[Bioc-devel] A question on adding data in R package development

[Li, Dongmei]

Hi Laurent,

Thanks so much for all your help! It works now.

Have a nice weekend!

Best,
Dongmei

On 2/28/15, 9:21 AM, "Laurent Gatto" <lg390 at cam.ac.uk> wrote:

>
>Dear Dongmei, 
>
>On 28 February 2015 14:08, Li, Dongmei wrote:
>
>> Hi,
>>
>> I have a question on adding data in R package development. This is my
>> first time to write a R package and I used the Rstudio for it. I save an
>> example data into .Rda format using the save() function in R and put in
>> into the data subdirectory in my package. When I used Rstudio to compile
>> the vignettes file, it works fine with the following R code:
>>
>> 
>>ovarian_cancer_ex<-load("~/Documents/RBM/data/ovarian_cancer_example.rda"
>>)
>> ovarian_cancer_ex
>> [1] "ovarian_cancer_methylation"
>> summary(ovarian_cancer_methylation)
>>
>>
>> The Rstudio also build the source package successfully. However, it
>>gives
>> me the following error message after I uploaded to the Bioconductor
>>(whey
>> they are trying to build packages for different systems using the source
>> package):
>> Warning in readChar(con, 5L, useBytes = TRUE) :
>>   cannot open compressed file
>> '/Users/pkgbuild/Documents/RBM/data/ovarian_cancer_example.rda',
>>probable
>> reason 'No such file or directory'
>>
>> Error: processing vignette 'RBM.Rnw' failed with diagnostics:
>>  chunk 7 
>> Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
>> Execution halted
>>
>>
>> I will really appreciate if anyone could give me a hint for solving this
>> issue. Thanks so much for all your help!
>
>You are right in putting your serialised object in the data
>subdirectory. Once your package is installed, these objects can be
>loaded by simply typing
>
>  data(ovarian_cancer_ex)
>
>Note that you will also need to write a man page.
>
>The reason you see the error is because the package is not build in its
>original location, and hence the file can not be found with the
>hardcoded path. In such situations, when you want to get the path to a
>file in a package, for example the extdata directory, you would
>
>  system.file("extdata", package = "Biobase")
>
>Hope this helps,
>
>Laurent
>
>
>> Best,
>> Dongmei
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> 
>>https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman
>>_listinfo_bioc-2Ddevel&d=AwIBAg&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQ
>>RxhA&r=azjhQW59umxfk67jsIXeg7AS2ugqKLkykGYJFRwaLto&m=b8-cQqHJDCcJQ12ZIGNG
>>lcYeOp1Y_eg7VSHmu-yUcMw&s=3XR8XyloI-O7xfLl86eOwOtj0F5oNaTLvrKsM-GBABE&e=
>