[Bioc-devel] Too many dependencies / MultiAssayExperiment + rtracklayer

[Michael Lawrence]

Hi Shraddha,

>From the rtracklayer perspective, it sounds like Rsamtools is
(indirectly) bringing in those system libraries. I would have expected
zlibbioc to cover the zlib dependency, and perhaps bz2 and lzma
support is optional. Perhaps a core member could comment on that.

In the past, I've used this package
https://github.com/Bioconductor/codetoolsBioC to identify missing
NAMESPACE imports. In theory, you could remove the rtracklayer import
and run functions in that package to identify the symbol-level
dependencies. The output is a bit noisy though.

Btw, using @importFrom only allows you to be selective of symbol-level
dependencies, not package-level.

Michael

On Mon, Sep 20, 2021 at 11:37 AM Shraddha Pai <shraddha.pai using utoronto.ca> wrote:
>
> Hello again,
> I'm trying to simplify the dependencies for my package "netDx", make it
> easier to install. It's currently got over 200(!) + some Unix libraries
> that need to be installed.
>
> 1. I ran pkgDepMetrics() from BiocPkgTools to find less-needed pkgs, and
> the package with the most dependencies is MultiAssayExperiment (see below
> email). I'm using MAE to construct a container - is there a way to use
> @importFrom calls to reduce MAE dependencies?
>
> 2. Another problem package is rtracklayer which requires Rhtslib, which
> requires some unix libraries: zlib1g-dev libbz2-dev liblzma-dev. I'm not
> sure which functionality in the package requires rtracklayer - how can I
> tell? Is there a way to simplify / reduce these deps so the user doesn't
> have to install all these unix packages?
>
> 3. Are there other "problem packages" you can see that I can remove? Let's
> assume for now ggplot2 stays because people find it useful to have plotting
> functions readily available.
>
> Thanks very much in advance,
> Shraddha
> ---
> "ImportedAndUsed" "Exported" "Usage" "DepOverlap" "DepGainIfExcluded"
> "igraph" 1 782 0.13 0.05 0
> "ggplot2" 1 520 0.19 0.19 0
> "pracma" 1 448 0.22 0.03 0
> "plotrix" 1 160 0.62 0.03 1
> "S4Vectors" 2 283 0.71 0.03 0
> "grDevices" 1 112 0.89 0.01 0
> "httr" 1 91 1.1 0.05 0
> "scater" 1 85 1.18 0.4 0
> "utils" 3 217 1.38 0.01 0
> "GenomeInfoDb" 1 60 1.67 0.06 0
> "stats" 12 449 2.67 0.01 0
> "bigmemory" 1 35 2.86 0.03 3
> "RCy3" 12 386 3.11 0.32 18
> "BiocFileCache" 1 29 3.45 0.23 3
> "glmnet" 1 24 4.17 0.07 2
> "parallel" 2 33 6.06 0.01 0
> "combinat" 1 13 7.69 0.01 1
> "MultiAssayExperiment" 4 46 8.7 0.22 1
> "foreach" 2 23 8.7 0.02 0
> "graphics" 8 87 9.2 0.01 0
> "GenomicRanges" 15 106 14.15 0.08 0
> "rappdirs" 1 7 14.29 0.01 0
> "reshape2" 1 6 16.67 0.05 0
> "RColorBrewer" 1 4 25 0.01 0
> "netSmooth" 1 3 33.33 0.82 3
> "Rtsne" 1 3 33.33 0.02 0
> "doParallel" 1 2 50 0.03 0
> "ROCR" 2 3 66.67 0.05 4
> "clusterExperiment" NA 122 NA 0.74 0
> "IRanges" NA 255 NA 0.04 0
>
>
> --
>
> *Shraddha Pai, PhD*
> Principal Investigator, OICR
> Assistant Professor, Department of Molecular Biophysics, University of
> Toronto
> shraddhapai.com; @spaiglass on Twitter
> https://pailab.oicr.on.ca
>
>
> *Ontario Institute for Cancer Research*
> MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G
> 0A3
> *@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
> <http://www.oicr.on.ca/>
>
>
>
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