[Bioc-devel] Confusing namespace issue with IRanges 1.99.17

[Martin Morgan]

Hi Leonardo --

On 07/07/2014 03:27 PM, Leonardo Collado Torres wrote:
> Hello BioC-devel list,
>
> I am currently confused on a namespace issue which I haven't been able
> to solve. To reproduce this, I made the simplest example I thought of.
>
>
> Step 1: make some toy data and save it on your desktop
>
> library(IRanges)
> DF <- DataFrame(x = Rle(0, 10), y = Rle(1, 10))
> save(DF, file="~/Desktop/DF.Rdata")
>
> Step 2: install the toy package on R 3.1.x
>
> library(devtools)
> install_github("lcolladotor/fooPkg")
> # Note that it passes R CMD check
>
> Step 3: on a new R session run
>
> example("foo", "fooPkg")
> # Change the location of DF.Rdata if necessary
>
>
> You will see that when running the example, the session information is
> printed listing:
>
> other attached packages:
> [1] fooPkg_0.0.1
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.11.3 IRanges_1.99.17     parallel_3.1.0
> S4Vectors_0.1.0     stats4_3.1.0        tools_3.1.0
>
>
> Then the message for loading IRanges is showed, which is something I
> was not expecting and thus the following session info shows:
>
> other attached packages:
> [1] IRanges_1.99.17     S4Vectors_0.1.0     BiocGenerics_0.11.3
> fooPkg_0.0.1
>
> loaded via a namespace (and not attached):
> [1] stats4_3.1.0 tools_3.1.0
>
> Meaning that IRanges, S4Vectors and BiocGenerics all went from "loaded
> via a namespace" to "other attached packages".
>
>
>
> All the fooPkg::foo() is doing is using a mapply() to go through a
> DataFrame and a list of indices to subset the data as shown at
> https://github.com/lcolladotor/fooPkg/blob/master/R/foo.R#L26 That is:
>
> res <- mapply(function(x, y) { x[y] }, DF, index)
>
> I thus thought that the only thing I would need to specify on the
> namespace is to import the '[' IRanges method.
>
> Checking with BiocCheck and codetoolsBioC suggests importing the
> method for mapply() from BiocGenerics. Doing so doesn't affect things
> and R still loads IRanges on that mapply() call. Importing the '['
> method from S4Vectors doesn't help either. Most intriging, importing
> the whole S4Vectors, BiocGenerics and IRanges still doesn't change the
> fact that IRanges is loaded when evaluating the same line of code
> shown above.
>
> Any clues on what I am missing or doing wrong?
>

This comes from S4Vectors::extractROWS

 > selectMethod(extractROWS, c("Rle", "integer"))
Method Definition:

function (x, i)
{
     if (!suppressWarnings(require(IRanges, quietly = TRUE)))
         stop("Couldn't load the IRanges package. You need to install ",
             "the IRanges\n  package in order to subset an Rle object.")

...

which moves the IRanges package from loaded to attached. Maybe that should be 
'suppressPackageStartupMessages' or if (!IRanges %in% loadedNamespaces()) and 
functions referenced by IRanges:::...



>
>
> In my use case, I'm trying to keep the namespace as small as possible
> (to minimize loading time) because it's for a tiny package that has a
> single function. This tiny package is then loaded on a
> BiocParallel::blapply() call using BiocParallel::SnowParam() which
> performs much better than BiocParallel::MulticoreParam() in terms of
> keeping the memory under control.

probably it is not desirable to move packages from loaded to attached, but I 
don't think this influences performance in a meaningful way?

Martin

>
>
>
>
> Thank you for your help!
> Leo
>
> Leonardo Collado Torres, PhD student
> Department of Biostatistics
> Johns Hopkins University
> Bloomberg School of Public Health
> Website: http://www.biostat.jhsph.edu/~lcollado/
> Blog: http://lcolladotor.github.io/
>
>
>
>
>
>
>
>
>
>
>
> Full output from running the example:
>
>
>
>
>> example("foo", "fooPkg")
>
> foo> ## Initial info
> foo> sessionInfo()
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (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] fooPkg_0.0.1
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.11.3 IRanges_1.99.17     parallel_3.1.0
> S4Vectors_0.1.0     stats4_3.1.0        tools_3.1.0
>
> foo> ## Load data
> foo> load("~/Desktop/DF.Rdata")
>
> foo> ## Run function
> foo> result <- foo(DF)
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (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] fooPkg_0.0.1
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.11.3 IRanges_1.99.17     parallel_3.1.0
> S4Vectors_0.1.0     stats4_3.1.0        tools_3.1.0
> Loading required package: parallel
>
> Attaching package: ‘BiocGenerics’
>
> The following objects are masked from ‘package:parallel’:
>
>      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
> clusterExport, clusterMap, parApply, parCapply, parLapply,
>      parLapplyLB, parRapply, parSapply, parSapplyLB
>
> The following object is masked from ‘package:stats’:
>
>      xtabs
>
> The following objects are masked from ‘package:base’:
>
>      anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
> do.call, duplicated, eval, evalq, Filter, Find, get,
>      intersect, is.unsorted, lapply, Map, mapply, match, mget, order,
> paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
>      rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table,
> tapply, union, unique, unlist
>
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (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] parallel  stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] IRanges_1.99.17     S4Vectors_0.1.0     BiocGenerics_0.11.3
> fooPkg_0.0.1
>
> loaded via a namespace (and not attached):
> [1] stats4_3.1.0 tools_3.1.0
>>
>
>
>
> The same thing happens with the following setup:
>
> R version 3.1.1 RC (2014-07-07 r66083)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> 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] parallel  stats     graphics  grDevices datasets  utils     methods
> [8] base
>
> other attached packages:
> [1] IRanges_1.99.17     S4Vectors_0.1.0     BiocGenerics_0.11.3
> [4] fooPkg_0.0.1        colorout_1.0-2
>
> loaded via a namespace (and not attached):
> [1] stats4_3.1.1 tools_3.1.1
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793