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

[Shraddha Pai]

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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