[R-SIG-Mac] R-SIG-Mac Digest, Vol 180, Issue 6
Ossenbruggen, Paul
Paul.Ossenbruggen at unh.edu
Fri Feb 16 20:15:18 CET 2018
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.
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:
********************************************************************************************************************************************
Send R-SIG-Mac mailing list submissions to
r-sig-mac at r-project.org<mailto:r-sig-mac at r-project.org>
To subscribe or unsubscribe via the World Wide Web, visit
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=S86paWuTkKAFxU7d9pmaDrGf5fQvUDN4lTfSAFihUSI&s=5USUZGu_N566kZFSUUNPm__bJ6mBMkTahr2mCeIwDXw&e=
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
r-sig-mac-owner at r-project.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-SIG-Mac digest..."
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
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=
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
r-sig-mac-owner at r-project.org
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
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=
------------------------------
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
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=S86paWuTkKAFxU7d9pmaDrGf5fQvUDN4lTfSAFihUSI&s=5USUZGu_N566kZFSUUNPm__bJ6mBMkTahr2mCeIwDXw&e=
------------------------------
End of R-SIG-Mac Digest, Vol 180, Issue 6
*****************************************
[[alternative HTML version deleted]]
More information about the R-SIG-Mac
mailing list