[R] Error w/ Start up Script
R. Michael Weylandt
michael.weylandt at gmail.com
Mon Jun 18 23:52:58 CEST 2012
You are perhaps not using suppressPackageStartupMessages() correctly
if you're getting those warnings: my .Rprofile has these lines:
suppressPackageStartupMessages(library("quantmod"))
suppressPackageStartupMessages(library("ggplot2"))
suppressPackageStartupMessages(library("lattice"))
but produces no warnings (the first does when loading in a clean
session without suppressing)
Best,
Michael
On Mon, Jun 18, 2012 at 4:08 PM, Lopez, Dan <lopez235 at llnl.gov> wrote:
> Ouch Bert. Not patience for the newbies, I see.
>
> I know what ?anything means which is why I didn't ask about ?Startup. But being that I just recently discovered what Rprofile.site is I thought it might do something different within the start-up file and tried it both ways.
>
> Besides I think what I really need is to just figure out as I said:
> I did however go to the Misc menu and select "List search path" and got the below results. Not exactly sure what it means but I do notice that several of the packages that popup at startup as being "masked" appear in this list. Maybe this is the problem? If so how do you take out what you don't need at startup?
>
> > search()
>
> [1] ".GlobalEnv" "package:stats" "package:graphics" "package:grDevices" "package:datasets"
>
> [6] "package:rattle" "package:R.utils" "package:utils" "package:R.oo" "package:R.methodsS3"
>
> [11] "package:methods" "Autoloads" "package:base"
>
>
>
> Dan
>
> From: Bert Gunter [mailto:gunter.berton at gene.com]
> Sent: Monday, June 18, 2012 1:50 PM
> To: Lopez, Dan
> Cc: David Winsemius; R help (r-help at r-project.org)
> Subject: Re: [R] Error w/ Start up Script
>
> I gave you the references you need. It's up to you to read and understand how to use them. You apparently need to work harder to do so. BTW
>
> ?anything
>
> is an alternative way to type
>
> help("anything")
>
> at the command line for R's help pages.
>
> -- Bert
> On Mon, Jun 18, 2012 at 1:34 PM, Lopez, Dan <lopez235 at llnl.gov<mailto:lopez235 at llnl.gov>> wrote:
> Hi Bert,
>
> I tried entering: "?suppressPackageStartupMessages" and then "suppressPackageStartupMessages" into my Rprofile.site file and the messages still came up.
>
> I did however go to the Misc menu and select "List search path" and got the below results. Not exactly sure what it means but I do notice that several of the packages that popup at startup as being "masked" appear in this list. Maybe this is the problem? If so how do you take out what you don't need at startup?
>
>> search()
> [1] ".GlobalEnv" "package:stats" "package:graphics" "package:grDevices" "package:datasets"
> [6] "package:rattle" "package:R.utils" "package:utils" "package:R.oo" "package:R.methodsS3"
> [11] "package:methods" "Autoloads" "package:base"
>> 0
>
> Thanks.
> Dan
>
> From: Bert Gunter [mailto:gunter.berton at gene.com<mailto:gunter.berton at gene.com>]
> Sent: Monday, June 18, 2012 1:10 PM
> To: Lopez, Dan
> Cc: David Winsemius; R help (r-help at r-project.org<mailto:r-help at r-project.org>)
> Subject: Re: [R] Error w/ Start up Script
>
> ?suppressPackageStartupMessages
>
> Put this into your appropriate startup file.
> ?Startup ## for details on starting R and what files are executed at startup.
>
> -- Bert
> On Mon, Jun 18, 2012 at 12:46 PM, Lopez, Dan <lopez235 at llnl.gov<mailto:lopez235 at llnl.gov>> wrote:
> David,
>
> Sorry I should have been more specific. They are not as much errors as they are extra script that is running at startup after "Type q() to quit R". It wasn't there before. And am thinking eventually it could become a problem.
>
> Thanks.
> Dan
>
> Here it is again...what it looks like when I first startup R (partial copy and paste):
>
> ....
> ...
> ..
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> Attempting to load the environment 'package:R.utils'
> R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?R.methodsS3 for help.
> R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.
>
> Attaching package: 'R.oo'
>
> The following object(s) are masked from 'package:R.methodsS3':
>
> throw.default
> ..
> ...
> ....
> -----Original Message-----
> From: David Winsemius [mailto:dwinsemius at comcast.net<mailto:dwinsemius at comcast.net>]
> Sent: Monday, June 18, 2012 12:12 PM
> To: Lopez, Dan
> Cc: R help (r-help at r-project.org<mailto:r-help at r-project.org>)
> Subject: Re: [R] Error w/ Start up Script
>
>
> On Jun 18, 2012, at 11:25 AM, Lopez, Dan wrote:
>
>> I noticed about a couple weeks ago that my R start up script starting
>> showing the below errors, following the line "Type 'q()' to quit R"
>>
>
> I didn't see any errors reported. I didn't see any warnings, either.
>
> --
> David.
>
>> Not sure what I did different and so far it hasn't caused major
>> problems but kind of fear that it will.
>>
>> Can you please help?
>> I also posted my Rprofile below.
>>
>> Attempting to load the environment 'package:R.utils'
>> R.methodsS3 v1.2.2 (2010-11-17) successfully loaded. See ?
>> R.methodsS3 for help.
>> R.oo v1.9.3 (2012-03-18) successfully loaded. See ?R.oo for help.
>>
>> Attaching package: 'R.oo'
>>
>> The following object(s) are masked from 'package:R.methodsS3':
>>
>> throw.default
>>
>> The following object(s) are masked from 'package:methods':
>>
>> getClass, getClasses, getMethods
>>
>> The following object(s) are masked from 'package:base':
>>
>> attach, detach, gc, load, save
>>
>> R.utils v1.12.1 (2012-03-20) successfully loaded. See ?R.utils for
>> help.
>>
>> Attaching package: 'R.utils'
>>
>> The following object(s) are masked from 'package:utils':
>>
>> timestamp
>>
>> The following object(s) are masked from 'package:base':
>>
>> cat, commandArgs, getOption, inherits, isOpen, lapply, parse,
>> warnings
>>
>> And here is my Rprofile.site file specs:
>> # Things you might want to change
>> # options(papersize="a4")
>> # options(editor="notepad")
>> # options(pager="internal")
>>
>> # set the default help type
>> # options(help_type="text")
>> options(help_type="html")
>>
>> # set a site library
>> # .Library.site <- file.path(chartr("\\", "/", R.home()), "site-
>> library")
>>
>> # set a CRAN mirror
>> local({r <- getOption("repos")
>> r["CRAN"] <- "http://cran.cnr.Berkeley.edu"
>> options(repos=r)})
>>
>> # Give a fortune cookie, but only to interactive sessions # (This
>> would need the fortunes package to be installed.) # if
>> (interactive())
>> # fortunes::fortune()
>>
>>
>> Daniel Lopez
>> Workforce Analytics & Metrics Team
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org<mailto:R-help at r-project.org> mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius, MD
> West Hartford, CT
>
> ______________________________________________
> R-help at r-project.org<mailto:R-help at r-project.org> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
>
>
>
>
> --
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
> Internal Contact Info:
> Phone: 467-7374
> Website:
> http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
>
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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