[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
> 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



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