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

[Shraddha Pai]

Hi Michael,
Thanks! Looks like the package trying to load 'rtracklayer' was 'TCGAutils'
(see graph from Zugang above, generated using pkgndep - looks to be quite
useful). Turns out TCGAutils really wasn't necessary for my package so I
just took it out and removed all associated dependencies - mercifully an
easier fix.

Thanks for your help,
Shraddha

On Mon, Sep 20, 2021 at 2:57 PM Michael Lawrence <lawrence.michael using gene.com>
wrote:

> 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
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> >
> >
> >
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>
> --
> Michael Lawrence
> Principal Scientist, Director of Data Science and Statistical Computing
> Genentech, A Member of the Roche Group
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