[R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
Spencer Graves
@pencer@gr@ve@ @end|ng |rom prod@y@e@com
Fri May 15 06:04:55 CEST 2020
Hi, Peter et al.:
I'm still overwhelmed.
To limit changes to things I think I understand, my
'/usr/local/texlive' directory contains subdirectories 2014, 2015, 2016,
2020, and texmf-local. From your comments, I gather that the following
would be wise:
sudo rm -r /usr/local/texlive/2014
sudo rm -r /usr/local/texlive/2015
sudo rm -r /usr/local/texlive/2016
I did this, and "R CMD check Ecfun_0.2-4.tar.gz" still ran to
completion without errors.
I don't understand "ls -l /usr/local/bin | grep 'texlive/2016' |
awk '{print $9}'", but I did "ls -l /usr/local/bin | grep 'texlive/20' >
texlive_20.txt" and examined texlive_20.txt in R. I found it contained
451 lines like the following:
lrwxr-xr-x 1 sbgraves admin 48 Jan 13 17:42 a2ping ->
/usr/local/texlive/2016/bin/x86_64-darwin/a2ping
All had "2016". I'm inferring from your comments that if
anything I do calls any of those 451 operations like "a2ping", I will
get "not found". If I get that, I gather I'm supposed to "sudo rm
/usr/local/bin/a2ping" and hope that solves the problem.
???
Thanks very much.
Spencer Graves
On 2020-05-14 02:51, peter dalgaard wrote:
> 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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