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/2016I 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. -pdOn 14 May 2020, at 01:21 , Spencer Graves <spencer.gra...@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/texbinFinder 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 UninstallPKGHow 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 likeI 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 gawkI 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.txtI 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 MacTeXBasicI 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 --selfI 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 texhashI 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[...]_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
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