load_all on package with S4 classes fails

[DarwinAwardWinner]

I'm trying to do some development on BiocParallel (https://github.com/Bioconductor/BiocParallel), which defines an S4 class hierarchy across several R files. When I attempt to use load_all() on it, I get:

> load_all()
Loading BiocParallel
Error in getClass(what, where = where) (from BatchJobsParam-class.R#9) : 
  "BiocParallelParam" is not a defined class

This looks kind of like #623, but the error message is different, so I'm not sure if it's the same issue.

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grDevices datasets  parallel  graphics  stats4    stats     utils    
[8] methods   base     

other attached packages:
[1] devtools_1.8.0.9000  foreach_1.4.2        plyr_1.8.2          
[4] stringr_1.0.0        IRanges_2.2.1        ggplot2_1.0.1       
[7] S4Vectors_0.6.0      BiocGenerics_0.14.0  BiocInstaller_1.18.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6          git2r_0.10.1         futile.logger_1.4.1 
 [4] bitops_1.0-6         futile.options_1.0.0 iterators_1.0.7     
 [7] tools_3.2.0          digest_0.6.8         memoise_0.2.1       
[10] gtable_0.1.2         proto_0.3-10         httr_0.6.1          
[13] roxygen2_4.1.1       rversions_1.0.0      grid_3.2.0          
[16] snow_0.3-13          XML_3.98-1.1         reshape2_1.4.1      
[19] lambda.r_1.1.7       magrittr_1.5         scales_0.2.4        
[22] codetools_0.2-11     MASS_7.3-40          colorspace_1.2-6    
[25] stringi_0.4-1        RCurl_1.96-0         munsell_0.4.2    

[Geoff99]

Hi @DarwinAwardWinner , Issue #623 should be fixed in the versions of devtools and roxygen2 your sessionInfo report mentions, so it's probably not that.

Just a guess - have you got #' @include filename.r type roxygen2 comments in your various files, to ensure that the collate sequence in the DESCRIPTION file is correct. By default devtools loads files in alphabetical order of the filenames, which can lead to code being out of order and hence R may be trying to create a subclass before it knows about the superclass (if the correct collate order is not alphabetical). PS If you have manually entered the collate sequence in the DESCRIPTION file don't use the #' @include approach - it would wipe out all the manual entries :-(

Or alternatively, if the missing superclass (BiocParallelParam) comes from another package, you might be missing an #' @importClassesFrom whateverpkg BiocParallelParam type statement.

Emphasise these are both just guesses. Hope they help though.

PPS Both guesses wrong - sorry. Just had a look at your github link and you have manually created collate sequences in the DESCRIPTION file, which have BioParallelParam defined before BatchJobsParam. Maybe something to do with the fact you have both Collate.unix and Collate.windows entries is confusing devtools or roxygen2?

I'll have to leave this to someone more knowledgeable than me.

Collate.unix: AllGenerics.R BiocParallelParam-class.R ErrorHandling.R 
 bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpmapply-methods.R 
 bpiterate-methods.R bpschedule-methods.R bpstart-methods.R bpstop-methods.R 
 bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R 
 bpaggregate-methods.R bpvalidate.R SnowParam-class.R MulticoreParam-class.R 
 register.R SerialParam-class.R DoparParam-class.R SnowParam-utils.R 
 BatchJobsParam-class.R progress.R utilities.R unix/pvec.R  
 unix/mclapply.R unix/zzz.R 

Collate.windows: AllGenerics.R BiocParallelParam-class.R ErrorHandling.R 
 bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpmapply-methods.R 
 bpiterate-methods.R bpschedule-methods.R bpstart-methods.R bpstop-methods.R 
 bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R 
 bpaggregate-methods.R bpvalidate.R SnowParam-class.R MulticoreParam-class.R 
 register.R SerialParam-class.R DoparParam-class.R SnowParam-utils.R 
 BatchJobsParam-class.R progress.R utilities.R windows/zzz.R 

[hadley]

The problem is that you're using collate.unix and collate.windows which devtools doesn't know about. I'd be happy to accept a PR to add support (you'd need to patch https://github.com/hadley/devtools/blob/master/R/load-code.r#L40-L65). They're rare enough that I don't have the time to add support myself.

[lock]

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