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 <lcoll...@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@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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