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

[Martin Maechler]

>>>>> 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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