search

kasperdanielhansen / genbioconductor

Materials for Genomics Data Science: Introduction to Bioconductor
Other
92 stars 79 forks source link

biomaRt error: Error in scan file: line 1 did not have 3 elements #17

Closed caloto closed 4 years ago

caloto commented 4 years ago

Good morning,

This error is sent after:

ensembl <- useMart("ensembl") ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl) all.genes <- getBM(attributes=c('chromosome_name', 'band', 'start_position', 'end_position', 'strand', 'hgnc_symbol'), mart=ensembl)

This code has been correctly run in the past. Do you have any idea why is broken now?

Thank you in advance!

kasperdanielhansen commented 4 years ago

Are you using an updated version of biomaRt? Occasionally Ensembl change their formats so the R package needs to change.

On Fri, Oct 9, 2020 at 11:11 AM caloto notifications@github.com wrote:

Good morning,

This error is sent after:

ensembl <- useMart("ensembl") ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl) all.genes <- getBM(attributes=c('chromosome_name', 'band', 'start_position', 'end_position', 'strand', 'hgnc_symbol'), mart=ensembl)

This code has been correctly run in the past. Do you have any idea why is broken now?

Thank you in advance!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/kasperdanielhansen/genbioconductor/issues/17, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH2FF7I4WZFEFVO4EYTSJ3HT5ANCNFSM4SJ2EJ4Q .

-- Best, Kasper

caloto commented 4 years ago

I am using biomaRt 2.40.5 version. I tried to reinstall it but the error persists.

In other Q&A, I could see 8 years ago somebody with the same problem due to RCurl update...

caloto commented 4 years ago

https://support.bioconductor.org/p/48335/ This is the link to that conversation

caloto commented 4 years ago

In any case, this is not working for me... Since the error is thrown at the first line, I would suggest a new format in the downloaded files not supported previously due to any third part update biomaRt is dependent on (??)

caloto commented 4 years ago

Okay, now working. Actually, i have no idea how the issue has been self-solved... Amazing

My apologies for the inconvenience!

kasperdanielhansen commented 4 years ago

This works for me right now using R-4.0 with Bioconductor 3.11 and R-4.0.3-patched with Bioconductor 3.12. Now, both of these installations needs some package updating which I'm doing and then trying again.

On Fri, Oct 9, 2020 at 12:34 PM caloto notifications@github.com wrote:

In any case, this is not working for me... Since the error is thrown at the first line, I would suggest a new format in the downloaded files not supported previously due to any third part update biomaRt is dependent on (??)

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/kasperdanielhansen/genbioconductor/issues/17#issuecomment-706105457, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABF2DH2EXTMSZUURQZMMT6DSJ3RMVANCNFSM4SJ2EJ4Q .

-- Best, Kasper