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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Issue with GDCprepare #548

Closed Lattesnow closed 1 year ago

Lattesnow commented 1 year ago

This is what I got from GDCprepare

Starting to add information to samples => Add clinical information to samples => Adding TCGA molecular information from marker papers => Information will have prefix 'paper_' prad subtype information from:doi:10.1016/j.cell.2015.10.025 Available assays in SummarizedExperiment : => unstranded => stranded_first => stranded_second => tpm_unstrand => fpkm_unstrand => fpkm_uq_unstrand => Saving file: TCGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData Error in gzfile(file, "wb") : cannot open the connection In addition: Warning message: In gzfile(file, "wb") : cannot open compressed file 'TCGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData', probable reason 'Invalid argument'

manwarA commented 1 year ago

Hi, I am not an expert, but if you are working on Windows, this file name is problematic "CGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData", Windows can not create anything with ":" in its name. You can manually assign a file name and then try again.

=> Saving file: TCGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData Error in gzfile(file, "wb") : cannot open the connection ## cannot save the file with this name In addition: Warning message: In gzfile(file, "wb") : cannot open compressed file 'TCGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData', probable reason 'Invalid argument' ## no saving and then no opening

I encountered the same error recently.

Lattesnow commented 1 year ago

Hi, I am not an expert, but if you are working on Windows, this file name is problematic "CGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData", Windows can not create anything with ":" in its name. You can manually assign a file name and then try again.

=> Saving file: TCGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData Error in gzfile(file, "wb") : cannot open the connection ## cannot save the file with this name In addition: Warning message: In gzfile(file, "wb") : cannot open compressed file 'TCGA-PRADTranscriptome_ProfilingWed_Oct_19_23:39:22_2022.RData', probable reason 'Invalid argument' ## no saving and then no opening

I encountered the same error recently.

Solved the problem, thank you