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

[Dr Eberhard W Lisse]

Spencer,

If you just google

	https://www.google.com/search?q=uninstallpkg

the first link coming up is the right one.  But see below.


Do you have a ~/Downloads directory?  Did you look in there?


So the removing of /usr/local/bin/pdflatex did not remove the old 2019
version.  Which is why I proposed uninstallPKG to get rid of all the old
crud.

To be honest, I reckon you should run TimeMachine and then re-install
Catalina after reformatting your hard disk, restore your home directory
and then carefully (step by step) install the Xcode Command Lime Tools,
homebrew, MacTeX and R, which will give you a known state.

I like to have a consistent, known state, with only one (the latest if
possible) version of everything and if possible via the Software Update
or a package manager (homebrew).


homebrew has what is called Casks, which installs proper MacApps (often
from the original developers’ site).  I check regularly whether there
are (new) casks for apps I have manually installed which I then install
(overwrite) so a

	brew upgrade
	brew cask upgrade

will sort me out

btw, I just looked and

	brew cask install uninstallpkg

will do the deed nicely.

el

On 2020-05-13 23:31 , Spencer Graves wrote:
>       Thank you all for your comments on this.  I'm overwhelmed, not
> just with the volume of the discussion, but my own ignorance of the
> standard command line protocols.
>
>
>       After trying some but on all of Eberhard Lisse's and Peter
> Dalgaard's suggestions below, the problem disappeard after I executed
> "sudo rm /usr/local/bin/pdflatex".  I tested "R CMD check
> Ecfun_0.2-4.tar.gz" right before I did that, and the problem was still
> there.  It disappeared right after I did that.
>
>
>       Lisse's "UninstallPKG" might have been more graceful, but I
> couldn't find the key to that padlock, so I used something that seems
> more like boltcutters instead -- and it worked.
>
>
>       Thanks again,
>       Spencer Graves
>
>
> On 2020-05-13 09:57, Dr Eberhard W Lisse wrote:
>> Peter,
>>
>> as far as I understand this the idea is to make the binaries of whatever
>> MacTeX you use available in
>>
>>     /Library/TeX/texbin
>
>
>       Finder says this was installed yesterday, presumably when I
> installed MacTex.
>>
>> so that it survives the (annual) upgrade of MacTeX or a switch from the
>> Basic to the Big MacTeX or whatever.
>>
>>
>> I would personally not remove the pdflatex, but find something like
>> UninstallPKG
>
>
>       How do I find something like "UninstallPKG"?
>
>
>> and then locate MacTeX in there and remove that (all
>> versions, so all old crud goes away.
>>
>> If you, like me, use MacTeXBasic you can do something like
>
>
>       I don't think I'm using MacTexBasic, but I'm not a big LaTeX user,
> beyond trying to make RMarkdown work these days (and having used LaTeX
> when writing "Functional Data Analysis with R and Matlab with Ramsay and
> Hooker over a decade ago).
>
>>
>>     if [ ! -x /usr/local/bin/gawk ]
>
>
>       I don't seem to have gawk installed, at least not there, and
> "gawk" at a Terminal prompt returned, "-bash: gawk: command not found".
>
>>     then
>>         brew install gawk
>
>
>       I did that, and it seemed to work.  It started "Updating
> Homebrew..." and ended 'For compilers to find readline you may need to
> set:  export LDFLAGS="-L/usr/local/opt/readline/lib";  export
> CPPFLAGS="-I/usr/local/opt/readline/include"'.
>
>>     fi
>>     tlmgr list --only-installed \
>>        | gawk '{gsub(/:/, ""); print $2}' \
>>        > ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt
>
>
>       I tried that.  It executed quickly with no output.
>>
>> before uninstalling the old packages,
>
>
>       I don't know what to uninstall nor how to do it nor how to even
> find what I should uninstall, other than ask here (or maybe at
> tex.stackexchange, as Dirk Eddelbuettel had suggested).
>
>
>> then you install the latest and
>> greatest MacTeXBasic
>
>
>       I installed MacTex yesterday, as I indicated earlier in this
> thread.  That may not be enough, but I will skip that for the moment.
>
>
>> and run something like
>>
>>     tlmgr update --self
>
>
>       I did this in /Library/TeX/texbin as follows:
>
>
> texbin sbgraves$ tlmgr update --self
>
> tlmgr: Local TeX Live (2019) is older than remote repository (2020).
> Cross release updates are only supported with
>   update-tlmgr-latest(.sh/.exe) --update
> See https://tug.org/texlive/upgrade.html for details.
>
>
>       That link starts with, "By default, please get the new TL by doing
> a new installation instead of proceeding here."  Clicking "here" took me
> to where I was yesterday, when I installed MacTex-2020, which seems to
> have gone into "/user/local/texlive/2020".  I also found under
> "/user/local/texlive" subdirectories for 2014, and 2016 but not 2019.
>
>
>>     tlmgr install $(cat ~/Downloads/texlive.$(date
>> +%Y-%m-%d).installed.txt)
>
>
>       This gave me the same message as "tlmgr update --self".
>>
>> and, perhaps
>>
>>     perl -i -p \
>>         -e 's+\$SELFAUTOPARENT/+/usr/local/texlive/+' \
>>         /usr/local/texlive/2020basic/texmf.cnf
>>     texhash
>
>
>       I have "/user/local/texlive/2020" but not "2020basic", as I
> indicated above.  I think I'll skip this for the moment.
>>
>> :-)-O
>>
>> Nowadays, you can just
>>
>>     sudo rm -rf /usr/local/texlive/2019basic
>>
>> and if you use homebrew you might have /usr/local owned by yourself so
>> you don't need the sudo.
>>
>> Time Machine is your friend (as I just noticed) :-)-O
>>
>> el
>>
>>
>> On 13/05/2020 15:34, peter dalgaard wrote:
>>> Hmm, like Eberhard, I'm not too sure this is right.
>>>
>>> A look at ls -l /usr/local/bin should be informative though.
>
>
> ls -l /usr/local/bin
> total 460456
[...]
>>>
>>> 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
[...]

-- 
Dr. Eberhard W. Lisse   \         /       Obstetrician & Gynaecologist
el using lisse.NA             / *      |  Telephone: +264 81 124 6733 (cell)
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10007, Namibia           ;____/ Sect 20 of Act No. 4 of 2019 may apply