[R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 6
David Winsemius
dwinsemius at comcast.net
Fri Feb 16 22:11:30 CET 2018
> On Feb 16, 2018, at 11:15 AM, Ossenbruggen, Paul <Paul.Ossenbruggen at unh.edu> wrote:
>
> First of all, I want to thank David Wensemius and Brandon Hurr.
>
> Next, I want to say that my problem was more complicated than removing the invisible file, .RData. After removal and startup of RStudio, I received:
>
> Error: object 'CF.mb' not found.
>
> I removed the following files: .Rhistory .Rprfile .Rprofile .Rdata. After removing them, my error message went away.
That makes sense. The history files can get corrupted as well. You can also get a clean load of R by running from the command line with the --vanilla flag.
For those using the R.app GUI, the history file in use is .Rapp.history rather than .Rhistory. See the R-MAC-FAQ.
David.
>
> Paul
>
>
>
> On Feb 16, 2018, at 6:00 AM, r-sig-mac-request at r-project.org<mailto:r-sig-mac-request at r-project.org> wrote:
>
>
>
> ********************************************************************************************************************************************
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>
> Today's Topics:
>
> 1. Re: R-SIG-Mac Digest, Vol 180, Issue 5 (Ossenbruggen, Paul)
> 2. Re: R-SIG-Mac Digest, Vol 180, Issue 5 (David Winsemius)
> 3. Re: R-SIG-Mac Digest, Vol 180, Issue 5 (Brandon Hurr)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 15 Feb 2018 14:18:45 +0000
> From: "Ossenbruggen, Paul" <Paul.Ossenbruggen at unh.edu>
> To: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 5
> Message-ID: <E70BF2CE-F724-4D3B-AAA4-276387E6890E at unh.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Given David Winsemius’ reply, I obtained the following information:
>
>
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".*" -ls
>
> 52645352 24 -rw-r--r-- 1 PJO staff 8196 Feb 9 13:20 /Users/PJO/Library/R/3.4/library/CF//.DS_Store
>
> 52645353 16 -rw-r--r-- 1 PJO staff 6148 Feb 9 13:20 /Users/PJO/Library/R/3.4/library/CF//extdata/.DS_Store
>
> The following
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname "CF.Rdata" -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname "CF.mb" -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".mb" -ls
> return nothing or
> PJO:SDE PJO$
>
> I hope this information is of some use.
>
> Thanks,
> Paul
>
> On Feb 15, 2018, at 6:00 AM, r-sig-mac-request at r-project.org wrote:
>
> Caution - External Email;
>
> ********************************************************************************************************************************************
> Send R-SIG-Mac mailing list submissions to
> r-sig-mac at r-project.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> or, via email, send a message with subject or body 'help' to
> r-sig-mac-request at r-project.org
>
> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of R-SIG-Mac digest..."
>
>
> Today's Topics:
>
> 1. R installation error caused by a bogus file. (Ossenbruggen, Paul)
> 2. Re: Update of RcppParallel failed (Marc Girondot)
> 3. Re: R installation error caused by a bogus file.
> (David Winsemius)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Feb 2018 15:01:46 +0000
> From: "Ossenbruggen, Paul" <Paul.Ossenbruggen at unh.edu>
> To: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
> Subject: [R-SIG-Mac] R installation error caused by a bogus file.
> Message-ID: <0B742675-F1EB-4F2B-9F5D-F8587D399278 at unh.edu>
> Content-Type: text/plain; charset="utf-8"
>
> I receive the following error whenever I restart R and reload R onto my computer:
>
> Error: object 'CF.mb' not found
> [R.app GUI 1.70 (7463) x86_64-apple-darwin15.6.0]
>
> The object 'CF.mb’ file is a bogus file. In actually, it does not and should not exist and R should not attempting to load it.
>
> I suspect that I created it by mistake when I worked with RStudio in creating a R package called “CF”. Most likely I typed “CF.mb" instead of “CF.md.” The extension “.md” makes sense. It is extension for a Markdown file. “.mb” stands for some animation program extension, which I am not using.
>
> QUESTION: How do I stop R from looking for this object?
>
> Apparently, R has saved a call to the 'CF.mb’ file somewhere in its memory. My guess if I erase this call, I will be running R the way it is designed.
>
> Thanks,
>
> Paul
>
>
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 14 Feb 2018 16:11:11 +0100
> From: Marc Girondot <marc_grt at yahoo.fr>
> To: Keith O'Hara <keith.ohara at nyu.edu>, r-sig-mac R
> <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] Update of RcppParallel failed
> Message-ID: <14a19e19-d1aa-d189-961d-dc0f988dc9db at yahoo.fr>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi Keith,
>
> When I try just now, a new version of RcppParallel was available
> (4.3.20.2; previous one was 4.3.20.1):
>
> essai de l'URL 'https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_src_contrib_RcppParallel-5F4.3.20.2.tar.gz&d=DwIGaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=vXaWf90_eNvgohBfU4b0GVo02vigVp6lPSTKMqr0RwQ&m=cb_FXbPhkXtSllNWIRAvnjDKHGCFqirdYqn2-fCXn3E&s=tR-Ab93uBbFJM8JTcIhOKJjwcpsCBojt9HslLckRpD0&e='
>
> And it compiles without problem !
>
> So the problem is solved !
>
> Thanks
>
> Marc
>
>
>
>
> Le 14/02/2018 à 14:58, Keith O'Hara a écrit :
> This looks like an issue to bring up with the Rcpp guys, not R… but can you provide a full printout of the error? I’m guessing this failed when compiling a C file, not C++.
>
>
> On Feb 14, 2018, at 8:43 AM, Marc Girondot via R-SIG-Mac <r-sig-mac at r-project.org> wrote:
>
> This morning I had an update to apply for RcppParallel but it failed
>
> Here are some information:
>
> update.packages()
> RcppParallel :
> Version 4.3.20 installed in /Library/Frameworks/R.framework/Versions/3.5/Resources/library
> Version 4.3.20.1 available at https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org&d=DwIGaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=vXaWf90_eNvgohBfU4b0GVo02vigVp6lPSTKMqr0RwQ&m=cb_FXbPhkXtSllNWIRAvnjDKHGCFqirdYqn2-fCXn3E&s=Q1PNswfQSKGd9Ow-GalzQ1NXiyozpmVIw8u15cvI6vo&e=
> ....
> During instal, I had this error
>
> error: invalid argument '-std=gnu++11' not allowed with 'C'
>
> It failed with the two versions of clang that I have installed:
>
> clang++ --version
> clang version 5.0.1 (tags/RELEASE_501/final)
> Target: x86_64-apple-darwin17.4.0
> Thread model: posix
> InstalledDir: /usr/local/opt/llvm/bin
>
> or
>
> clang++ --version
> Apple LLVM version 9.0.0 (clang-900.0.39.2)
> Target: x86_64-apple-darwin17.4.0
> Thread model: posix
> InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
>
> Do you have some idea about what's happened and how to solve this problem ?
>
> Thanks
>
> Marc
>
> _________________
>
> Information on my R version:
>
> R.Version()
> $platform
> [1] "x86_64-apple-darwin15.6.0"
>
> $arch
> [1] "x86_64"
>
> $os
> [1] "darwin15.6.0"
>
> $system
> [1] "x86_64, darwin15.6.0"
>
> $status
> [1] "Under development (unstable)"
>
> $major
> [1] "3"
>
> $minor
> [1] "5.0"
>
> $year
> [1] "2018"
>
> $month
> [1] "02"
>
> $day
> [1] "13"
>
> $`svn rev`
> [1] "74247"
>
> $language
> [1] "R"
>
> $version.string
> [1] "R Under development (unstable) (2018-02-13 r74247)"
>
> $nickname
> [1] "Unsuffered Consequences"
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dmac&d=DwIGaQ&c=c6MrceVCY5m5A_KAUkrdoA&r=vXaWf90_eNvgohBfU4b0GVo02vigVp6lPSTKMqr0RwQ&m=cb_FXbPhkXtSllNWIRAvnjDKHGCFqirdYqn2-fCXn3E&s=lWzj9K1TzXbvPZJx5dD70IvjNFcxTS-iuZY36R4qlDo&e=
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 14 Feb 2018 08:26:38 -0800
> From: David Winsemius <dwinsemius at comcast.net>
> To: "Ossenbruggen, Paul" <Paul.Ossenbruggen at unh.edu>
> Cc: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] R installation error caused by a bogus file.
> Message-ID: <F149708C-6939-4CC1-ACE0-D042E0FFB64C at comcast.net>
> Content-Type: text/plain; charset="utf-8"
>
>
> On Feb 14, 2018, at 7:01 AM, Ossenbruggen, Paul <Paul.Ossenbruggen at unh.edu> wrote:
>
> I receive the following error whenever I restart R and reload R onto my computer:
>
> Error: object 'CF.mb' not found
> [R.app GUI 1.70 (7463) x86_64-apple-darwin15.6.0]
>
> The object 'CF.mb’ file is a bogus file. In actually, it does not and should not exist and R should not attempting to load it.
>
> I suspect that I created it by mistake when I worked with RStudio in creating a R package called “CF”. Most likely I typed “CF.mb" instead of “CF.md.” The extension “.md” makes sense. It is extension for a Markdown file. “.mb” stands for some animation program extension, which I am not using.
>
> QUESTION: How do I stop R from looking for this object?
>
> Apparently, R has saved a call to the 'CF.mb’ file somewhere in its memory. My guess if I erase this call, I will be running R the way it is designed.
>
>
> Have you deleted your `.Rdata` file? It's an invisible file and you may need to use Terminal.app to remove it from you startup directory. Where exactly that might be depends on how Rstudio is configured.
>
> --
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law
>
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> R-SIG-Mac mailing list
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>
>
> ------------------------------
>
> End of R-SIG-Mac Digest, Vol 180, Issue 5
> *****************************************
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 15 Feb 2018 08:42:47 -0800
> From: David Winsemius <dwinsemius at comcast.net>
> To: "Ossenbruggen, Paul" <Paul.Ossenbruggen at unh.edu>
> Cc: "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 5
> Message-ID: <71215AC9-0AF2-444E-9B3F-96D6B5672F91 at comcast.net>
> Content-Type: text/plain; charset="utf-8"
>
>
> On Feb 15, 2018, at 6:18 AM, Ossenbruggen, Paul <Paul.Ossenbruggen at unh.edu> wrote:
>
> Given David Winsemius’ reply, I obtained the following information:
>
>
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".*" -ls
>
> 52645352 24 -rw-r--r-- 1 PJO staff 8196 Feb 9 13:20 /Users/PJO/Library/R/3.4/library/CF//.DS_Store
>
> 52645353 16 -rw-r--r-- 1 PJO staff 6148 Feb 9 13:20 /Users/PJO/Library/R/3.4/library/CF//extdata/.DS_Store
>
> The following
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname "CF.Rdata" -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname "CF.mb" -ls
> PJO:SDE PJO$ find /Users/PJO/Library/R/3.4/library/CF/ -type f -iname ".mb" -ls
> return nothing or
> PJO:SDE PJO$
>
> I hope this information is of some use.
>
> 1) When you reply to a posting you get from mailing list you should aggressively trim the stuff that is not needed to understand you query.
>
> 2) My approach to managing my invisible files in the MacOS is to make thm visible with this at a Terminal session:
>
> defaults write com.apple.finder AppleShowAllFiles YES
>
> Then you can find .Rdata files in whatever directory they might reside. I say "they" becaus you might have one in any directory that was your working directory at the time of a shutdown where you accept the R.app's offer to save work.
>
> So, don't just look at your Library sub directory, which is not a typical place to house a working directory. Instead look everywhere:
>
> find /Users/username/ -iname ".R*"
>
>
>
>
>
> Thanks,
> Paul
>
>
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 15 Feb 2018 15:13:52 -0800
> From: Brandon Hurr <brandon.hurr at gmail.com>
> To: David Winsemius <dwinsemius at comcast.net>
> Cc: "Ossenbruggen, Paul" <Paul.Ossenbruggen at unh.edu>,
> "r-sig-mac at r-project.org" <r-sig-mac at r-project.org>
> Subject: Re: [R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 5
> Message-ID:
> <CAG2OMvujVXfVPG3e9n1iFSCN1gh1Q3XipQ5QWhw_Yz3p0EXXQQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> A newish shortcut also makes this easier.
>
> CMD + Shift + .
>
> This toggles hidden files without using terminal.
>
> 2) My approach to managing my invisible files in the MacOS is to make thm visible with this at a Terminal session:
>
> defaults write com.apple.finder AppleShowAllFiles YES
>
>
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> R-SIG-Mac mailing list
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>
>
> ------------------------------
>
> End of R-SIG-Mac Digest, Vol 180, Issue 6
> *****************************************
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
David Winsemius
Alameda, CA, USA
'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law
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