500_Effectively_Using_the_DelayedArray_Framework.Rmd

[lwaldron]

I'm creating an issue for each workshop, to be closed when both 1) the workshop is complete, and 2) it compiles without problems. Please note problems and status updates here.

ERROR: can't open file @line 559

[lwaldron]

Quitting from lines 568-586 (500_Effectively_Using_the_DelayedArray_Framework.Rmd) 
Error in h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : 
  Error in h5checktypeOrOpenLoc(). Cannot open file. File 'hdf5_mat.h5' does not exist.
Calls: <Anonymous> ... eval -> eval -> <Anonymous> -> h5checktypeOrOpenLoc
Execution halted

[PeteHaitch]

Will fix this week (just off flight from US to Aus)

[PeteHaitch]

The immediate issue should be fixed in db5c813158e069474cca296ea226ca56a44a9056

I'll continue to work on material

[LiNk-NY]

Hi Pete, @PeteHaitch I'm not sure why this is coming up:

label: unnamed-chunk-19

Quitting from lines 669-682 (500_Effectively_Using_the_DelayedArray_Framework.Rmd) 
Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  : 
  long vectors not supported yet: connections.c:5861
Calls: local ... <Anonymous> -> <Anonymous> -> lazyLoadDBinsertVariable
Execution halted
Error in Rscript_render(f, render_args, render_meta) : 
  Failed to compile 500_Effectively_Using_the_DelayedArray_Framework.Rmd
Calls: <Anonymous> ... render_new_session -> tryCatch -> tryCatchList -> Rscript_render
Execution halted

Exited with status 1.

Could it have something to do with the cache? I'll delete and re-run.

[lshep]

it is a caching issue but the r code chunk needs to have the cache=FALSE - the cache=FALSE corrects this ERROR

[LiNk-NY]

Thanks Lori. I'll try this.

[seandavi]

The

Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  : 
  long vectors not supported yet: connections.c

is fixed by f29aa79.

[LiNk-NY]

@seandavi Do we want to use cache.lazy = TRUE for all chunks? I can add it to our _common.R file.

[seandavi]

I don't know the answer to that. I see that it is really just for very large caches; there were only two workflows that showed this error and I have corrected them.

On Thu, Jul 19, 2018 at 3:09 PM Marcel Ramos notifications@github.com wrote:

@seandavi https://github.com/seandavi Do we want to use cache.lazy = TRUE for all chunks? I can add it to our _common.R file.

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[LiNk-NY]

Thanks for that Sean