If you're willing to depend on R (>= 4.0.0), then tools::R_user_dir() can replace the 'rappdirs' package.
/Henrik On Mon, Oct 18, 2021, 09:05 Shraddha Pai <shraddha....@utoronto.ca> wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel