[Bioc-devel] Moving minfi classes definition to a lighter package
顾祖光
jokergoo @end|ng |rom gm@||@com
Thu Mar 4 10:29:08 CET 2021
Hi all,
I have a package `pkgndep` (
https://cran.r-project.org/web/packages/pkgndep/index.html) which can make
a dependency heatmap for a specific package. As shown in the following
figure for minfi package (version 1.30.0)
https://jokergoo.github.io/pkgndep/stat/image/minfi.png
Rows are the packages minfi depends on, grouped by whether they are in
Depends, Imports or Suggests fields,
and columns are the namespaces each package brings to the R session. For
this version of minfi (1.30.0), loading
minfi will bring 89 namespaces and if also loading the packages in
Suggests, there will be 117 namespaces loaded.
If we only look at the dependency for Depends and Imports, actually there
are three packages: bumphunter, GEOquery
and genefilter which are the major reasons for the heavy dependency of
minfi. If there is a way to move these three
packages to Suggests, the dependency will be reduced to 30+.
Best,
Zuguang
On Wed, 3 Mar 2021 at 14:43, Robert Castelo <robert.castelo using upf.edu> wrote:
> hi,
>
> about a year ago we had a developer's forum session devoted to this
> subject, you might find useful the discussion we had starting on minute
> 29th here:
>
> https://www.youtube.com/watch?v=xsM4nN85cok
>
> part of the result of that discussion is in section 7 of this vignette:
>
>
> http://bioconductor.org/packages/release/bioc/vignettes/BiocPkgTools/inst/doc/BiocPkgTools.html#dependency-burden
>
> which illustrates how to calculate some metrics on the dependency burden
> of a package using functionality we implemented in the package
> BiocPkgTools, in the case of minfi, this is the output:
>
> library(BiocPkgTools)
> depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"),
> dependencies=c("Depends", "Imports"))
> minfidepmetrics <- pkgDepMetrics("minfi", depdf)
> minfidepmetrics
> ImportedAndUsed Exported Usage DepOverlap
> DepGainIfExcluded
> DelayedArray 1 188 0.53
> 0.11 0
> grDevices 1 112 0.89
> 0.01 0
> data.table 1 100 1.00
> 0.01 1
> MASS 1 78 1.28
> 0.04 0
> limma 4 310 1.29
> 0.04 0
> reshape 1 67 1.49
> 0.03 2
> nlme 2 109 1.83
> 0.05 1
> utils 4 216 1.85
> 0.01 0
> lattice 3 144 2.08
> 0.05 0
> BiocGenerics 5 141 3.55
> 0.04 0
> stats 16 449 3.56
> 0.01 0
> siggenes 2 51 3.92
> 0.13 3
> genefilter 2 49 4.08
> 0.38 3
> Biobase 6 128 4.69
> 0.05 0
> GenomeInfoDb 3 60 5.00
> 0.09 0
> preprocessCore 2 39 5.13
> 0.02 1
> GEOquery 1 17 5.88
> 0.32 4
> HDF5Array 5 72 6.94
> 0.15 4
> bumphunter 1 14 7.14
> 0.76 25
> BiocParallel 6 68 8.82
> 0.07 0
> Biostrings 23 240 9.58
> 0.11 0
> graphics 9 87 10.34
> 0.01 0
> IRanges 40 254 15.75
> 0.06 0
> S4Vectors 47 278 16.91
> 0.05 0
> DelayedMatrixStats 14 74 18.92
> 0.14 2
> GenomicRanges 23 106 21.70
> 0.12 0
> RColorBrewer 1 4 25.00
> 0.01 1
> SummarizedExperiment 23 82 28.05
> 0.19 0
> illuminaio 1 3 33.33
> 0.04 2
> quadprog 1 2 50.00
> 0.01 1
> beanplot 1 1 100.00
> 0.01 1
> mclust NA 271 NA
> 0.04 1
> nor1mix NA 38 NA
> 0.02 1
>
> so, with the exception of 'bumphunter', it doesn't look like the removal
> of a single dependency will give you much gain. it seems that minfi
> imports a single functionality from bumphunter:
>
> imp <- pkgDepImports("minfi")
> imp[imp$pkg %in% "bumphunter", ]
> # A tibble: 1 x 2
> pkg fun
> <chr> <chr>
> 1 bumphunter bumphunter
>
> you can explore the gain by excluding combinations of package
> dependencies with the function 'pkgCombDependencyGain()':
>
> pcd <- pkgCombDependencyGain("minfi", depdf, maxNbr=2L)
> dim(pcd)
> [1] 561 3
> head(pcd[order(pcd$DepGain, decreasing = TRUE), ])
> Packages NbrExcl DepGain
> 160 bumphunter, GEOquery 2 43
> 175 bumphunter, genefilter 2 40
> 98 BiocParallel, bumphunter 2 31
> 161 bumphunter, HDF5Array 2 29
> 165 bumphunter, siggenes 2 28
> 157 bumphunter, DelayedMatrixStats 2 27
>
> have fun with the dependency exploration game! :)
>
> robert.
>
> On 3/3/21 1:28 PM, Kasper Daniel Hansen wrote:
> > I am happy to engage in a discussion about this, although I'm not sure
> that
> > I am ultimately interested in having two packages.
> >
> > But first I would like to look at some dependency graphs. I am wondering
> > what makes the dependency tree this big (and my tree is smaller than
> yours,
> > but still big: library(minfi) gives me 16 attached packages and 89 loaded
> > packages for the current release). This includes some part of the
> tidyverse
> > which we don't really use much though (and which could probably get
> removed
> > from the package with almost no work).
> >
> > What's the current best tool for dependency graphs in Bioconductor?
> > pkgDepTools?
> >
> > Best,
> > Kasper
> >
> > On Mon, Mar 1, 2021 at 6:24 PM Carlos Ruiz <carlos.ruiz using isglobal.org>
> wrote:
> >
> >> Dear Bioc developers,
> >>
> >> I have been developing different packages to analyze DNA methylation. In
> >> all of them, I have used minfi's class GenomicRatioSet to manage DNA
> >> methylation data, in order to take profit of the features of
> >> RangedSummarizedExperiment.
> >>
> >> Although I am very happy with the potential of the class, importing its
> >> definition from minfi, makes me add the package to imports. As minfi
> has a
> >> high number of dependencies (129 in the current release), my packages
> end
> >> up having hundreds of dependencies too. This is particularly
> problematic as
> >> I do not use any of the other functions of minfi.
> >>
> >> I am wondering whether it could be possible to move minfi's class (or at
> >> least GenomicRatioSet) to a lighter package, so people developing
> packages
> >> on DNA methylation could rely on this class without having to import the
> >> whole minfi package and its dependencies.
> >>
> >> Thank you very much,
> >> --
> >>
> >> Carlos Ruiz
> >>
> >> --
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> --
> Robert Castelo, PhD
> Associate Professor
> Dept. of Experimental and Health Sciences
> Universitat Pompeu Fabra (UPF)
> Barcelona Biomedical Research Park (PRBB)
> Dr Aiguader 88
> E-08003 Barcelona, Spain
> telf: +34.933.160.514
> fax: +34.933.160.550
>
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