[BioC] install pdInfoBuilder package

[James W. MacDonald]

Hi Julie,

On 11/27/12 8:10 PM, Julie Collet wrote:
> Hi Benito,
>
> Many thanks for your help.
> I initially tried:
>> setwd("C:/Users/uqjcol10/Desktop")
>> install.packages("pd.110608.dser.sc.expr.zip", repos=NULL)
>> library(pd.110608.dser.sc.expr)
> Error in library(pd.110608.dser.sc.expr) :
>    'pd.110608.dser.sc.expr' is not a valid installed package
>
This is because you used winzip or whatever to zip up the package you 
made. What you want to be pointing to is the directory that existed 
before you ran winzip. You might be able to just unzip and then run 
install.packages(), but you may need to recreate the package first.

Also note that Benilton advised you to use the additional argument type 
= "source". So you should be doing something like

install.packages("pd.110608.dser.sc.expr", repos = NULL, type = "source")

Best,

Jim



> So the installation didn't give any error message, I could just not access the library. Following your message I tried:
>
>> install.packages("pd.110608.dser.sc.expr", repos=NULL, type='source')
> --- Please select a CRAN mirror for use in this session ---
> * installing *source* package 'pd.110608.dser.sc.expr' ...
> ** R
> ** data
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> *** arch - i386
> Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>    there is no package called 'SQLite'
> *** arch - x64
> Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>    there is no package called 'SQLite'
>
>
> * DONE (pd.110608.dser.sc.expr)
>> library(pd.110608.dser.sc.expr)
> Warning message:
> In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>    there is no package called 'SQLite'
>
> Should I worry about the Warning message or is it completely normal?
>
> It surely looks much more promising. Many thanks for your help,
> Julie
>
>
>
> From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com]
> Sent: Tuesday, 27 November 2012 8:04 PM
> To: Julie Collet
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] install pdInfoBuilder package
>
> Hi Julie,
>
> The first step is to identify where you have the directory (containing the package) created by pdInfoBuilder.
>
> I don't have a Windows machine to try with more realistic "names", but suppose you the directory 'pd.110608.dser.sc.expr' is inside the 'folder' "C:/MyDocuments".
>
> So, I'd do the following (from within R):
>
> setwd("C:/MyDocuments")
> install.packages('pd.110608.dser.sc.expr', type='source')
>
> and that would be it...
>
> Can you please try and let me know exactly what output you get?
>
> b
>
> On 27 November 2012 07:10, Julie Collet<j.collet at uq.edu.au<mailto:j.collet at uq.edu.au>>  wrote:
> Dear all,
>
> I created an annotation package with pdInfoBuilder. All looked like it worked. I first tried to install it directly with R by
> - Creating a zip file (with winzip or 7 zip)
> - Installing it directly with R by install.packages("pd.110608.dser.sc.expr.zip", repos=NULL)
> All looked like it worked until I call the library and get
>> library(pd.110608.dser.sc.expr)
> Error in library(pd.110608.dser.sc.expr) :
>    'pd.110608.dser.sc.expr' is not a valid installed package
>
> I then tried with R tools following http://www.biostat.wisc.edu/~kbroman/Rintro/Rwinpack.html
> And got the following message error on the gcc-4.6.3 session
> Starting program: CMD INSTALL -build pd.110608.dser.sc.expr
> No executable specified, use 'target exec'.
> I played around with various combinations of path that would make sense to me. But 1) I'm not sure this is where the problem come from 2) I have a very limited notion of what 'path' means so I'm not sure what should actually be in the path and in what order.
>
> You'd have guessed, I'm on Windows (7).
>
> Many thanks for your help,
> Julie
>
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