[R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?

Marc Schwartz m@rc_@chw@rtz @end|ng |rom me@com
Wed May 13 14:16:12 CEST 2020 

Spencer,

FWIW, this may be a situation where you need to remove your current/older installations of TeXLive and start fresh with a clean install of TeXLive 2020. It is possible that there is some conflict or corruption of the current multiple installations.

That 'which pdflatex' is pointing directly to an executable in /usr/local/bin, rather than to a symlink in the TeXLive tree, suggests that there is something amiss with your installation.

There are two primary folder trees that would need to be removed:

  /Library/TeX

and 

  /usr/local/texlive

The former path will show in Finder, but the latter will not, unless you have hidden folders set to show. If not, then you can use the Finder menu option:

  Go -> Go to Folder

and enter:

  /usr/local

That will then show you the texlive folder, which you can then right click on and delete.

Both folder trees will require your Admin password to delete.

Once you do this, if you elect to do so, you will then need to re-install TeXLive 2020 and hopefully start fresh.

Regards,

Marc Schwartz


> On May 13, 2020, at 7:00 AM, Spencer Graves <spencer.graves using prodsyse.com> wrote:
> 
> Hi, Peter et al.:
> 
> 
>       It looks like you've properly diagnosed my problem.  How do I fix it?
> 
> 
>       "which pdflatex" and "echo $PATH" are as follows:
> 
> 
> $ which pdflatex
> /usr/local/bin/pdflatex
> 
> 
> $ echo $PATH
> /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin
> 
> 
>       I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but "which pdflatex" doesn't find it.
> 
> 
>       Thanks,
>       Spencer Graves
> 
> 
> On 2020-05-13 01:31, peter dalgaard wrote:
>> You typically need to ensure that you have the right TeX installation in your PATH (and not an older one earlier in the path). You should see something like this
>> 
>> Peters-MacBook-Air:BUILD pd$ which pdflatex
>> /Library/TeX/texbin/pdflatex
>> Peters-MacBook-Air:BUILD pd$ pdflatex -version
>> pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019)
>> kpathsea version 6.3.1
>> ....
>> Peters-MacBook-Air:BUILD pd$ echo $PATH
>> /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin
>> 
>> (Notice that if I had older TeX stuff in /usr/local, I could be in similar trouble...)
>> 
>> -pd
>> 
>> 
>>> On 13 May 2020, at 06:15 , Spencer Graves <spencer.graves using prodsyse.com> wrote:
>>> 
>>> Hi, Ken et al.:
>>> 
>>> 
>>>       Thanks for the info.  I tried to do what you suggested but still have the problem.
>>> 
>>> 
>>>       Specifically, a web search for TexLive 2020 led me to "https://tug.org/texlive/".  That invited me to download and install MacTex 2020 from "https://tug.org/mactex/mactex-download.html", which I did.   Everything seemed to go smoothly, but when I ran "R CMD build Ecfun" and "R CMD check Ecfun_0.2-4.tar.gz", I got the same error.  This is running those commands in a Terminal.  When I invoked "r" there just now and requested "sessionInfo()", I got the following:
>>> 
>>> 
>>> R version 4.0.0 (2020-04-24)
>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>> Running under: macOS Catalina 10.15.4
>>> 
>>> Matrix products: default
>>> BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>>> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>>> 
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>> 
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods base
>>> 
>>> loaded via a namespace (and not attached):
>>> [1] compiler_4.0.0
>>> 
>>> 
>>>       Might you have other suggestions?
>>> 
>>> 
>>>       Thanks very much for eliminating one possible source of this problem.
>>> 
>>> 
>>>       Spencer Graves
>>> 
>>> 
>>> On 2020-05-12 20:12, Ken Beath wrote:
>>>> Your package passes checks on my machine perfectly. It has R 4.0.0 with RStudio and TexLive 2020 with updates to a week or two ago.
>>>> 
>>>> Ken
>>>> 
>>>>> On 13 May 2020, at 8:17 am, Spencer Graves<spencer.graves using prodsyse.com>  wrote:
>>>>> 
>>>>> Hello, All:
>>>>> 
>>>>> 
>>>>>       Might "R CMD check" on Mac use obsolete LaTeX software?
>>>>> 
>>>>> 
>>>>>       I ask, because "R CMD check" on my Mac started reporting LaTeX
>>>>> errors on *.Rd files that previously passed "R CMD check" without
>>>>> problems.  Dirk Eddelbuettel recommended I ask tex.stackexchange about
>>>>> that.  I did that and got the following:
>>>>> 
>>>>> 
>>>>>             * "In a current tex system \textasciigrave should work with
>>>>> your families - they don't have the glyph but latex will fall back
>>>>> without error. In older systems it could give an error."
>>>>> 
>>>>> 
>>>>> See:
>>>>> 
>>>>> 
>>>>> https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
>>>>> 
>>>>> 
>>>>>       Comments?
>>>>>       Thanks,
>>>>>       Spencer Graves
>>>>> 
>>>>> 
>>>>> p.s.  An earlier post on this issue to r-pkg-devel is copied below.
>>>>> 
>>>>> 
>>>>> -------- Forwarded Message --------
>>>>> Subject: 	[R-pkg-devel] Error: Symbol \textasciigrave not provided by
>>>>> (textcomp)
>>>>> Date: 	Sun, 16 Feb 2020 14:21:17 -0600
>>>>> From: 	Spencer Graves<spencer.graves using effectivedefense.org>
>>>>> To: 	r-package-devel using r-project.org
>>>>> 
>>>>> 
>>>>> 
>>>>> Hello, All:
>>>>> 
>>>>> 
>>>>>       "R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the
>>>>> following:
>>>>> 
>>>>> 
>>>>> ! Package textcomp Error: Symbol \textasciigrave not provided by
>>>>> (textcomp)                font family zi4 in TS1 encoding.
>>>>> (textcomp)                Default family used instead.
>>>>> 
>>>>> See the textcomp package documentation for explanation.
>>>>> * checking PDF version of manual without hyperrefs or index ... ERROR
>>>>> * DONE
>>>>> 
>>>>> 
>>>>>       This is using R 3.6.2 under macOS 10.15.3 applied to the current
>>>>> development version of"https://github.com/sbgraves237/Ecfun".  Travis
>>>>> CI reported that the build passed;  see
>>>>> "https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification&utm_source=email".
>>>>> 
>>>>> 
>>>>> 
>>>>>       This looks to me like it's complaining about the use of the back
>>>>> tick character ("`", below "~" on the top left key on a standard
>>>>> American English keyboard), which I assume is equivalent to
>>>>> "\textasciigrave" in certain contexts.
>>>>> 
>>>>> 
>>>>>       Six out of those 8 repetitions occur in the examples sections of
>>>>> files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and
>>>>> "subNonStandardNames.Rd". Those functions were written to fix parsing
>>>>> errors with names like "Raúl" that had been mangled by different
>>>>> software before I could get it into R.
>>>>> 
>>>>> 
>>>>>       After a day's work failed to produce a work around, I decided to
>>>>> ask this group.
>>>>> 
>>>>> 
>>>>>       What do you suggest?
>>>>>       Thanks,
>>>>>       Spencer Graves

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