search

genomicsclass / labs

Rmd source files for the HarvardX series PH525x
http://genomicsclass.github.io/book
MIT License
2.01k stars 1.95k forks source link

Trouble building biocintro_5x / bioc1_LiftOver.Rmd #63

Closed shwetagopaul92 closed 5 years ago

shwetagopaul92 commented 7 years ago

@vjcitn
Building the biocintro_5x / bioc1_LiftOver.Rmd throws an error:

Quitting from lines 66-70 (bioc1_liftOver.Rmd) Error in seqlevels<-(*tmp*, force = TRUE, value = "chr1") : unused argument (force = TRUE) Calls: ... handle -> withCallingHandlers -> withVisible -> eval -> eval

vjcitn commented 7 years ago

thanks, removed force setting in seqlevels

vjcitn commented 7 years ago

I have further modified this vignette to use AnnotationHub to get the chain file, commenting out the reference to the home folder. @shwetagopaul92 could you check this new version? You will need to install AnnotationHub package.

vjcitn commented 7 years ago

I have further modified this vignette to use AnnotationHub to get the chain file, commenting out the reference to the home folder. @shwetagopaul92 could you check this new version? You will need to install AnnotationHub package.

On Mon, May 15, 2017 at 3:37 PM, Shweta Gopaulakrishnan < notifications@github.com> wrote:

@vjcitn https://github.com/vjcitn Building the biocintro_5x / bioc1_LiftOver.Rmd throws an error:

Quitting from lines 66-70 (bioc1_liftOver.Rmd) Error in seqlevels<-(tmp, force = TRUE, value = "chr1") : unused argument (force = TRUE) Calls: ... handle -> withCallingHandlers -> withVisible -> eval -> eval

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/genomicsclass/labs/issues/63, or mute the thread https://github.com/notifications/unsubscribe-auth/AEaOwuThvdnFUDj0BGleSgrFZg8oi2U2ks5r6Kl7gaJpZM4Nbly3 .

shwetagopaul92 commented 7 years ago

@vjcitn Yes, this is building fine now! Thanks!