Yes, I think so. On Tue, 21 Sept 2021 at 15:53, Shraddha Pai <shraddha....@utoronto.ca> wrote:
> 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
