[Bioc-devel] IRanges - PartitioningByEnd not found when package method runs.

[Ben Ward (TGAC)]

Hi All,

I am having an issue with an un-exported method in a package I am developing, the package imports Biostrings and IRanges.

I have created a minimal, reproducible example, (many many thanks to Martin Morgan for telling me how to do this) in this repo branch: https://github.com/Ward9250/testRpkg/tree/PartByEnd

The method, as you will see from the branch, is called subsetSites, and is supposed to cut a DNAString set down to only the sites/base positions indicated by a provided vector of integers. It does this by indexing the DNAStringSet with re.int.

If I try to run this however, it seems to fail, indicating that it cannot find the PartitioningByEnd function. This puzzles me as I know the function is part of IRanges, which is imported in the package, and I would assume Biostrings would import any IRanges functionality it needed for the DNAStringSet indexing operator.

Below is an example run of what I see, and my session info.

If anyone can see what my issue is or knows how to solve this it would be a big help.

Many Thanks,
Ben W.


bward at n78620:/tmp$ git clone git at github.com:ward9250/testRpkg.git -b PartByEnd
Cloning into 'testRpkg'...
remote: Counting objects: 18, done.
remote: Compressing objects: 100% (10/10), done.
remote: Total 18 (delta 1), reused 18 (delta 1), pack-reused 0
Receiving objects: 100% (18/18), done.
Resolving deltas: 100% (1/1), done.
Checking connectivity... done.
bward at n78620:/tmp$ cd testRpkg
bward at n78620:/tmp/testRpkg$ R CMD INSTALL .
* installing to library ‘/usr/users/TGAC_ga002/bward/R/x86_64-pc-linux-gnu-library/3.2’
* installing *source* package ‘testRpkg’ ...
** R
** preparing package for lazy loading
** help
No man pages found in package  ‘testRpkg’
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (testRpkg)
bward at n78620:/tmp/testRpkg$ R --vanilla -e "sessionInfo(); testRpkg::doit()"
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

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Type 'contributors()' for more information and
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> sessionInfo(); testRpkg::doit()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

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

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
Error in end(PartitioningByEnd(x)) :
  error in evaluating the argument 'x' in selecting a method for function 'end': Error: could not find function "PartitioningByEnd"
Calls: <Anonymous> ... subset_List_by_List -> fast_path_FUN -> .unlist_NL_subscript -> end
Execution halted



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