Hi Shraddha, Note that the badge on the landing page is using this formula (~ from the `biocViews` package):
```r db <- available.packages(repos = BiocManager::repositories()) deps <- tools::package_dependencies("netDx", db, recursive = TRUE, reverse = FALSE, which = "strong") lengths(deps) #' netDx #' 109 ``` This number is not matching up with the value listed in the badge. Hervé is currently looking into it and will have an update soon. Best regards, Marcel On 10/18/21 12:05 PM, Shraddha Pai 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 --- Marcel Ramos Bioconductor Core Team Roswell Park Comprehensive Cancer Center Dept. of Biostatistics & Bioinformatics Elm St. & Carlton St. Buffalo, New York 14263 This email message may contain legally privileged and/or...{{dropped:4}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel