DefineClones fatal error: could not find function "slidingArrayOf5mers"

[Former user]

DefineClones fails to run with error :

Error in FUN(c("NNTGTGCAAGAGGAATACGATTTTTGGAGTGGTTACCTACGTACAACTGGTTCGACCCCTGGNN", : could not find function "slidingArrayOf5mers" In addition: Warning message: replacing previous import by ‘seqinr::count’ when loading ‘shm’

(Hope this is not user error. This might be the first time I've tried to run hs5f. I did "hg update" for shm and changeo manually, and nothing with the name seqinr in my shm repo has a modified date before Feb5. slidingArrayOf5mers funcion is in selection.R, and there is only one file by that name on my system so I don't think it's a path issue.)

[Former user]

1 - I built/installed on the master node but in order to run the job on another node via SGE, i have to build/install updated code on each of those non-master nodes. I thought building the source on an NFS-shared drive was sufficient, but obviously i don't really understand what's going on. Anyway, not your problem.

2 - I didn't have the R package doSNOW; this one is a bit more mysterious because it's loaded for shm installation successfully in the past..... shm installation now tries to get it from CRAN but fails with "trying to use CRAN without setting a mirror" ... not sure if that's a line that needs to be set in shm install or maybe it would work to set it in my .Rprofile

[Jason Vander Heiden]

1 - Hrm. Curious. Maybe your ~/R directory isn't on the NSF share? You can add R package locations to you .Rprofile with:

    .libPaths(c(.libPaths(), "/nfs/drive/in/outerspace")) 

2 - I believe this can be resolved in your .Rprofile by setting the default mirror (see below .Rprofile addition). The SHM dependcy config looks to be correct. However, I'll also add an install_deps() step to the update script, as it would be best to do that before build() anyway. Also, any time you run install.packages("somepackage", type="source", repos=NULL) it won't install dependencies from CRAN because repos=NULL... Just for further annoyance.

    .First <- function() {
    options(
      repos = c(CRAN = "http://cran.rstudio.com/"),
      browserNLdisabled = TRUE,
      deparse.max.lines = 2)
    }
    if (interactive()) {
      suppressMessages(require(devtools))
    }