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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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getGEOSuppFiles function bug #63

Closed ibilgen closed 6 years ago

ibilgen commented 6 years ago

I am using getGEOSuppFiles function to download supplementary files for each of the series_id in the list. It usually returns an error after a progressing. The problem is that sometimes it gives error and stops but in some cases it works successfully.

below the code, it shows the code I run and the error. The problem is seen in trying URL. After "..suppl//" part, a string starting with "mailto:" comes.

getGEOSuppFiles("GSE939", baseDir = "supp_files/", makeDirectory = T) https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE939/suppl/ OK trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE939/suppl//mailto:%5bno%20address%20given%5d' Error in download.file(file.path(url, i), destfile = file.path(storedir, : cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE939/suppl//mailto:%5bno%20address%20given%5d' In addition: Warning message: In download.file(file.path(url, i), destfile = file.path(storedir, : cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE939/suppl//mailto:%5bno%20address%20given%5d': HTTP status was '404 Not Found'

seandavi commented 6 years ago

Thanks for the report, @ibilgen. I fixed this recently. The new behavior is to return NULL when no supplementary files are available. Could you update GEOquery the most recent version to check that is the behavior you now see?

seandavi commented 6 years ago

Closing for now. @ibilgen, feel free to update this issue if you are still noticing problems after upgrading. If you do, the output of sessionInfo() would be helpful.