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

[Duncan Murdoch]

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]]
> 
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