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

[Shraddha Pai]

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*
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>> >
>> >
>> >
>> > *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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