[Bioc-devel] Too many dependencies / MultiAssayExperiment + rtracklayer
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 at 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.* This message and any attachments may contain confident...{{dropped:22}}