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

Mon Oct 18 23:58:57 CEST 2021

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
>>>>
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>>
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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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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com