Hi all, Despite moving rarely-used packages to Suggests and eliminating some (e.g. TCGAutils), the number of dependencies is still listed as 200 for our package netDx. https://www.bioconductor.org/packages/devel/bioc/html/netDx.html#since Is there anything else we can do to cut down on dependencies?
Thank you, Shraddha On Tue, Sep 21, 2021 at 5:35 PM Shraddha Pai <shraddha....@utoronto.ca> wrote: > Hi Michael, > Thanks! Looks like the package trying to load 'rtracklayer' was > 'TCGAutils' (see graph from Zugang above, generated using pkgndep - looks > to be quite useful). Turns out TCGAutils really wasn't necessary for my > package so I just took it out and removed all associated dependencies - > mercifully an easier fix. > > Thanks for your help, > Shraddha > > On Mon, Sep 20, 2021 at 2:57 PM Michael Lawrence < > lawrence.mich...@gene.com> wrote: > >> 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....@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 >> >> >> >> -- >> Michael Lawrence >> Principal Scientist, Director of Data Science and Statistical Computing >> Genentech, A Member of the Roche Group >> Office +1 (650) 225-7760 >> micha...@gene.com >> >> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
