Rapporter/rapport

namespace collision with GenomicRanges

leipzig opened this issue · 6 comments

leipzig commented

Not sure if this is avoidable:

> source("http://bioconductor.org/biocLite.R")
> biocLite("GenomicRanges")
> library("GenomicRanges")
> library("rapport")
> tpl.export(tpl.example('example', 'all'))
Error in envRefSetField(x, what, refObjectClass(x), selfEnv, value) : 
  "time" is not a field in class “Report”
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] rapport_0.31        reshape_0.8.4       plyr_1.7.1         
[4] RColorBrewer_1.0-5  lattice_0.20-0      evaluate_0.4.1     
[7] ascii_2.1           GenomicRanges_1.6.7 IRanges_1.12.6     

loaded via a namespace (and not attached):
[1] grid_2.14.1 stringr_0.6
ramnathv commented

I get the same error without loading the GenomicRange package. So it is likely that the conflict is due to a different package. Here is my sessionInfo

R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] rapport_0.2        RJSONIO_0.98-0     reshape_0.8.4      plyr_1.7.1        
 [5] RColorBrewer_1.0-5 lattice_0.20-0     evaluate_0.4.1     ascii_2.1         
 [9] tikzDevice_0.6.2   cacheSweave_0.6    formatR_0.3-4      optparse_0.9.4    
[13] getopt_1.17        highlight_0.3.1    parser_0.0-14      Rcpp_0.9.9        
[17] codetools_0.2-8    stashR_0.3-4       filehash_2.2      

loaded via a namespace (and not attached):
[1] digest_0.5.1    grid_2.14.1     knitr_0.2       pgfSweave_1.2.1 stringr_0.6
daroczig commented

Thank you both for providing details!
I am checking out how could we resolve that and will give some feedback soon.

ramnathv commented

By the way, it works fine for me when I use the Mac RGUI. The error occurs only with RStudio. So I am thinking, one way to zero in on the source of the error is to look at packages loaded by RStudio, and not by the Mac RGUI, and intersecting it with those loaded by GenomicRanges. Here is my sessionInfo for the Mac RGUI, where things work.

R version 2.14.1 (2011-12-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] rapport_0.2        RJSONIO_0.98-0     reshape_0.8.4     
[4] plyr_1.7.1         RColorBrewer_1.0-5 lattice_0.20-0    
[7] evaluate_0.4.1     ascii_2.1         

loaded via a namespace (and not attached):
[1] grid_2.14.1 stringr_0.6
aL3xa commented

@leipzig, @ramnathv thanks for feedback. I tried replicating the bugs you've posted, but without success. I tried both on Linux and Windows (in VM). However, that's irrelevant, 'cause both of you guys are using MacOS. However, @daroczig could replicate it, and he's working on bugfix now.

(sorry for packageVersion info... my mistake. turn.on("brain", "Alex"))

daroczig commented

Thank you all again for details!
I could replicate the bug after loading the IRanges package on Windows RGUI, but not in RStudio.

Anyway, imho this bug is fixed, but please test and provide some feedback if the GH version does work for you.
I suggest you to install it with devtools.

If everything goes right, then we could send a hotfix today to CRAN too.

ramnathv commented

I checked and it works for me. Thanks.