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boutroslab / caRpools

Exploratory data analysis for pooled CRISPR/Cas9 screens
http://www.crispr-analyzer.de
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CaRpools-extended-PDF.Rmd errors #7

Open xuguorong2016 opened 6 years ago

xuguorong2016 commented 6 years ago

Hi,

I installed the virtual box and loaded the image on my mac machine. When I launched the R-studio to run the test command and I got the below error. I also tried other R markdown templates and all failed. Any thoughts?

library(caRpools) use.caRpools(type=NULL, file="CaRpools-extended-PDF.Rmd", miaccs="MIACCS.xls", check=TRUE, work.dir=NULL)

Quitting from lines 342-382 (CaRpools-extended-PDF.Rmd) Show Traceback

Rerun with Debug Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing

Thanks, Michael

jos4uke commented 6 years ago

Hi maybe a little bit late, I also encountered the same error using the provided VM and on the sample dataset.

This seems related to Gene Annotation with biomaRt. This is controlled in the MIACCS.xls file (lines 84-91). Especially the lines 85 (Convert gene identifier?) and 90 (Annotate final gene hit list?). By default they are all TRUE. When disabled (FALSE), use.caRpools() run untill the end without errors and you get your report.

So if you don't need converting/annotating gene with biomaRt, you can disable these options.

jos4uke commented 6 years ago

Maybe upgrade biomart package could fix this issue as stated here https://support.bioconductor.org/p/79422/

While i am using the provided VM, and not my own install, I didn't try yet