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

[Marcel Ramos]

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.*
>>>>
>>>>
>>>>
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>>>
>>>
>>> --
>>> 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
>>>
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---
Marcel Ramos
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Dept. of Biostatistics & Bioinformatics
Elm St. & Carlton St.
Buffalo, New York 14263


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