[R-SIG-Mac] Solved via deleting .RData & .Rhistory problem loading ggplot2 package
David Winsemius
dwinsemius at comcast.net
Tue Mar 8 16:22:03 CET 2011
Posting this as a SOLVED message and perhaps a clue to the next
sufferer. (I had sent a private shot in the dark solution that turned
out to work.)
--
david.
Begin forwarded message:
> From: linsleys <linsleys at comcast.net>
> Date: March 8, 2011 10:02:10 AM EST
> To: David Winsemius <dwinsemius at comcast.net>
> Subject: Re: [R-SIG-Mac] problem loading ggplot2 package
>
> David-
> Thanks for your help. I deleted the .Rdata files and the .Rhistory
> files, un- and re-installed R and ggplot now works. I'm happy!
>
> p
>
> On Sun, Mar 6, 2011 at 10:57 AM, David Winsemius <dwinsemius at comcast.net
> > wrote:
>>
>> On Mar 6, 2011, at 12:47 PM, linsleys wrote:
>>
>>> Ben-
>>> Thanks for the useful ideas. I've spent some time with them and
>>> they
>>> yielded a clue: ggplot2 lods correctly when I login as another user.
>>> Any further suggestions?
>>>
>>> p
>>>
>>> My answers to your specific questions are below:
>>>
>>> -I don't know how to examine .Rprofile
>>
>> If you did not make one, then it does not exist.
>>
>> (By default dot files, of which .Rprofile is but one instance, are
>> not
>> displayed by Finder.app.)
>>
>> You can change the default behavior of Finder.app. You can also
>> delete the
>> hidden .RData file that gets loaded on startup, although I don't
>> have any
>> idea whether that will help.)
>>
>> http://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#R_002eapp-GUI-crashes-on-startup_0021
>>
>> (Which I understand may not apply but does describe trouble-
>> shooting methods
>> for dot files.)
>>
>> --
>> David
>>
>>> -I have the same problem whether I use the GUI ot command line to
>>> load
>>> ggplot2
>>> -proto loads fine
>>> -ggplot2 lods correctly when I login as another user
>>> - I repaired permissions, but it didn't help
>>>
>>> On Sat, Mar 5, 2011 at 7:12 PM, Ben Bond-Lamberty <bpbond at gmail.com>
>>> wrote:
>>>>
>>>> I have no special knowledge, but a few questions to try to narrow
>>>> things
>>>> down:
>>>>
>>>> - Is there anything unusual in your .Rprofile?
>>>> - Did you try installing ggplot using the "Package Installer" menu
>>>> item in the GUI?
>>>> - Is it ggplot, or actually the load of 'proto' that's failing?
>>>> (Can
>>>> you "library(proto)" OK?)
>>>> - Try creating a new user on your Mac, logging in, installing R and
>>>> then ggplot2.
>>>>
>>>> Re permissions, seems unlikely, but running the voodoo "Repair
>>>> Permissions" in Disk Utility won't hurt...
>>>>
>>>> Ben
>>>>
>>>>
>>>> On Sat, Mar 5, 2011 at 2:50 PM, linsleys <linsleys at comcast.net>
>>>> wrote:
>>>>>
>>>>> None of these suggestions fixed my problem. Uninstalled R,
>>>>> re-installed the latest version and re-loaded ggplot2. Still
>>>>> get the
>>>>> same error message. I'm wondering about the env = envir part of
>>>>> the
>>>>> error message- could it be a permissions problem?
>>>>>
>>>>> p
>>>>>
>>>>>
>>>>>> library(ggplot2)
>>>>>
>>>>> Loading required package: reshape
>>>>> Loading required package: plyr
>>>>>
>>>>> Attaching package: 'reshape'
>>>>>
>>>>> The following object(s) are masked from 'package:plyr':
>>>>>
>>>>> round_any
>>>>>
>>>>> Loading required package: grid
>>>>> Loading required package: proto
>>>>> Error in assign(names[i], dots[[i]], env = envir) :
>>>>> invalid first argument
>>>>> Error : unable to load R code in package 'ggplot2'
>>>>> Error: package/namespace load failed for 'ggplot2'
>>>>>
>>>>>
>>>>>
>>>>> $version.string
>>>>> [1] "R version 2.12.2 (2011-02-25)"
>>>>>
>>>>>> SystemInfo()
>>>>>
>>>>> Error: could not find function "SystemInfo"
>>>>>>
>>>>>> Sys.info()
>>>>>
>>>>> sysname
>>>>>
>>>>> "Darwin"
>>>>>
>>>>> release
>>>>>
>>>>> "10.6.0"
>>>>>
>>>>> version
>>>>> "Darwin Kernel Version 10.6.0: Wed Nov 10 18:13:17 PST 2010;
>>>>> root:xnu-1504.9.26~3/RELEASE_I386"
>>>>>
>>>>> nodename
>>>>>
>>>>> "MacBook-Chef.local"
>>>>>
>>>>> machine
>>>>>
>>>>> "i386"
>>>>>
>>>>> login
>>>>>
>>>>> "linsleys"
>>>>>
>>>>> user
>>>>>
>>>>> "linsleys"
>>>>>>
>>>>>
>>>>> On Fri, Mar 4, 2011 at 6:13 PM, Anirban Mukherjee <anirbanm at smu.edu.sg
>>>>> >
>>>>> wrote:
>>>>>>
>>>>>> I would suggest updating R to 2.12.2. That should be fairly
>>>>>> seamless/painless.
>>>>>>
>>>>>> A
>>>>>>
>>>>>> --
>>>>>> Anirban Mukherjee | Assistant Professor, Marketing
>>>>>> LKCSB, Singapore Management University
>>>>>> 5056 School of Business, 50 Stamford Road
>>>>>> Singapore 178899 | +65-6828-1932
>>>>>>
>>>>>>
>>>>>> On Mar 5, 2011, at 12:14 AM, MacQueen, Don wrote:
>>>>>>
>>>>>>> Peter,
>>>>>>>
>>>>>>> There should not be a problem with ggplot2 on a Mac; I was
>>>>>>> able to
>>>>>>> install
>>>>>>> and load it without difficulty just now (see below). (though
>>>>>>> apparently
>>>>>>> some dependencies are not available, so perhaps some ggplot2
>>>>>>> functions
>>>>>>> won't work properly; I don't know)
>>>>>>>
>>>>>>> This does tend to suggest something is awry with your R
>>>>>>> installation,
>>>>>>> as
>>>>>>> Bob Bond-Lamberty suggested in his response. Note that I have
>>>>>>> 32 bit R
>>>>>>> 2.12.2 whereas you have 64 bit 2.12.1. I don't think the 32 vs
>>>>>>> 64 bit
>>>>>>> is
>>>>>>> the problem, since I can run R64 and load ggplot2.
>>>>>>>
>>>>>>> Does
>>>>>>> traceback()
>>>>>>> used immediately after the error, give any useful information?
>>>>>>>
>>>>>>> Not much help, I know...
>>>>>>>
>>>>>>> -Don
>>>>>>>
>>>>>>>> install.packages('ggplot2',dep=TRUE)
>>>>>>>
>>>>>>> --- Please select a CRAN mirror for use in this session ---
>>>>>>> Loading Tcl/Tk interface ... done
>>>>>>> Warning: dependencies 'marray', 'affy', 'Biobase' are not
>>>>>>> available
>>>>>>> also installing the dependencies 'logspline', 'digest',
>>>>>>> 'quantreg',
>>>>>>> 'hexbin'
>>>>>>>
>>>>>>> trying URL
>>>>>>>
>>>>>>> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/logspline_2.1
>>>>>>> .3.tgz'
>>>>>>> Content type 'application/x-gzip' length 409453 bytes (399 Kb)
>>>>>>> opened URL
>>>>>>> ==================================================
>>>>>>> downloaded 399 Kb
>>>>>>>
>>>>>>> trying URL
>>>>>>>
>>>>>>> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/digest_0.4.2
>>>>>>> .
>>>>>>> tgz'
>>>>>>> Content type 'application/x-gzip' length 120633 bytes (117 Kb)
>>>>>>> opened URL
>>>>>>> ==================================================
>>>>>>> downloaded 117 Kb
>>>>>>>
>>>>>>> trying URL
>>>>>>>
>>>>>>> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/quantreg_4.57
>>>>>>> .tgz'
>>>>>>> Content type 'application/x-gzip' length 2818374 bytes (2.7 Mb)
>>>>>>> opened URL
>>>>>>> ==================================================
>>>>>>> downloaded 2.7 Mb
>>>>>>>
>>>>>>> trying URL
>>>>>>>
>>>>>>> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/hexbin_1.24.0
>>>>>>> .tgz'
>>>>>>> Content type 'application/x-gzip' length 690100 bytes (673 Kb)
>>>>>>> opened URL
>>>>>>> ==================================================
>>>>>>> downloaded 673 Kb
>>>>>>>
>>>>>>> trying URL
>>>>>>>
>>>>>>> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/ggplot2_0.8.9
>>>>>>> .tgz'
>>>>>>> Content type 'application/x-gzip' length 2481399 bytes (2.4 Mb)
>>>>>>> opened URL
>>>>>>> ==================================================
>>>>>>> downloaded 2.4 Mb
>>>>>>>
>>>>>>>
>>>>>>> The downloaded packages are in
>>>>>>>
>>>>>>>
>>>>>>> /var/folders/pa/pamYryRNGGKLDVNRYyxBt+++m+c/-Tmp-//RtmplZqsQp/
>>>>>>> downloaded_pa
>>>>>>> ckages
>>>>>>>
>>>>>>>> require(ggplot2)
>>>>>>>
>>>>>>> Loading required package: ggplot2
>>>>>>> Loading required package: reshape
>>>>>>> Loading required package: plyr
>>>>>>>
>>>>>>> Attaching package: 'reshape'
>>>>>>>
>>>>>>> The following object(s) are masked from 'package:plyr':
>>>>>>>
>>>>>>> round_any
>>>>>>>
>>>>>>> Loading required package: grid
>>>>>>> Loading required package: proto
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> sessionInfo()
>>>>>>>
>>>>>>> R version 2.12.2 (2011-02-25)
>>>>>>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>>>>>>
>>>>>>> locale:
>>>>>>> [1] C
>>>>>>>
>>>>>>> attached base packages:
>>>>>>> [1] grid stats graphics grDevices utils datasets
>>>>>>> methods
>>>>>>> [8] base
>>>>>>>
>>>>>>> other attached packages:
>>>>>>> [1] ggplot2_0.8.9 proto_0.3-8 reshape_0.8.4 plyr_1.4
>>>>>>>
>>>>>>> loaded via a namespace (and not attached):
>>>>>>> [1] tcltk_2.12.2 tools_2.12.2
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Don MacQueen
>>>>>>>
>>>>>>> Lawrence Livermore National Laboratory
>>>>>>> 7000 East Ave., L-627
>>>>>>> Livermore, CA 94550
>>>>>>> 925-423-1062
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 3/4/11 7:19 AM, "linsleys" <linsleys at comcast.net> wrote:
>>>>>>>
>>>>>>>> I'm having trouble loading ggplot2 using R version 2.12.1, as
>>>>>>>> shown
>>>>>>>> below. I can't seem to find a relevant post that fixes my
>>>>>>>> problem.
>>>>>>>> Any
>>>>>>>> help would be very much appreciated. Thanks,
>>>>>>>>
>>>>>>>> peter l
>>>>>>>>
>>>>>>>>> install.packages('ggplot2', dep = TRUE)
>>>>>>>>
>>>>>>>> trying URL
>>>>>>>>
>>>>>>>> 'http://cran.cnr.Berkeley.edu/bin/macosx/leopard/contrib/2.12/ggplot2_0.8
>>>>>>>> .
>>>>>>>> 9.tgz'
>>>>>>>> Content type 'application/x-gzip' length 2481399 bytes (2.4 Mb)
>>>>>>>> opened URL
>>>>>>>> =================================================
>>>>>>>> downloaded 2.4 Mb
>>>>>>>>
>>>>>>>>
>>>>>>>> The downloaded packages are in
>>>>>>>>
>>>>>>>>
>>>>>>>> /var/folders/XF/XF0tU7gdGTeF4Th7KhKYDk+++TI/-Tmp-//RtmpFMnqLB/
>>>>>>>> downloaded_p
>>>>>>>> ackages
>>>>>>>>>
>>>>>>>>> library(ggplot2)
>>>>>>>>
>>>>>>>> Error in assign(names[i], dots[[i]], env = envir) :
>>>>>>>> invalid first argument
>>>>>>>> Error : unable to load R code in package 'ggplot2'
>>>>>>>> Error: package/namespace load failed for 'ggplot2'
>>>>>>>>
>>>>>>>> sessionInfo() R version 2.12.1 (2010-12-16) Platform:
>>>>>>>> x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1]
>>>>>>>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached
>>>>>>>> base
>>>>>>>> packages: [1] grid stats graphics grDevices utils datasets
>>>>>>>> methods
>>>>>>>> [8]
>>>>>>>> base other attached packages: [1] proto_0.3-8 reshape_0.8.4
>>>>>>>> plyr_1.4
>>>>>>>> loaded via a namespace (and not attached): [1] tcltk_2.12.2
>>>>>>>> tools_2.12.2
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Peter and Leslie Linsley
>>>>>>>> 2528 11th Ave W
>>>>>>>> Seattle, WA 98119
>>>>>>>> linsleys at comcast.net
>>>>>>>> 206.818.3206 P-cell
>>>>>>>> 206-818-3167 L-cell
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> R-SIG-Mac mailing list
>>>>>>>> R-SIG-Mac at r-project.org
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac at r-project.org
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Peter and Leslie Linsley
>>>>> 2528 11th Ave W
>>>>> Seattle, WA 98119
>>>>> linsleys at comcast.net
>>>>> 206.818.3206 P-cell
>>>>> 206-818-3167 L-cell
>>>>>
>>>>> _______________________________________________
>>>>> R-SIG-Mac mailing list
>>>>> R-SIG-Mac at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>
>>>
>>>
>>>
>>> --
>>> Peter and Leslie Linsley
>>> 2528 11th Ave W
>>> Seattle, WA 98119
>>> linsleys at comcast.net
>>> 206.818.3206 P-cell
>>> 206-818-3167 L-cell
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>>
>>
>
>
>
> --
> Peter and Leslie Linsley
> 2528 11th Ave W
> Seattle, WA 98119
> linsleys at comcast.net
> 206.818.3206 P-cell
> 206-818-3167 L-cell
David Winsemius, MD
West Hartford, CT
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