Undocumented prerequisites

[jankowtf]

First of: kudos for trying to ensure reproducibility!

Forgive me if I might have overlooked it, but I think you forgot to document some prerequisites that must be met in order to get your package up and running.

After reading your post and trying to install gRAN (or GRANBase as it's called in your post?), I experienced the following issues due to missing package dependencies:

1. BiocInstaller needs to be installed first.

2. BiocStyle needs to be installed first.

3. After installing these packages, I still get the following error:

   • checking for file 'C:\Users\jat\AppData\Local\Temp\RtmpYXNZw4\devtools1ef44d404295\gRAN-master/DESCRIPTION' ... OK
   • preparing 'GRANBase':
   • checking DESCRIPTION meta-information ... OK
   • installing the package to build vignettes
   • creating vignettes ...Warning: running command '"Q:/home/apps/RAPPTO~1/apps/r/R-31~1.1/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1 ERROR

   Error: processing vignette 'GRAN-Overview.Rnw' failed with diagnostics: chunk 3 Error in GRANonGRAN(repo) : copy failed Execution halted

This is the code I ran:

source("http://bioconductor.org/biocLite.R")
biocLite("BiocInstaller")
biocLite("BiocStyle")

require("devtools")
install_github("gRAN", "gmbecker")

My sessionInfo():

R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
[1] BiocInstaller_1.14.2 devtools_1.5        

loaded via a namespace (and not attached):
 [1] digest_0.6.4    evaluate_0.5.5  httr_0.4        memoise_0.2.1  
 [5] packrat_0.4.0.4 parallel_3.1.1  RCurl_1.95-4.3  stringr_0.6.2  
 [9] tools_3.1.1     whisker_0.3-2  

[gmbecker]

@Rappster,

Thanks for trying it out (and caring about reproducibility!).

BiocInstaller is indeed required (and listed as such in the DESCRIPTION file). BiocStyle is suggested, which means it's required to build the vignette, but not for the core package functionality to work. It is a (major) limitation of install_github (though an understandable one) that it doesn't grab package dependencies.

Parts of GRAN (sorry about the capitalization inconsistency) aren't currently supported on windows (namely the mechanism for constructing permanent, continuously integrated repositories). That is what is failing in the vignette.

The stuff for finding old package versions, however, IS.

I'd say in the short term, install using install_github it with build_vignettes=FALSE, while I gradually try to increase Windows support for other portions of the package.

~G