscores disappear, and hopefully using Duncan's suggestion will result
in less trouble in the future.

I really appreciate the rapid responses to my question in the list.

Best regards,
Yaoyong

On Sat, Jun 11, 2022 at 1:38 PM Duncan Murdoch <murdoch.duncan using gmail.com>
wrote:

> As Martin said, just remove the \.
>
> The other thing I'd do is use \sQuote{_AAseq.txt.gz} instead of entering
> the quotes yourself.  Then you don't need to worry about the difference
> between plain quotes and directional quotes, R will use whichever is
> appropriate.
>
> Duncan Murdoch
>
> On 11/06/2022 8:29 a.m., Martin Maechler wrote:
> >>>>>> Yaoyong Li
> >>>>>>      on Sat, 11 Jun 2022 12:29:25 +0100 writes:
> >
> >      > Hello,
> >
> >      > I just got a problem in a function document in a package I
> developed.The
> >      > file containing the document is generatingCDSaaFile.Rd. The
> problem is
> >      > related to the underscore I used in the following sentence
> >
> >      > and the last part is ‘\_AAseq.txt.gz’
> >
> >      > I got a 'note' message when the package was checked in the CRAN:
> >
> >      > checkRd: (-1) generatingCDSaaFile.Rd:72: Escaped LaTeX specials:
> \_
> >
> >      > I don't think I saw this kind of message in the past (say six
> months
> >      > ago).
> >
> > Yes, you are right.. this is quite new.  Some of my
> > <pkg>/man/*.Rd  files have been affected similarly.
> >
> > AFAIK there is a history behind, where the   Rd -> LaTeX
> > translation code was partly buggy  for quite a long time, and hence
> > such  `\`-escapes where necessary in *.Rd such that the produced
> > *.tex was LaTeX-able.
> >
> > However, these Rd2latex bugs/problems have been fixed and now
> > almost all such \-escapes are not only unneeded but actually the
> > `\` become visible, hence ugly looking
> > ==> hence the NOTE.
> >
> >      > A copy of the check result in CRAN is appended below. As you can
> >      > see, I also got the same problem in other places in the document.
> I
> >      > have been trying to fix the problem via searching Google. I have
> tried
> >      > to replace "\_" with "\textunderscore " as some internet post
> >      > suggested, but this did not solve the problem.
> >
> >      > So I just wonder if anyone can help me with the problem. Please
> let me
> >      > know if any more information is needed.
> >
> > In all cases in my packages,  just removing the `\` (or
> > sometimes `\\` ?)  was perfect, so I think you can and should do
> > just that.
> >
> > Best,
> > Martin
> >
> >
> >      > Best regards,
> >
> >      > Yaoyong
> >
> >      > #####################################################
> >
> >      > CRAN Package Check Results for Package geno2proteo
> >      > <https://cran.r-project.org/web/packages/geno2proteo/index.html>
> >
> >      > Last updated on 2022-06-11 11:52:26 CEST.
> >      > FlavorVersionTinstallTcheckTtotalStatusFlags
> >      > r-devel-linux-x86_64-debian-clang
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-clang
> >
> >      > 0.0.5 17.31 170.54 187.85 NOTE
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/geno2proteo-00check.html
> >
> >      > r-devel-linux-x86_64-debian-gcc
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-debian-gcc
> >
> >      > 0.0.5 12.00 130.58 142.58 NOTE
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/geno2proteo-00check.html
> >
> >      > r-devel-linux-x86_64-fedora-clang
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-fedora-clang
> >
> >      > 0.0.5 220.04 NOTE
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/geno2proteo-00check.html
> >
> >      > r-devel-linux-x86_64-fedora-gcc
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-devel-linux-x86_64-fedora-gcc
> >
> >      > 0.0.5 229.54 NOTE
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/geno2proteo-00check.html
> >
> >      > r-devel-windows-x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-devel-windows-x86_64
> >
> >      > 0.0.5 242.00 470.00 712.00 NOTE
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/geno2proteo-00check.html
> >
> >      > r-patched-linux-x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-patched-linux-x86_64
> >
> >      > 0.0.5 12.58 164.99 177.57 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-patched-linux-x86_64/geno2proteo-00check.html
> >
> >      > r-release-linux-x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-release-linux-x86_64
> >
> >      > 0.0.5 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-release-linux-x86_64/geno2proteo-00check.html
> >
> >      > r-release-macos-arm64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-release-macos-arm64
> >
> >      > 0.0.5 65.00 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/geno2proteo-00check.html
> >
> >      > r-release-macos-x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-release-macos-x86_64
> >
> >      > 0.0.5 89.00 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/geno2proteo-00check.html
> >
> >      > r-release-windows-x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-release-windows-x86_64
> >
> >      > 0.0.5 195.00 363.00 558.00 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-release-windows-x86_64/geno2proteo-00check.html
> >
> >      > r-oldrel-macos-arm64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-oldrel-macos-arm64
> >
> >      > 0.0.5 57.00 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-oldrel-macos-arm64/geno2proteo-00check.html
> >
> >      > r-oldrel-macos-x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-oldrel-macos-x86_64
> >
> >      > 0.0.5 84.00 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-oldrel-macos-x86_64/geno2proteo-00check.html
> >
> >      > r-oldrel-windows-ix86+x86_64
> >      > <
> https://cran.r-project.org/web/checks/check_flavors.html#r-oldrel-windows-ix86_x86_64
> >
> >      > 0.0.5 32.00 145.00 177.00 OK
> >      > <
> https://www.r-project.org/nosvn/R.check/r-oldrel-windows-ix86+x86_64/geno2proteo-00check.html
> >
> >      > Check
> >      > Details
> >
> >      > Version: 0.0.5
> >      > Check: Rd files
> >      > Result: NOTE
> >      > checkRd: (-1) generatingCDSaaFile.Rd:23: Escaped LaTeX specials:
> \_ \_
> >      > checkRd: (-1) generatingCDSaaFile.Rd:72: Escaped LaTeX specials:
> \_
> >
> >      > Flavors: r-devel-linux-x86_64-debian-clang
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/geno2proteo-00check.html
> >,
> >      > r-devel-linux-x86_64-debian-gcc
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/geno2proteo-00check.html
> >,
> >      > r-devel-linux-x86_64-fedora-clang
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/geno2proteo-00check.html
> >,
> >      > r-devel-linux-x86_64-fedora-gcc
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/geno2proteo-00check.html
> >,
> >      > r-devel-windows-x86_64
> >      > <
> https://www.r-project.org/nosvn/R.check/r-devel-windows-x86_64/geno2proteo-00check.html
> >
> >
> >      >
> ##########################################################################
> >
> >      > [[alternative HTML version deleted]]
> >
> >      > ______________________________________________
> >      > R-package-devel using r-project.org mailing list
> >      > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
> > ______________________________________________
> > R-package-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>

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