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