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

[Spencer Graves]

Hi, Eberhard:


       Please excuse:  I've already solved this problem.  "sudo rm 
/usr/local/bin/pdflatex" did the trick.


        You may be right that I should reformat my hard drive and 
restore from my TimeMachine.  However, that sounds too much like 
"do-it-yourself lobotomy" to me.  I don't plan to try that right now.


       Thanks again for your suggestions.
       Spencer


On 2020-05-13 18:16, Dr Eberhard W Lisse wrote:
> 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
> [...]
>