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

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

     >

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