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

peter dalgaard pd@|gd @end|ng |rom gm@||@com
Wed May 13 15:34:31 CEST 2020 

Hmm, like Eberhard, I'm not too sure this is right.

A look at ls -l /usr/local/bin should be informative though.

I haven't been paying that close attention, but I think the history is that TeX programs used to live in /usr/local/bin, but then Apple did something(?) so now they go to Library/TeX/texbin (and are really links that via several levels of indirection end up somewhere in /usr/local/texlive). However, old installs may still have binaries or links in /usr/local/bin. I would guess that a simple

sudo rm /usr/local/bin/pdflatex

could work (possibly remove some other  *tex programs as well).

-pd

> On 13 May 2020, at 14:16 , Marc Schwartz <marc_schwartz using me.com> wrote:
> 
> 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
> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com

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