All good and no more warning message.

Thanks a lot for your time and your help,
Julie


From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com]
Sent: Wednesday, 28 November 2012 11:23 AM
To: Julie Collet
Cc: bioconductor@r-project.org
Subject: Re: [BioC] install pdInfoBuilder package

your installation isn't up-to-date... you need to update the installed packages... the current pdInfoBuilder is 1.22.0... and, if the problem persists, I'll address it asap. b

On 28 November 2012 01:19, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> wrote:
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pd.110608.dser.sc.expr_0.0.1 pdInfoBuilder_1.20.0         oligo_1.20.4
[4] oligoClasses_1.18.0          affxparser_1.28.1            RSQLite_0.11.2
[7] DBI_0.2-5                    Biobase_2.16.0               BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] affyio_1.24.0         BiocInstaller_1.4.7   Biostrings_2.24.1     bit_1.1-8
 [5] codetools_0.2-8       ff_2.2-7              foreach_1.4.0         IRanges_1.14.4
 [9] iterators_1.0.6       preprocessCore_1.18.0 splines_2.15.1        stats4_2.15.1
[13] tools_2.15.1          zlibbioc_1.2.0

From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com<mailto:beniltoncarvalho@gmail.com>]
Sent: Wednesday, 28 November 2012 11:17 AM

To: Julie Collet
Cc: bioconductor@r-project.org<mailto:bioconductor@r-project.org>
Subject: Re: [BioC] install pdInfoBuilder package

I'm pretty sure I had addressed that issue (of SQLite)... what's the result for sessionInfo()  ?

On 28 November 2012 01:10, Julie Collet <j.collet@uq.edu.au<mailto:j.collet@uq.edu.au>> 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

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@gmail.com<mailto:beniltoncarvalho@gmail.com>]
Sent: Tuesday, 27 November 2012 8:04 PM
To: Julie Collet
Cc: bioconductor@r-project.org<mailto:bioconductor@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@uq.edu.au<mailto:j.collet@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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