Fix [BioC] yeastCC installs ok, but won't load; R2.0.1

[Robert Gentleman]

On Feb 5, 2005, at 10:04 PM, JDCGo at aol.com wrote:

> Received a suggestion from Jim MacDonald to look for and extract this  
> zip file, and then try to load.
>
> C:\Program Files\R\rw2001\library\yeastCC\data\Rdata.zip
>
> Extracted this zip file which created yeastCC.RData, which is a file  
> of type "R Workspace".  Then dragged yeastCC.Rdata onto the RGui to do  
> the load as shown here:
>

I'm pretty confused by what you are doing.
In R, if you want to access data from a package, like yeastCC,
you first install the package. All that that does is to download it and  
put it in the right place.
You need to use R's tools for doing that:
  on windows either use the menu or install.packages("yeastCC"). You  
cannot download the zip file and unpack it, since R does some  
manipulation on the files when it installs them.
So if you have not installed this way, then you should do it this way.

Then, any (and hence every) time you want to use the package you will  
need to load it.
so
  library("yeastCC")

does that.
Then search(), should report that it is there (I have no concept of why  
you are calling .packages() )

At this point data(), with no arguments will list all the data sets you  
have access to. Data in packages that are installed, but not loaded (or  
attached)  is not available. Data in packages that were incorrectly  
installed (using unzip, for example) are also not available.

Why are you calling load? It would help if you could point me to the  
documentation that gave you some of these ideas, as I would like to try  
and correct it. There is rather a lot (like the Introduction to R) that  
should give you somewhat better instructions.

Robert

>> load("C:/Program  
>> Files/R/rw2001/library/yeastCC/data/Rdata/yeastCC.RData")
>

This will load exactly the data file, but it is certainly not the  
recommended way to do that.
If it worked without error then you do have a data file at the location  
given by that path.

> Although still get same error:
>
>> library(yeastCC)
> Error in open.connection(con, "rb") : unable to open connection

So your library was not correctly installed, not much good can happen  
until this is fixed.

> In addition: Warning message:
> cannot open compressed file  
> `C:/PROGRA~1/R/rw2001/library/yeastCC/data/yeastCC.RData'
> Error in library(yeastCC) : .First.lib failed for 'yeastCC'

Yes, well a comparison of this path with the one above certainly ought  
to suggest what the problem is.


>>
>
> and don't see yeastCC in packages:
>
>> (.packages())
> [1] "multtest"   "genefilter" "survival"   "splines"    "affy"        
> "reposTools" "annotate"
> [8] "Biobase"    "tools"      "methods"    "stats"      "graphics"    
> "grDevices"  "utils"
> [15] "datasets"   "base"
>>
>

  Well, you got an error loading, why do you suppose it would have  
loaded anyways? And as I said above use search(), to see which packages  
are attached.

> and get warning with data command:
>
>> data(yeastCC)
> Warning message:
> Data set 'yeastCC' not found in: data(yeastCC)
>>

Yes, well, again, you got that error message above, repeating the  
command, will give you the same error message.

>
> exprs works:
>
>> dat <- exprs(yeastCC)
>> dim(dat)
> [1] 6178   77
>>
>

  And again, you directly loaded the data, using load, so it is there,  
no surprise, your sequence of commands, and the errors and warnings  
seem to suggest that the package is incorrectly installed. I would try  
to fix that first.

Robert

> and see data:
>
>> dat[1:5,1:5]
>       cln3.1 cln3.2 clb2.2 clb2.1 alpha0
> YAL001C   0.15     NA  -0.22   0.07  -0.15
> YAL002W  -0.07  -0.76  -0.12  -0.25  -0.11
> YAL003W  -1.22  -0.27  -0.10   0.23  -0.14
> YAL004W  -0.09   1.20   0.16  -0.14  -0.02
> YAL005C  -0.60   1.01   0.24   0.65  -0.05
>>
>
> Thanks,
>
> John Garner
>
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> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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