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.r...@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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