[R-SIG-Mac] “pdflatex is not available” from “R CMD check”
Hello: What should I do to diagnose and fix “pdflatex is not available” from “R CMD check” on a Mac running OS X 10.10.1 (see below for more details including sessionInfo.)? A blog on Building R packages: missing path to pdflatex” (http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/ http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/) suggested the following: Sys.which(pdflatex”) # Sys.getenv(PATH) # [1] /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin” However, the suggested fix did not work for me. 1. How can I determine if pdflatex is installed? 2. If it is, how can I find it? If it’s not, what i the recommended install procedure? Thanks Spencer Graves ## R CMD check … ... * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -rf /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//RtmpjOTCtB/Rd2pdf1651fa89c1’ # sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) 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 [7] base loaded via a namespace (and not attached): [1] tools_3.1.2 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] R Freezes while Document editing
I have the same problem. I get convertPointFromBase when I start and at various other times; I also frequently get segfault errors and have to force close the app. R version 3.1.2 (2014-10-31) -- Pumpkin Helmet Platform: x86_64-apple-darwin13.4.0 (64-bit) [R.app GUI 1.65 (6833) x86_64-apple-darwin13.4.0] On Thursday, December 4, 2014 at 9:14:48 PM UTC-8, John Magnotti wrote: If it helps, a colleague of mine and I also get the freezing + segfaults a few times a day. They also occur while typing into the code editor in R.app [both of us are using R version 3.1.2 (2014-10-31); Platform: x86_64-apple-darwin13.4.0 (64-bit) ]. They seem to be more frequent while trying to use command+z (undo) several times in a row. Maybe some thread is scanning/parsing the file after each change and it can't keep up with rapid undo? John On Thu, Dec 4, 2014 at 10:43 PM, Boris Steipe boris@utoronto.ca javascript: wrote: Ah - sorry if this was unclear: I don't know if the warning is related to the segfault. I just started noticing both at about the same time. When the segfault occurs, R is frozen. The console displays an options dialogue for shutting it down, but accepts no input. With several more freezes today a pattern seems to emerge: once I have edited for a while, the freeze happens when I select a part of a line of code. B. On Dec 4, 2014, at 5:06 PM, peter dalgaard pda...@gmail.com javascript: wrote: On 04 Dec 2014, at 21:16 , Boris Steipe boris@utoronto.ca javascript: wrote: For a couple of days I have been seeing a (system generated) warning after I open a document, when I change focus into that document: 2014-12-04 15:05:21.336 R[73463:707] *** WARNING: Method convertPointFromBase: in class NSView is deprecated on 10.7 and later. It should not be used in new applications. This occurs also if the document is empty, however not with a document that has been freshly created in a new session. As well, I have experienced freezes (application not responding) right after R displays the segfault message, while editing the script file. The freezes are intermittent, after about an hour of coding or so - I can't reproduce them yet. Updating to 3.1.2 has solved neither of the problems. Is this a known problem? Is there anything I can contribute to get it solved? Thanks! Boris It's a warning. A programming paradigm used in older versions of OS X fell from favor in version 10.7. We still maintain a Snow Leopard (i.e. OS X 10.6) build. The question is whether the intended paradigm replacement actually works in 10.6; otherwise, it could be undesirable to maintain two different codes for the two different builds. I don't see the warning as related to any segfault? Being able to continue work following a segfault would be quite unusual so I suspect that you're using the term incorrectly. If you want to contribute, you might dig into the source code for R.app and figure out what it is that needs to be replaced and by what. And then whether the what is present in the Snow Leopard toolchain. The closest I can get is stuff like this: http://oleb.net/blog/2011/08/whats-new-for-developers-in-lion-part-2/ Mind you, Simon might already know all about this and just needs to get around to sorting things out. - Mac OS 10.9.5 R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base ___ R-SIG-Mac mailing list r-si...@r-project.org javascript: https://stat.ethz.ch/mailman/listinfo/r-sig-mac -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk javascript: Priv: pda...@gmail.com javascript: ___ R-SIG-Mac mailing list r-si...@r-project.org javascript: https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list r-si...@r-project.org javascript: 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] “pdflatex is not available” from “R CMD check”
On Jan 26, 2015, at 6:20 PM, Spencer Graves spencer.gra...@prodsyse.com wrote: Hello: What should I do to diagnose and fix “pdflatex is not available” from “R CMD check” on a Mac running OS X 10.10.1 (see below for more details including sessionInfo.)? A blog on Building R packages: missing path to pdflatex” (http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/ http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/) suggested the following: Sys.which(pdflatex”) # Sys.getenv(PATH) # [1] /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin” However, the suggested fix did not work for me. 1. How can I determine if pdflatex is installed? 2. If it is, how can I find it? If it’s not, what i the recommended install procedure? Thanks Spencer Graves ## R CMD check … ... * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -rf /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//RtmpjOTCtB/Rd2pdf1651fa89c1’ Spencer, First question would be, have you installed MacTex, which includes all the required components? If not, then visit: https://tug.org/mactex/ MacTex 2014 is the current version. There are also some Yosemite specific notes here: http://www.tug.org/mactex/yosemite.html The package should modify your $PATH upon installation, so that it includes: /usr/texbin and Sys.which(pdflatex) in the R console run from the OS X terminal should return: Sys.which(pdflatex) pdflatex /usr/texbin/pdflatex I would check: $PATH and: which pdflatex from the OS X terminal (not in an R session), just to be sure that you don't get different results there, as compared to what you are getting in R. In theory, the OS X terminal should provide the definitive response, whereas running some applications/GUI's, may not pick up (inherit) the system path. You can also check: ls /usr/texbin which contains links to the actual installation in: ls /usr/local/texlive/2014/bin/x86_64-darwin to see if MacTex 2014 has been installed (it should show a large number of files and links, including pdflatex). If you have a prior version, then the path would be: ls /usr/local/texlive//... Regards, Marc Schwartz ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] “pdflatex is not available” from “R CMD check”
I just noticed the date on this message as having been sent on Jan 26 but not received until today (Feb22). I'm also seeing several other R-SIG-Mac items from prior months showing up today. Am I the only one getting delayed delivery? -- David. On Jan 26, 2015, at 4:20 PM, Spencer Graves wrote: Hello: What should I do to diagnose and fix “pdflatex is not available” from “R CMD check” on a Mac running OS X 10.10.1 (see below for more details including sessionInfo.)? A blog on Building R packages: missing path to pdflatex” (http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/ http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/) suggested the following: Sys.which(pdflatex”) # Sys.getenv(PATH) # [1] /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin” However, the suggested fix did not work for me. 1. How can I determine if pdflatex is installed? 2. If it is, how can I find it? If it’s not, what i the recommended install procedure? Thanks Spencer Graves ## R CMD check … ... * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -rf /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//RtmpjOTCtB/Rd2pdf1651fa89c1’ # sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) 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 [7] base loaded via a namespace (and not attached): [1] tools_3.1.2 [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] “pdflatex is not available” from “R CMD check”
On Feb 22, 2015, at 6:31 AM, Marc Schwartz wrote: On Jan 26, 2015, at 6:20 PM, Spencer Graves spencer.gra...@prodsyse.com wrote: Hello: What should I do to diagnose and fix “pdflatex is not available” from “R CMD check” on a Mac running OS X 10.10.1 (see below for more details including sessionInfo.)? A blog on Building R packages: missing path to pdflatex” (http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/ http://www.r-bloggers.com/building-r-packages-missing-path-to-pdflatex/) suggested the following: Sys.which(pdflatex”) That had fancy-quotes. When corrected I see: Sys.which(pdflatex) pdflatex /usr/texbin/pdflatex # Sys.getenv(PATH) # [1] /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin” However, the suggested fix did not work for me. 1. How can I determine if pdflatex is installed? 2. If it is, how can I find it? If it’s not, what i the recommended install procedure? Thanks Spencer Graves ## R CMD check … ... * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. * checking PDF version of manual without hyperrefs or index ... ERROR Re-running with no redirection of stdout/stderr. Hmm ... looks like a package Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : pdflatex is not available Error in running tools::texi2pdf() You may want to clean up by 'rm -rf /var/folders/mh/mrm_14nx19g13lsnj9zmvwjrgn/T//RtmpjOTCtB/Rd2pdf1651fa89c1’ Spencer, First question would be, have you installed MacTex, which includes all the required components? If not, then visit: https://tug.org/mactex/ MacTex 2014 is the current version. There are also some Yosemite specific notes here: http://www.tug.org/mactex/yosemite.html The package should modify your $PATH upon installation, so that it includes: /usr/texbin and Sys.which(pdflatex) in the R console run from the OS X terminal should return: Sys.which(pdflatex) pdflatex /usr/texbin/pdflatex I would check: $PATH and: which pdflatex When I run that in a Terminal session I get (nothing) whereas I do have MacTex installed: david-winsemiuss-mac-pro:~ davidwinsemius$ which pdflatex david-winsemiuss-mac-pro:~ davidwinsemius$ ls /usr/texbin T1Wrap dvilj gftopk mktexpk pooltypetexdiff a2ping dvilj2p gftype mktextfmppower4 texdirflatten afm2afm dvilj4 gsftopk mllatex ps2eps texdoc afm2pl dvilj4l hbf2gf mltex ps2frag texdoctk Snipped output from the OS X terminal (not in an R session), just to be sure that you don't get different results there, as compared to what you are getting in R. In theory, the OS X terminal should provide the definitive response, whereas running some applications/GUI's, may not pick up (inherit) the system path. You can also check: ls /usr/texbin which contains links to the actual installation in: ls /usr/local/texlive/2014/bin/x86_64-darwin to see if MacTex 2014 has been installed (it should show a large number of files and links, including pdflatex). If you have a prior version, then the path would be: ls /usr/local/texlive//... The paths for Terminal sessions are different than for R sessions (and I'm the wrong person to ask why, or how to synchronize, or even whether they _should_ be synchronized.) Regards, Marc Schwartz ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac David Winsemius Alameda, CA, USA ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
