[Bioc-devel] Windows-only issue with downloading a Rdata file and loading it with R

[Gabe Becker]

I wonder if raw only means "raw after line return munging"? can you attach
the file that gets downloaded  via email? (off list is fine)

On Fri, Jun 17, 2016 at 1:44 PM, Leonardo Collado Torres <lcollado at jhu.edu>
wrote:

> Hi,
>
> I'm trying to figure out what is going wrong with an error that pops
> up on Windows only. It's currently the only error for a package that I
> recently submitted to Bioc. The function is fairly simple: it
> downloads a Rdata file from the web and loads it.
>
> If I try to download and load the file with R, the following error
> occurs (only on Windows):
>
>
> > library('downloader')
> > download('
> https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true',
> destfile = 'test.Rdata')
> trying URL '
> https://github.com/leekgroup/recount-website/blob/master/metadata/metadata_clean_sra.Rdata?raw=true
> '
> Content type 'application/octet-stream' length 2531337 bytes (2.4 MB)
> downloaded 2.4 MB
>
> > load('test.Rdata')
> Error: ReadItem: unknown type 50, perhaps written by later version of R
> > traceback()
> 1: load("test.Rdata")
> > options(width = 120)
> > devtools::session_info()
> Session info
> -----------------------------------------------------------------------------------------------------------
>  setting  value
>  version  R version 3.3.0 (2016-05-03)
>  system   x86_64, mingw32
>  ui       Rgui
>  language (EN)
>  collate  English_United States.1252
>  tz       America/New_York
>  date     2016-06-17
>
> Packages
> ---------------------------------------------------------------------------------------------------------------
>  package    * version date       source
>  devtools     1.11.1  2016-04-21 CRAN (R 3.3.0)
>  digest       0.6.9   2016-01-08 CRAN (R 3.3.0)
>  downloader * 0.4     2015-07-09 CRAN (R 3.3.0)
>  memoise      1.0.0   2016-01-29 CRAN (R 3.3.0)
>  withr        1.0.1   2016-02-04 CRAN (R 3.3.0)
> >
>
>
> If I open the same url on my browser and manually download the file,
> then everything works as shown below:
>
> > load('metadata_clean_sra.Rdata')
> > metadata_clean
> Loading required package: S4Vectors
> Loading required package: stats4
> Loading required package: BiocGenerics
> Loading required package: parallel
> ## removed more output
>
> > options(width = 120)
> > devtools::session_info()
> Session info
> -----------------------------------------------------------------------------------------------------------
>  setting  value
>  version  R version 3.3.0 (2016-05-03)
>  system   x86_64, mingw32
>  ui       Rgui
>  language (EN)
>  collate  English_United States.1252
>  tz       America/New_York
>  date     2016-06-17
>
> Packages
> ---------------------------------------------------------------------------------------------------------------
>  package      * version date       source
>  BiocGenerics * 0.19.1  2016-06-17 Bioconductor
>  devtools       1.11.1  2016-04-21 CRAN (R 3.3.0)
>  digest         0.6.9   2016-01-08 CRAN (R 3.3.0)
>  IRanges      * 2.7.2   2016-06-07 Bioconductor
>  memoise        1.0.0   2016-01-29 CRAN (R 3.3.0)
>  S4Vectors    * 0.11.3  2016-06-03 Bioconductor
>  withr          1.0.1   2016-02-04 CRAN (R 3.3.0)
> > print(object.size(metadata_clean), units = 'Mb')
> 30.5 Mb
>
> The object itself is a DataFrame and was created using R 3.3.1 with
> S4Vectors version 0.11.4. I get the same error if using a Unix machine
> I re-save the data using R 3.3.0 (with S4Vectors from Bioc-release).
>
> Some google leads are "corrupt file" or something about a hidden
> session Rdata file. But from the manual test, everything looks line.
> Unless downloader::download() (or alternatively utils::download.file()
> ) is corrupting the file.
>
>
> An option would be to include the data in the package, but I'd like to
> avoid doing so to minimize the package size. It already has a big
> data.frame that is necessary for the package to work. This short
> function is there for convenience.
>
> Best,
> Leo
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>


-- 
Gabriel Becker, Ph.D
Associate Scientist
Bioinformatics and Computational Biology
Genentech Research

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