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

[peter dalgaard]

Well, you solved the immediate problem. However, you could get in trouble later with other tools from the 2016 TeXlive set, which seems to be what you have lingering. 

There doesn't seem to be an uninstaller that removes the symlinks on Mac. So...

Either: (a) remove all links manually plus the entire /usr/local/texlive/2016 tree. 
Or: (b) ensure that the current TeXlive stuff is found ahead of /usr/local/bin

(a) is a bit painful when it comes to the symlinks. There are likely around 450 of them. Of course, only a handful are ever used, so once /usr/local/texlive/2016 is gone, you just get a 'not found' type error and can remove the offending link one at a time. It is possible to automate it, but a bit dangerous if you get it wrong... Something like

ls -l /usr/local/bin | grep 'texlive/2016' | awk '{print $9}'

should give you a list. (...which with a bit of diligence, you can have removed in one swoop, but...)

(b) is more expedient (but leaves the mess in /usr/local/bin): edit /etc/paths with, like,

sudo nano /etc/paths

insert /Library/TeX/texbin at the top and save. Then, for good measure

sudo rm /etc/paths.d/TeX

so that it isn't in $PATH twice.


-pd

> On 14 May 2020, at 01:21 , Spencer Graves <spencer.graves using prodsyse.com> wrote:
> 
> 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
>> [...]
>> 
> 
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-- 
Peter Dalgaard, Professor,
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