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Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download usin...

Dear all, I've been diving a bit deeper into this per request of Tomas Kalibra, and found the following : - the lock on the file is only after trying to read it using oligo, so that's not a R problem in itself. The problem is independent of extrenal packages. - using Windows' fc utility and cygwin's cmp utility I found out that every so often the download.file() function inserts an extra byte. There's no rea...

On 05/02/2018 03:21 PM, Joris Meys wrote: > Dear all, > > I've noticed by trying to download gz files from here : > https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 > > At the bottom one can download GSM907811.CEL.gz . If I download this > manually and try > > oligo::read.celfiles("GSM907811.CEL.gz") > > everything works fine. (oligo is a bioConduct...

Use mode="wb" when you download the file. See https://github.com/HenrikBengtsson/Wishlist-for-R/issues/30. R core, and others, is there a good argument for why we are not making this the default download mode? It seems like a such a simple fix to such a common "mistake". Henrik On Thu, May 3, 2018, 00:44 Joris Meys <jorism...

...olves it. Apologies for not trying the obvious. Cheers Joris On Thu, May 3, 2018 at 2:10 PM, Martin Morgan <martin.morgan at roswellpark.org > wrote: > > > On 05/02/2018 03:21 PM, Joris Meys wrote: > >> Dear all, >> >> I've noticed by trying to download gz files from here : >> https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 >> >> At the bottom one can download GSM907811.CEL.gz . If I download this >> manually and try >> >> oligo::read.celfiles("GSM907811.CEL.gz") >> >> everything works...