Hi Zugang, Thanks for the tip on pkgndep - very helpful visualization. If I understand correctly, rows in the matrix are sorted by number of dependency packages loaded by a package required by netDx. Can see the long stripes for the packages you mention. Those packages are used by 1-2 minor functions for visualizing results so I could indeed move them to Suggests.
Question: When moving packages from Depends to SUGGESTS, I should also remove the @imports tag from inline Roxygen2 documentation? And then in the function itself, should I qualify the functions used by package name? e.g. if I remove RCy3 from the Depends section, I would remove @imports RCy3 from the function doc of the corresponding function. Then within that function wherever I use a function I would prepend with RCy3:: (e.g. RCy3::commandsGET() instead of commandsGET()). Is this correct? Thanks,Shraddha On Mon, Sep 20, 2021 at 3:41 PM 顾祖光 <joker...@gmail.com> wrote: > An analysis with the pkgndep package (https://github.com/jokergoo/pkgndep) > shows > the three heaviest packages are RCy3, clusterExperiment and netSmooth. If > you can > move these three packages to SUGGESTS (where the packages are loaded only > when related > functions are called), I think the number of dependent packages will be > reduced > to 130~150, or maybe less. > > library(pkgndep) > x = pkgndep("netDx") > plot(x) > > The plot is here > https://github.com/jokergoo/ComplexHeatmap/files/7198274/test.pdf > > Cheers, > Zuguang > > > On Mon, 20 Sept 2021 at 20:37, Shraddha Pai <shraddha....@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 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. >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
