object 'OUTPUT_DIR' not found

[wleepang]

I'm getting the following error when I run the example code for SPADE.driver:

Error in paste(OUTPUT_DIR, "tables", sep = "/") : 
  object 'OUTPUT_DIR' not found
> traceback()
3: paste(OUTPUT_DIR, "tables", sep = "/")
2: dir.create(paste(OUTPUT_DIR, "tables", sep = "/"), recursive = TRUE, 
       showWarnings = FALSE) at driver.R#227
1: SPADE.driver(data_file_path, out_dir = "../../tmp", cluster_cols = c("marker1", 
       "marker2"))

Perhaps this was supposed to be out_dir as specified in the function arguments?

(note: I installed the github version since the "official" version on BioConductor still lists igraph0 as a dependency)

[zbjornson]

:) You happened to download the github version while I've been hacking at it without much QA. Just fixed this bug, thanks for catching. Try installing again.

[wleepang]

Greatly appreciate the impressively rapid turnaround :)

Unfortunately, I'm now getting another error:

Producing tables...
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file 'U:/tmp//tables/bySample/U:/tmp/SimulatedRawData.fcs.density.fcs.cluster.fcs.anno.Rsave_table.csv': No such file or directory
> traceback()
7: file(file, ifelse(append, "a", "w"))
6: write.table(pivot, file = paste(out_dir, "/tables/bySample/", 
       name, "_table", ".csv", sep = ""), row.names = FALSE, col.names = TRUE, 
       sep = ",", dec = ".", qmethod = "double")
5: eval(expr, envir, enclos)
4: eval(expr, p)
3: eval.parent(Call)
2: write.csv(pivot, file = paste(out_dir, "/tables/bySample/", name, 
       "_table", ".csv", sep = ""), row.names = FALSE) at driver.R#262
1: SPADE.driver(data_file_path, out_dir = "U:/tmp", cluster_cols = c("marker1", 
       "marker2"))

perhaps using file.path() and sprintf() instead of paste():

file=file.path(out_dir, 'tables', 'bySample', sprintf('%s_table.csv', name))

[zbjornson]

Ugh, sorry. Until I fix that, you might try downloading this instead, which no longer depends on igraph0 and doesn't have that bit of code I added that's breaking.

https://github.com/nolanlab/spade/archive/2f2d21a22a522918807eb270cd3fe30526aed651.zip

[wleepang]

Thanks, using the older commit works without error.