[R-SIG-Mac] [R-sig-mac] Hmisc installed but won't load
Don McKenzie
dmck at u.washington.edu
Mon Mar 24 23:18:56 CET 2014
Thanks David, Steven, and Berend. Good things to try.
Don
On Mar 24, 2014, at 1:58 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>
> On Mar 24, 2014, at 1:23 PM, Don McKenzie wrote:
>
>> The plot thickens. I do indeed have latticeExtra installed, but observe. Is it turtles on down…? (and yes I have lattice installed too)
>>
>>> library("latticeExtra")
>> Loading required package: RColorBrewer
>> Loading required package: lattice
>> Error in gzfile(file, "rb") : cannot open the connection
>> In addition: Warning messages:
>> 1: '.find.package' is deprecated.
>> Use 'find.package' instead.
>> See help("Deprecated")
>> 2: In gzfile(file, "rb") :
>> cannot open compressed file '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/latticeExtra/data/Rdata.rdx', probable reason 'No such file or directory'
>> Error: package or namespace load failed for ‘latticeExtra’
>>
>> Thanks for your response Steve. Ideas?
>
> I would trash your .Rdata image, restart R, and try again.
>
> (I just updated to that version of Hmisc and also updated rms, lattice and latticeExtra and I'm having no trouble loading rms and Hmisc, which I load in my .Rprofile at startup.)
>
> You should post output from sessionInfo() and .libPaths(). My prior problems with keeping all packages up to date has lead me to use only one library directory.
>
> --
> David.
>>
>> Don
>>
>>
>> On Mar 24, 2014, at 1:13 PM, Steven McKinney <smckinney at bccrc.ca> wrote:
>>
>>> The complaint is about a component in package latticeExtra.
>>>
>>> Do you have this package installed?
>>>
>>> (latticExtra does not show as required when I load Hmisc
>>>
>>>> require("Hmisc")
>>> Loading required package: Hmisc
>>> Loading required package: grid
>>> Loading required package: lattice
>>> Loading required package: survival
>>> Loading required package: splines
>>> Loading required package: Formula
>>>
>>> but I do see latticeExtra in my installed library directory
>>>
>>> /Library/Frameworks/R.framework/Versions/Current/Resources/library )
>>>
>>>
>>>
>>>
>>> Steven McKinney
>>>
>>> Statistician
>>> Molecular Oncology and Breast Cancer Program
>>> British Columbia Cancer Research Centre
>>>
>>> ________________________________________
>>> From: r-sig-mac-bounces at r-project.org [r-sig-mac-bounces at r-project.org] On Behalf Of Don McKenzie [dmck at u.washington.edu]
>>> Sent: March 24, 2014 12:35 PM
>>> To: r-sig-mac at r-project.org
>>> Subject: [R-SIG-Mac] [R-sig-mac] Hmisc installed but won't load
>>>
>>> My apologies if this has been addressed recently. Searching the archive and google brought me only to older posts.
>>>
>>> I’m not understanding the error message below when I try to load Hmisc. I reinstalled it using the syntax suggested by Simon in an earlier post. I am using the vanilla R GUI ("R 3.0.3 GUI 1.63 Snow Leopard build (6660)”) on OSX 10.9.2.
>>>
>>> Thanks in advance.
>>>
>>>
>>>> install.packages("Hmisc",,"http://cran.r-project.org")
>>> trying URL 'http://cran.r-project.org/bin/macosx/contrib/3.0/Hmisc_3.14-3.tgz'
>>> Content type 'application/x-gzip' length 1555868 bytes (1.5 Mb)
>>> opened URL
>>> ==================================================
>>> downloaded 1.5 Mb
>>>
>>> The downloaded binary packages are in
>>> /var/folders/d1/r1hsc_s91pg18v_t23bq27tw0000gn/T//RtmpIPxtRG/downloaded_packages
>>>
>>>
>>>
>>>> library("Hmisc")
>>> Error in gzfile(file, "rb") : cannot open the connection *****************
>>> In addition: Warning message:
>>> In gzfile(file, "rb") :
>>> cannot open compressed file '/Library/Frameworks/R.framework/Versions/3.0/Resources/library/latticeExtra/data/Rdata.rdx', probable reason 'No such file or directory'
>>> Error: package or namespace load failed for ‘Hmisc’
>>>
>>>
>>>
>>>> installed.packages()
>>> .
>>> .
>>> .
>>> Hmisc "Hmisc" "/Library/Frameworks/R.framework/Versions/3.0/Resources/library" "3.14-3” NA
>>> .
>>> .
>>> .
>>>
>>>
>>>> sessionInfo()
>>> R version 3.0.3 (2014-03-06)
>>> Platform: x86_64-apple-darwin10.8.0 (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] splines grid stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] Formula_1.1-1 survival_2.37-7 lattice_0.20-27 lavaan_0.5-15 MASS_7.3-29 plspm_0.4.1 turner_0.1.7 tester_0.1.7 diagram_1.6.2 shape_1.4.1 amap_0.8-12
>>>
>>> loaded via a namespace (and not attached):
>>> [1] mnormt_1.4-7 pbivnorm_0.5-1 quadprog_1.5-5 RColorBrewer_1.0-5 stats4_3.0.3 tools_3.0.3
>>>
>>>
>>>
>>>
>>> Don McKenzie
>>> Research Ecologist
>>> Pacific Wildland Fire Sciences Lab
>>> US Forest Service
>>>
>>> Affiliate Professor
>>> School of Environmental and Forest Sciences
>>> University of Washington
>>> dmck at uw.edu
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>
>> Don McKenzie
>> Research Ecologist
>> Pacific Wildland Fire Sciences Lab
>> US Forest Service
>>
>> Affiliate Professor
>> School of Environmental and Forest Sciences
>> University of Washington
>> dmck at uw.edu
>>
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac at 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 at r-project.org
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Don McKenzie
Research Ecologist
Pacific Wildland Fire Sciences Lab
US Forest Service
Affiliate Professor
School of Environmental and Forest Sciences
University of Washington
dmck at uw.edu
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