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 confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.
"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
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