lgatto
commented
7 years ago Thank you very much for the report, @moghbaie. I think this was a temporary glitch, as I managed to run the chunk.
> px <- PXDataset("PXD002412")
> px
Object of class "PXDataset"
Id: PXD002412 with 1037 files
[1] 'FINV_uniprot_sprot_human_BSA_TRY_BCN_GFP_TEV_062911.fasta' ... [1037] 'interact-JO_120120_OT3_TRIM28-P004.prot.xml'
Use 'pxfiles(.)' to see all files.
> pxfiles(px)[6]
[1] "GR_130124_14_OT3_SIRT5_IB001_1_HEK293.mzXML"
> mzf <- pxget(px, pxfiles(px)[6])
Downloading 1 file
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/07/PXD002412/GR_130124_14_OT3_SIRT5_IB001_1_HEK293.mzXML'
Content type 'unknown' length 278025154 bytes (265.1 MB)
==================================================
> library(mzR)
Loading required package: Rcpp
> openMSfile(mzf)
Mass Spectrometry file handle.
Filename: GR_130124_14_OT3_SIRT5_IB001_1_HEK293.mzXML
Number of scans: 28561 Still thanks for reporting it, as there have been some issues in the past with the server at the ISB and reports like this might help them to identify when/what goes wrong.
I'll close the issue, but do not hesitate to re-open it if you still hit issues.
I'm trying to get xml data from PRIDE and I'm getting this error: px <- PXDataset("PXD002412") pxfiles(px) mzf <- pxget(px, pxfiles(px)[6])
Downloading 1 file trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/07/PXD002412/interact-HG_130628_84_OT3_WDR5_IB001_1_293.prot.xml' Error in download.file(urls[i], toget[i], ...) : cannot open URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/07/PXD002412/interact-HG_130628_84_OT3_WDR5_IB001_1_293.prot.xml' In addition: Warning message: In download.file(urls[i], toget[i], ...) : InternetOpenUrl failed: 'The login request was denied '