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

[Henrik Bengtsson]

If you're willing to depend on R (>= 4.0.0), then tools::R_user_dir() can
replace the 'rappdirs' package.

/Henrik

On Mon, Oct 18, 2021, 09:05 Shraddha Pai <shraddha.pai using utoronto.ca> wrote:

> Hi all,
> Despite moving rarely-used packages to Suggests and eliminating some (e.g.
> TCGAutils), the number of dependencies is still listed as 200 for our
> package netDx.
> https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since
> Is there anything else we can do to cut down on dependencies?
>
> Thank you,
> Shraddha
>
> On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai <shraddha.pai using utoronto.ca>
> wrote:
>
> > 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
> >> > 0A3
> >> > *@OICR_news* <https://twitter.com/oicr_news> | *www.oicr.on.ca*
> >> > <http://www.oicr.on.ca/>
> >> >
> >> >
> >> >
> >> > *Collaborate. Translate. Change lives.*
> >> >
> >> >
> >> >
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> >>
> >>
> >>
> >> --
> >> Michael Lawrence
> >> Principal Scientist, Director of Data Science and Statistical Computing
> >> Genentech, A Member of the Roche Group
> >> Office +1 (650) 225-7760
> >> michafla using gene.com
> >>
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