RnBeads Error Message

[jae-bum Bae]

Hi all

I recentyl start to use RnBeads and pretty new to R, when setting analysis, I got below error message

working directory is C:\Users\Administrator\Documents

report.dir <- "~/RnBeads/analysis/reports"

> rnb.run.analysis(dir.reports=report.dir, sample.sheet=sample.annotation,data.dir=idat.dir, data.type="infinium.idat.dir")

2014-12-29 13:34:48     5.7  STATUS                                                             STARTED RnBeads Pipeline

2014-12-29 13:34:48     5.7    INFO                                                                 Initialized report index and saved to index.html

2014-12-29 13:34:48     5.7  STATUS                                                                 STARTED Loading Data

2014-12-29 13:34:48     5.7    INFO                                                                     Number of cores: 1

2014-12-29 13:34:48     5.7    INFO                                                                     Loading data of type "infinium.idat.dir"

2014-12-29 13:34:48     5.7  STATUS                                                                     STARTED Loading Data from IDAT Files

2014-12-29 13:34:48     5.7    INFO                                                                         Added column barcode to the provided sample annotation table

2014-12-29 13:35:48     6.2  STATUS                                                                     COMPLETED Loading Data from IDAT Files

2014-12-29 13:35:52     5.4  STATUS                                                                     Loaded data from E:\image data//9829119091

2014-12-29 13:35:53     5.5  STATUS                                                                     Added data loading section to the report

2014-12-29 13:35:53     5.5  STATUS                                                                     Loaded 1 samples and 485577 sites

2014-12-29 13:35:53     5.5    INFO                                                                     Output object is of type RnBeadRawSet

2014-12-29 13:35:53     5.6  STATUS                                                                 COMPLETED Loading Data

we found following errors, setwd(dfile) : cannot change working directory

 warnings:

In dir.create(dfile, recursive = TRUE) :

  directory 'C:\Users\Administrator\Documents\C:\Users'

Can anyone give me a clue how to solve this error?

Thanks

Jae-Bum

[Yassen Assenov]

Hello Jae-Bum,

Sorry for the late reply. RnBeads has a bug that causes this error in
some cases when saving datasets in Windows. We fixed the bug and plan to
release the new version of RnBeads next week. I can send you a download
link once it is released.

Greetings,
Yassen

> Hi all
>
> I recentyl start to use RnBeads and pretty new to R, when setting
> analysis, I got below error message
>

> working directory is *C:\Users\Administrator\Documents
> *
> *report.dir <- "~/RnBeads/analysis/reports"
>
> *

> *

> we found following errors, setwd(dfile) : cannot change working directory

> *
> * warnings:*
> *In dir.create(dfile, recursive = TRUE) :*
> * directory 'C:\Users\Administrator\Documents\C:\Users'*

>
> Can anyone give me a clue how to solve this error?
>
> Thanks
>
> Jae-Bum
>

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[Diana Van Der Plaat]

Hi all, 

I have a similar problem as Jae-Bum

working directory is C:/Users/Data/Methylation/

analysis.dir <- "~/RnBeads"

report.dir <- file.path(analysis.dir, "reports")

When i give the following commant, i get this error:

rnb.run.analysis(dir.reports=data.dir, sample.sheet=sample.annotation,data.dir=idat.dir, data.type="infinium.idat.dir")

Error in rnb.run.analysis(dir.reports = data.dir, sample.sheet = sample.annotation,  : 

Could not initialize reports in ~/RnBeads/reports ; make sure this path does not exist.

I am absolutely sure that the path is not existing, but I keep getting this error.

What can i do?

Kind regards, 

Diana 

Op maandag 29 december 2014 08:11:11 UTC+1 schreef jae-bum Bae:

[Brenna Hott]

Hi Diana,

Did you ever figure this out? I am having the same issue. 

Brenna

[Fadl AlAkwaa]

Dear Yassen,
Yesterday I try to run RnBeads on your dataset and it works fine, but today I have the below error:

Error in setwd(dfile) : cannot change working directory

I do not know why it works fine first time without this error?

When I create a new user in my server, this problem solved, why?
So I need to create a new user if I want to use RnBeads in A new dataset.

I appreciate your reply.

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