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

2020-05-17 Thread Eberhard W Lisse
Spencer, you are welcome. As before, it is really helpful to have a “known state”. As I may have written before, being disciplined about this (having a “handbook”), may be boring, but makes especially uncommon tasks easy. I have recently gone so far as to replacing all manually uploaded Apps

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

2020-05-17 Thread Spencer Graves
  I did more tidying.  "ls -l /usr/local/bin/" contained 854 objects before I did "rm" on 451 that were alias for objects in "/usr/local/texlive/2016".  After I did that, "ls -l /usr/local/bin/" contained 403 = 854-451 objects.   Thanks again to Ken Beath, Peter Dalgaard, Eberhard W

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

2020-05-17 Thread peter dalgaard
So you should be set. Anything more is just tidying. I have two of the three programs mentioned in /library/TeX xindy.mem nowhere in sight, but they are pretty obscure. -pd > On 17 May 2020, at 05:18 , Spencer Graves wrote: > > > > > > I did "which" for all 451 executables found by

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

2020-05-16 Thread Spencer Graves
On 2020-05-15 03:34, peter dalgaard wrote: On 15 May 2020, at 06:04 , Spencer Graves wrote: 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

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

2020-05-15 Thread peter dalgaard
> On 15 May 2020, at 06:04 , Spencer Graves wrote: > > 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

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

2020-05-15 Thread Dr Eberhard W Lisse
Spencer, MacTeX 2020 "works" differently from MacTeX 2016. I had 2016 myself but don't remember what the difference was and when it changed. The MacTeX 2020 installation creates /etc/paths.d/TeX which contains '/Library/TeX/texbin' which via a convoluted mechanism survives upgrades to

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

2020-05-14 Thread Spencer Graves
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

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

2020-05-14 Thread 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

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

2020-05-13 Thread 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

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

2020-05-13 Thread 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

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

2020-05-13 Thread Spencer Graves
  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

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

2020-05-13 Thread Dr Eberhard W Lisse
Peter, as far as I understand this the idea is to make the binaries of whatever MacTeX you use available in /Library/TeX/texbin 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,

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

2020-05-13 Thread Dr Eberhard W Lisse
Ah, yes, brew install coreutils :-)-O Existing accounts using bash remain under bash when upgrading to Catalina. And bash remains available so all bash script will continue to run :-)-O el On 13/05/2020 15:44, Marc Schwartz wrote: > Hi, > > I will stand to be corrected, but from

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

2020-05-13 Thread Marc Schwartz via R-SIG-Mac
Hi, I will stand to be corrected, but from what I can tell, 'realpath' is not part of a default macOS installation, and would need to be installed from a third party repo (e.g. homebrew). There appear to be shell script incantations that would accomplish the same functionality, but in the

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

2020-05-13 Thread Adrian Dușa
Not sure if this helps, but for some reason my TeX Live was not installed in Library/TeX/texbin, but in: ~ % realpath $(which pdflatex) /usr/local/texlive/2019/bin/x86_64-darwin/pdftex > On 13 May 2020, at 16:34, peter dalgaard wrote: > > Hmm, like Eberhard, I'm not too sure this is right.

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

2020-05-13 Thread peter dalgaard
Hmm, like Eberhard, I'm not too sure this is right. A look at ls -l /usr/local/bin should be informative though. 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

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

2020-05-13 Thread Marc Schwartz via R-SIG-Mac
Spencer, FWIW, this may be a situation where you need to remove your current/older installations of TeXLive and start fresh with a clean install of TeXLive 2020. It is possible that there is some conflict or corruption of the current multiple installations. That 'which pdflatex' is pointing

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

2020-05-13 Thread Dr Eberhard W Lisse
realpath $(which pdflatex) pdflatex --version On 13/05/2020 13:00, Spencer Graves wrote: > Hi, Peter et al.: > > >   It looks like you've properly diagnosed my problem.  How do I fix it? > > >   "which pdflatex" and "echo $PATH" are as follows: > > > $ which pdflatex >

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

2020-05-13 Thread Spencer Graves
Hi, Peter et al.:   It looks like you've properly diagnosed my problem.  How do I fix it?   "which pdflatex" and "echo $PATH" are as follows: $ which pdflatex /usr/local/bin/pdflatex $ echo $PATH

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

2020-05-13 Thread peter dalgaard
You typically need to ensure that you have the right TeX installation in your PATH (and not an older one earlier in the path). You should see something like this Peters-MacBook-Air:BUILD pd$ which pdflatex /Library/TeX/texbin/pdflatex Peters-MacBook-Air:BUILD pd$ pdflatex -version pdfTeX

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

2020-05-12 Thread Spencer Graves
Hi, Ken et al.:   Thanks for the info.  I tried to do what you suggested but still have the problem.   Specifically, a web search for TexLive 2020 led me to "https://tug.org/texlive/".  That invited me to download and install MacTex 2020 from

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

2020-05-12 Thread Ken Beath
Your package passes checks on my machine perfectly. It has R 4.0.0 with RStudio and TexLive 2020 with updates to a week or two ago. Ken > On 13 May 2020, at 8:17 am, Spencer Graves > wrote: > > Hello, All: > > > Might "R CMD check" on Mac use obsolete LaTeX software? > > > I

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

2020-05-12 Thread Simon Urbanek
Spencer, as Duncan pointed out that is an issue on your machine, so only you can fix it. The checks use whatever you give them. FWIW the macOS CRAN setup uses TeX Live 2019: $ pdflatex --version | head -n1 pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019) You can upgrade your TeX installation if

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

2020-05-12 Thread Duncan Murdoch
On 12/05/2020 6:17 p.m., Spencer Graves wrote: Hello, All:   Might "R CMD check" on Mac use obsolete LaTeX software?   I ask, because "R CMD check" on my Mac started reporting LaTeX errors on *.Rd files that previously passed "R CMD check" without problems.  Dirk Eddelbuettel

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

2020-05-12 Thread Spencer Graves
Hello, All:   Might "R CMD check" on Mac use obsolete LaTeX software?   I ask, because "R CMD check" on my Mac started reporting LaTeX errors on *.Rd files that previously passed "R CMD check" without problems.  Dirk Eddelbuettel recommended I ask tex.stackexchange about that.  I