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

6 messages · Shraddha Pai, Michael Lawrence, 顾祖光 +1 more

Original
Shraddha Pai
# 
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*
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Michael Lawrence
# 
Hi Shraddha,
(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 at utoronto.ca> wrote:
顾祖光
# 
An analysis with the pkgndep package (https://github.com/jokergoo/pkgndep)
shows
the three heaviest packages are RCy3, clusterExperiment and netSmooth. If
you can
move these three packages to SUGGESTS (where the packages are loaded only
when related
functions are called), I think the number of dependent packages will be
reduced
to 130~150, or maybe less.

library(pkgndep)
x = pkgndep("netDx")
plot(x)

The plot is here
https://github.com/jokergoo/ComplexHeatmap/files/7198274/test.pdf

Cheers,
Zuguang


On Mon, 20 Sept 2021 at 20:37, Shraddha Pai <shraddha.pai at utoronto.ca>
wrote:
Shraddha Pai
# 
Hi Zugang,
Thanks for the tip on pkgndep - very helpful visualization. If I understand
correctly, rows in the matrix are sorted by number of dependency packages
loaded by a package required by netDx. Can see the long stripes for the
packages you mention.
Those packages are used by 1-2 minor functions for visualizing results so I
could indeed move them to Suggests.

Question: When moving packages from Depends to SUGGESTS, I should also
remove the @imports tag from inline Roxygen2 documentation? And then in the
function itself, should I qualify the functions used by package name?
e.g. if I remove RCy3 from the Depends section, I would remove @imports
RCy3 from the function doc of the corresponding function. Then within that
function wherever I use a function I would prepend with RCy3:: (e.g.
RCy3::commandsGET() instead of commandsGET()).

Is this correct?

Thanks,Shraddha
On Mon, Sep 20, 2021 at 3:41 PM ??? <jokergoo at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Zuguang Gu
    

    

      
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Yes, I think so.

On Tue, 21 Sept 2021 at 15:53, Shraddha Pai <shraddha.pai at utoronto.ca>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Shraddha Pai
    

    

      
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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 at gene.com>
wrote: