[R-SIG-Mac] [R-sig-mac] Hmisc installed but won't load

[David Winsemius]

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