Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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
lrwxr-xr-x 1 root wheel 66 Nov 26 2018 2to3 ->
../../../Library/Frameworks/Python.framework/Versions/3.7/bin/2to3
lrwxr-xr-x 1 sbgraves wheel 70 Jun 8 2016 2to3-3.5 ->
../../../Library/Frameworks/Python.framework/Versions/3.5/bin/2to3-3.5
lrwxr-xr-x 1 root wheel 70 Nov 26 2018 2to3-3.7 ->
../../../Library/Frameworks/Python.framework/Versions/3.7/bin/2to3-3.7
lrwxr-xr-x 1 root admin 47 Apr 29 15:52 R ->
/Library/Frameworks/R.framework/Resources/bin/R
lrwxr-xr-x 1 root admin 53 Apr 29 15:52 Rscript ->
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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, but 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
if [ ! -x /usr/local/bin/gawk ]
then
brew install gawk
fi
tlmgr list --only-installed \
| gawk '{gsub(/:/, ""); print $2}' \
> ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt
before uninstalling the old packages, then you install the latest and
greatest MacTeXBasic and run something like
tlmgr update --self
tlmgr install $(cat ~/Downloads/texlive.$(date +%Y-%m-%d).installed.txt)
and, perhaps
perl -i -p \
-e 's+\$SELFAUTOPARENT/+/usr/local/texlive/+' \
/usr/local/texlive/2020basic/texmf.cnf
texhash
:-)-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.
>
> 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
[...]
--
Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist
e...@lisse.na / * | Telephone: +264 81 124 6733 (cell)
PO Box 8421 Bachbrecht \ / If this email is signed with GPG/PGP
10007, Namibia ;/ Sect 20 of Act No. 4 of 2019 may apply
___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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 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 end, in the absence of these > approaches, there is not an easy way, under a standard macOS install, > to trace through the layers of symlinks to the target file. > > You can also do this manually via the Finder, by right clicking on the > symlink and using Show Original to navigate as well. > > Also, note that under Catalina, the default shell changed from bash to > zsh. > > Regards, > > Marc ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on 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 end, in the absence of these approaches, there is not an easy way, under a standard macOS install, to trace through the layers of symlinks to the target file. You can also do this manually via the Finder, by right clicking on the symlink and using Show Original to navigate as well. Also, note that under Catalina, the default shell changed from bash to zsh. Regards, Marc > On May 13, 2020, at 9:00 AM, Dr Eberhard W Lisse wrote: > > Marc, > > this is not necessarily correct, it can be a symlink, hence my suggestion of > > realpath $(which pdflatex) > > which will give you the final executable, in my case > > /usr/local/texlive/2020basic/bin/x86_64-darwin/pdftex > > But, I agree, this looks like an ancient installation :-0-O > > > el > > > On 13/05/2020 14:16, Marc Schwartz via R-SIG-Mac wrote: >> 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 directly to an executable in >> /usr/local/bin, rather than to a symlink in the TeXLive tree, suggests >> that there is something amiss with your installation. >> >> There are two primary folder trees that would need to be removed: >> >> /Library/TeX >> >> and >> >> /usr/local/texlive >> >> The former path will show in Finder, but the latter will not, unless >> you have hidden folders set to show. If not, then you can use the >> Finder menu option: >> >> Go -> Go to Folder >> >> and enter: >> >> /usr/local >> >> That will then show you the texlive folder, which you can then right >> click on and delete. >> >> Both folder trees will require your Admin password to delete. >> >> Once you do this, if you elect to do so, you will then need to >> re-install TeXLive 2020 and hopefully start fresh. >> >> Regards, >> >> Marc Schwartz > > ___ > R-SIG-Mac mailing list > R-SIG-Mac@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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. > > 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 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 — Adrian Dusa University of Bucharest Romanian Social Data Archive Soseaua Panduri nr. 90-92 050663 Bucharest sector 5 Romania https://adriandusa.eu ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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 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 > On 13 May 2020, at 14:16 , Marc Schwartz wrote: > > 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 directly to an executable in > /usr/local/bin, rather than to a symlink in the TeXLive tree, suggests that > there is something amiss with your installation. > > There are two primary folder trees that would need to be removed: > > /Library/TeX > > and > > /usr/local/texlive > > The former path will show in Finder, but the latter will not, unless you have > hidden folders set to show. If not, then you can use the Finder menu option: > > Go -> Go to Folder > > and enter: > > /usr/local > > That will then show you the texlive folder, which you can then right click on > and delete. > > Both folder trees will require your Admin password to delete. > > Once you do this, if you elect to do so, you will then need to re-install > TeXLive 2020 and hopefully start fresh. > > Regards, > > Marc Schwartz > > >> On May 13, 2020, at 7:00 AM, 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 >> /usr/local/bin/pdflatex >> >> >> $ echo $PATH >> /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin >> >> >> I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but "which >> pdflatex" doesn't find it. >> >> >> Thanks, >> Spencer Graves >> >> >> On 2020-05-13 01:31, peter dalgaard wrote: >>> You typically need to ensure that you have the right TeX installation in >>> your PATH (and not an older one earlier in the path). You should see >>> something like this >>> >>> Peters-MacBook-Air:BUILD pd$ which pdflatex >>> /Library/TeX/texbin/pdflatex >>> Peters-MacBook-Air:BUILD pd$ pdflatex -version >>> pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019) >>> kpathsea version 6.3.1 >>> >>> Peters-MacBook-Air:BUILD pd$ echo $PATH >>> /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin >>> >>> (Notice that if I had older TeX stuff in /usr/local, I could be in similar >>> trouble...) >>> >>> -pd >>> >>> On 13 May 2020, at 06:15 , Spencer Graves wrote: 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 "https://tug.org/mactex/mactex-download.html;, which I did. Everything seemed to go smoothly, but when I ran "R CMD build Ecfun" and "R CMD check Ecfun_0.2-4.tar.gz", I got the same error. This is running those commands in a Terminal. When I invoked "r" there just now and requested "sessionInfo()", I got the following: R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Catalina 10.15.4 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.0.0 Might you have other suggestions? Thanks very much for eliminating one possible source of this problem. Spencer Graves On 2020-05-12 20:12, Ken Beath wrote: >
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on 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 directly to an executable in /usr/local/bin, rather than to a symlink in the TeXLive tree, suggests that there is something amiss with your installation. There are two primary folder trees that would need to be removed: /Library/TeX and /usr/local/texlive The former path will show in Finder, but the latter will not, unless you have hidden folders set to show. If not, then you can use the Finder menu option: Go -> Go to Folder and enter: /usr/local That will then show you the texlive folder, which you can then right click on and delete. Both folder trees will require your Admin password to delete. Once you do this, if you elect to do so, you will then need to re-install TeXLive 2020 and hopefully start fresh. Regards, Marc Schwartz > On May 13, 2020, at 7:00 AM, 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 > /usr/local/bin/pdflatex > > > $ echo $PATH > /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin > > > I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but "which > pdflatex" doesn't find it. > > > Thanks, > Spencer Graves > > > On 2020-05-13 01:31, peter dalgaard wrote: >> You typically need to ensure that you have the right TeX installation in >> your PATH (and not an older one earlier in the path). You should see >> something like this >> >> Peters-MacBook-Air:BUILD pd$ which pdflatex >> /Library/TeX/texbin/pdflatex >> Peters-MacBook-Air:BUILD pd$ pdflatex -version >> pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019) >> kpathsea version 6.3.1 >> >> Peters-MacBook-Air:BUILD pd$ echo $PATH >> /usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin >> >> (Notice that if I had older TeX stuff in /usr/local, I could be in similar >> trouble...) >> >> -pd >> >> >>> On 13 May 2020, at 06:15 , Spencer Graves >>> wrote: >>> >>> 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 "https://tug.org/mactex/mactex-download.html;, which I did. >>> Everything seemed to go smoothly, but when I ran "R CMD build Ecfun" and "R >>> CMD check Ecfun_0.2-4.tar.gz", I got the same error. This is running those >>> commands in a Terminal. When I invoked "r" there just now and requested >>> "sessionInfo()", I got the following: >>> >>> >>> R version 4.0.0 (2020-04-24) >>> Platform: x86_64-apple-darwin17.0 (64-bit) >>> Running under: macOS Catalina 10.15.4 >>> >>> Matrix products: default >>> BLAS: >>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib >>> LAPACK: >>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> loaded via a namespace (and not attached): >>> [1] compiler_4.0.0 >>> >>> >>> Might you have other suggestions? >>> >>> >>> Thanks very much for eliminating one possible source of this problem. >>> >>> >>> Spencer Graves >>> >>> >>> On 2020-05-12 20:12, Ken Beath wrote: 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 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 did that and got the following: > > > * "In a current tex system \textasciigrave should work with > your families - they don't have the glyph but latex will fall back > without error. In older systems it could give an
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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 > /usr/local/bin/pdflatex > > > $ echo $PATH > /Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin > > > I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but "which > pdflatex" doesn't find it. > > > Thanks, > Spencer Graves > [...] -- Dr. Eberhard W. Lisse \ / Obstetrician & Gynaecologist e...@lisse.na / * | Telephone: +264 81 124 6733 (cell) PO Box 8421 Bachbrecht \ / If this email is signed with GPG/PGP 10007, Namibia ;/ Sect 20 of Act No. 4 of 2019 may apply ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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 $PATH
/Library/Frameworks/Python.framework/Versions/3.7/bin:/Users/sbgraves/anaconda3/bin:/Library/Frameworks/Python.framework/Versions/3.7/bin:/opt/local/bin:/opt/local/sbin:/Users/sbgraves/anaconda/bin:/Library/Frameworks/Python.framework/Versions/3.5/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/opt/X11/bin:/usr/local/git/bin
I do find "/Library/TeX/texbin/pdflatex" on my hard drive, but
"which pdflatex" doesn't find it.
Thanks,
Spencer Graves
On 2020-05-13 01:31, peter dalgaard wrote:
You typically need to ensure that you have the right TeX installation in your
PATH (and not an older one earlier in the path). You should see something like
this
Peters-MacBook-Air:BUILD pd$ which pdflatex
/Library/TeX/texbin/pdflatex
Peters-MacBook-Air:BUILD pd$ pdflatex -version
pdfTeX 3.14159265-2.6-1.40.20 (TeX Live 2019)
kpathsea version 6.3.1
Peters-MacBook-Air:BUILD pd$ echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin
(Notice that if I had older TeX stuff in /usr/local, I could be in similar
trouble...)
-pd
On 13 May 2020, at 06:15 , Spencer Graves wrote:
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 "https://tug.org/mactex/mactex-download.html;, which I did. Everything seemed to go smoothly, but when I ran
"R CMD build Ecfun" and "R CMD check Ecfun_0.2-4.tar.gz", I got the same error. This is running those commands in a
Terminal. When I invoked "r" there just now and requested "sessionInfo()", I got the following:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.0
Might you have other suggestions?
Thanks very much for eliminating one possible source of this problem.
Spencer Graves
On 2020-05-12 20:12, Ken Beath wrote:
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 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 did that and got the following:
* "In a current tex system \textasciigrave should work with
your families - they don't have the glyph but latex will fall back
without error. In older systems it could give an error."
See:
https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
Comments?
Thanks,
Spencer Graves
p.s. An earlier post on this issue to r-pkg-devel is copied below.
Forwarded Message
Subject:[R-pkg-devel] Error: Symbol \textasciigrave not provided by
(textcomp)
Date: Sun, 16 Feb 2020 14:21:17 -0600
From: Spencer Graves
To: r-package-de...@r-project.org
Hello, All:
"R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the
following:
! Package textcomp Error: Symbol \textasciigrave not provided by
(textcomp)font family zi4 in TS1 encoding.
(textcomp)Default family used instead.
See the textcomp package documentation for explanation.
* checking PDF version of manual without hyperrefs or index ... ERROR
* DONE
This is using R 3.6.2 under macOS 10.15.3 applied to the current
development version of"https://github.com/sbgraves237/Ecfun;. Travis
CI reported that the build passed; see
"https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;.
This looks to me like it's complaining about the use of the back
tick character ("`", below "~" on the top left key on a standard
American English keyboard), which I assume is equivalent to
"\textasciigrave" in certain contexts.
Six out of those 8 repetitions occur in the examples sections of
files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and
Re: [R-SIG-Mac] obsolete LaTeX software in "R CMD check" on Mac?
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 3.14159265-2.6-1.40.20 (TeX Live 2019)
kpathsea version 6.3.1
Peters-MacBook-Air:BUILD pd$ echo $PATH
/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/gfortran/bin:/usr/local/clang8/bin:/Library/TeX/texbin:/opt/X11/bin
(Notice that if I had older TeX stuff in /usr/local, I could be in similar
trouble...)
-pd
> On 13 May 2020, at 06:15 , Spencer Graves wrote:
>
> 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 "https://tug.org/mactex/mactex-download.html;, which I did.
> Everything seemed to go smoothly, but when I ran "R CMD build Ecfun" and "R
> CMD check Ecfun_0.2-4.tar.gz", I got the same error. This is running those
> commands in a Terminal. When I invoked "r" there just now and requested
> "sessionInfo()", I got the following:
>
>
> R version 4.0.0 (2020-04-24)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Catalina 10.15.4
>
> Matrix products: default
> BLAS:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
> LAPACK:
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.0.0
>
>
> Might you have other suggestions?
>
>
> Thanks very much for eliminating one possible source of this problem.
>
>
> Spencer Graves
>
>
> On 2020-05-12 20:12, Ken Beath wrote:
>> 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 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 did that and got the following:
>>>
>>>
>>> * "In a current tex system \textasciigrave should work with
>>> your families - they don't have the glyph but latex will fall back
>>> without error. In older systems it could give an error."
>>>
>>>
>>> See:
>>>
>>>
>>> https://tex.stackexchange.com/questions/543783/package-textcomp-error-symbol-textasciigrave-not-provided
>>>
>>>
>>> Comments?
>>> Thanks,
>>> Spencer Graves
>>>
>>>
>>> p.s. An earlier post on this issue to r-pkg-devel is copied below.
>>>
>>>
>>> Forwarded Message
>>> Subject:[R-pkg-devel] Error: Symbol \textasciigrave not provided by
>>> (textcomp)
>>> Date: Sun, 16 Feb 2020 14:21:17 -0600
>>> From: Spencer Graves
>>> To: r-package-de...@r-project.org
>>>
>>>
>>>
>>> Hello, All:
>>>
>>>
>>> "R CMD check Ecfun_0.2-4.tar.gz" ends with 8 repetitions of the
>>> following:
>>>
>>>
>>> ! Package textcomp Error: Symbol \textasciigrave not provided by
>>> (textcomp)font family zi4 in TS1 encoding.
>>> (textcomp)Default family used instead.
>>>
>>> See the textcomp package documentation for explanation.
>>> * checking PDF version of manual without hyperrefs or index ... ERROR
>>> * DONE
>>>
>>>
>>> This is using R 3.6.2 under macOS 10.15.3 applied to the current
>>> development version of"https://github.com/sbgraves237/Ecfun;. Travis
>>> CI reported that the build passed; see
>>> "https://travis-ci.org/sbgraves237/Ecfun/builds/650505913?utm_medium=notification_source=email;.
>>>
>>>
>>>
>>> This looks to me like it's complaining about the use of the back
>>> tick character ("`", below "~" on the top left key on a standard
>>> American English keyboard), which I assume is equivalent to
>>> "\textasciigrave" in certain contexts.
>>>
>>>
>>> Six out of those 8 repetitions occur in the examples sections of
>>> files "grepNonStandardCharacters.Rd", "subNonStandardCharacters.Rd", and
>>> "subNonStandardNames.Rd". Those functions were written to fix parsing
>>> errors with names like "Raúl" that had been mangled by different
>>> software before I could get it into R.
>>>
>>>
>>> After a day's work failed to produce a work around, I decided to
>>> ask this group.
>>>
>>>
>>> What do you suggest?
>>> Thanks,
>>>
