[Bioc-devel] EXTERNAL: Re: Too many dependencies / MultiAssayExperiment + rtracklayer

Tue Oct 19 15:38:06 CEST 2021

Hi Marcel and Hervé,
Easiest fix ever, for me! :)

Whew, I'm glad all that sleuthing around dependencies brought down the
count significantly.

Thank you for following up on this,
Shraddha

On Mon, Oct 18, 2021 at 5:59 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Indeed. The wrong set of repos was used for the count:
>
>    db <-
> available.packages(repos=BiocManager::repositories(version="3.13"))
>
>    deps <- tools::package_dependencies("netDx", db, recursive=TRUE,
> reverse=FALSE, which="strong")
>
>    lengths(deps)
>
>    # netDx
>
>    #   200
>
>
> Fixed now: https://bioconductor.org/packages/3.14/netDx
>
> Sorry for the inconvenience.
>
> Cheers,
> H.
>
>
> On 18/10/2021 13:31, Marcel Ramos wrote:
> > 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.pai using 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.michael using 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.pai using 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 using 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
> >>>> michafla using gene.com
> >>>>
> >>>> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
> >>>>
> >>      [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioc-devel using 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 using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]