# Overview of BiocPkgTools

Shian Su1, Vince Carey2, Lori Shepherd3, Martin Morgan3 and Sean Davis4*

1Walter and Eliza Hall Institute, Melbourne, Australia
2Channing Lab, Brigham and Womens Hospital, Harvard University, Boston, MA USA
3Roswell Park Comprehensive Cancer Center, Buffalo, NY USA
4National Cancer Institute, National Institutes of Health, Bethesda, MD USA

*seandavi@gmail.com

#### 28 April 2020

#### Abstract

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R in a tidy data format. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

#### Package

BiocPkgTools 1.6.0

# 1 Introduction

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R in a tidy data format. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

Functionality includes access to :

- Download statistics
- General package listing
- Build reports
- Package dependency graphs
- Vignettes

# 2 Build reports

The Bioconductor build reports are available online as HTML pages. However, they are not very computable. The `biocBuildReport` function does some heroic parsing of the HTML to produce a tidy data.frame for further processing in R.

    library(BiocPkgTools)
    head(biocBuildReport())

    ## # A tibble: 6 x 9
    ##   pkg   version author commit last_changed_date   node  stage result
    ##   <chr> <chr>   <chr>  <chr>  <dttm>              <chr> <chr> <chr>
    ## 1 a4    1.35.1  Tobia~  da86~ 2020-04-03 12:45:54 malb~ inst~ OK
    ## 2 a4    1.35.1  Tobia~  da86~ 2020-04-03 12:45:54 malb~ buil~ OK
    ## 3 a4    1.35.1  Tobia~  da86~ 2020-04-03 12:45:54 malb~ chec~ WARNI~
    ## 4 a4    1.35.1  Tobia~  da86~ 2020-04-03 12:45:54 toka~ inst~ OK
    ## 5 a4    1.35.1  Tobia~  da86~ 2020-04-03 12:45:54 toka~ buil~ OK
    ## 6 a4    1.35.1  Tobia~  da86~ 2020-04-03 12:45:54 toka~ chec~ WARNI~
    ## # ... with 1 more variable: bioc_version <chr>

## 2.1 Personal build report

Because developers may be interested in a quick view of their own packages, there is a simple function, `problemPage`, to produce an HTML report of the build status of packages matching a given author regex. The default is to report only “problem” build statuses (ERROR, WARNING).

    problemPage()

When run in an interactive environment, the `problemPage` function will open a browser window for user interaction. Note that if you want to include all your package results, not just the broken ones, simply specify `includeOK = TRUE`.

# 3 Download statistics

Bioconductor supplies download stats for all packages. The `biocDownloadStats` function grabs all available download stats for all packages in all Experiment Data, Annotation Data, and Software packages. The results are returned as a tidy data.frame for further analysis.

    head(biocDownloadStats())

    ## # A tibble: 6 x 7
    ##   Package  Year Month Nb_of_distinct_IPs Nb_of_downloads repo     Date
    ##   <chr>   <int> <chr>              <int>           <int> <chr>    <date>
    ## 1 ABarray  2020 Jan                   56             117 Software 2020-01-01
    ## 2 ABarray  2020 Feb                   52             126 Software 2020-02-01
    ## 3 ABarray  2020 Mar                   70             154 Software 2020-03-01
    ## 4 ABarray  2020 Apr                   46              84 Software 2020-04-01
    ## 5 ABarray  2020 May                    0               0 Software 2020-05-01
    ## 6 ABarray  2020 Jun                    0               0 Software 2020-06-01

The download statistics reported are for all available versions of a package. There are no separate, publicly available statistics broken down by version.

# 4 Package details

The R `DESCRIPTION` file contains a plethora of information regarding package authors, dependencies, versions, etc. In a repository such as Bioconductor, these details are available in bulk for all inclucded packages. The `biocPkgList` returns a data.frame with a row for each package. Tons of information are avaiable, as evidenced by the column names of the results.

    bpi = biocPkgList()
    colnames(bpi)

    ##  [1] "Package"               "Version"               "Depends"
    ##  [4] "Suggests"              "License"               "MD5sum"
    ##  [7] "NeedsCompilation"      "Title"                 "Description"
    ## [10] "biocViews"             "Author"                "Maintainer"
    ## [13] "git_url"               "git_branch"            "git_last_commit"
    ## [16] "git_last_commit_date"  "Date/Publication"      "source.ver"
    ## [19] "win.binary.ver"        "mac.binary.ver"        "vignettes"
    ## [22] "vignetteTitles"        "hasREADME"             "hasNEWS"
    ## [25] "hasINSTALL"            "hasLICENSE"            "Rfiles"
    ## [28] "dependencyCount"       "Enhances"              "dependsOnMe"
    ## [31] "Imports"               "importsMe"             "suggestsMe"
    ## [34] "LinkingTo"             "Archs"                 "VignetteBuilder"
    ## [37] "URL"                   "SystemRequirements"    "BugReports"
    ## [40] "Video"                 "linksToMe"             "OS_type"
    ## [43] "PackageStatus"         "License_restricts_use" "License_is_FOSS"
    ## [46] "organism"

Some of the variables are parsed to produce `list` columns.

    head(bpi)

    ## # A tibble: 6 x 46
    ##   Package Version Depends Suggests License MD5sum NeedsCompilation Title
    ##   <chr>   <chr>   <list>  <list>   <chr>   <chr>  <chr>            <chr>
    ## 1 a4      1.35.1  <chr [~ <chr [6~ GPL-3   1bb32~ no               Auto~
    ## 2 a4Base  1.35.1  <chr [~ <chr [3~ GPL-3   aea7e~ no               Auto~
    ## 3 a4Clas~ 1.35.1  <chr [~ <chr [2~ GPL-3   f2201~ no               Auto~
    ## 4 a4Core  1.35.1  <chr [~ <chr [1~ GPL-3   c34f1~ no               Auto~
    ## 5 a4Prep~ 1.35.1  <chr [~ <chr [2~ GPL-3   428c3~ no               Auto~
    ## 6 a4Repo~ 1.35.1  <chr [~ <chr [1~ GPL-3   4935c~ no               Auto~
    ## # ... with 38 more variables: Description <chr>, biocViews <list>,
    ## #   Author <list>, Maintainer <list>, git_url <chr>, git_branch <chr>,
    ## #   git_last_commit <chr>, git_last_commit_date <chr>,
    ## #   `Date/Publication` <chr>, source.ver <chr>, win.binary.ver <chr>,
    ## #   mac.binary.ver <chr>, vignettes <list>, vignetteTitles <list>,
    ## #   hasREADME <chr>, hasNEWS <chr>, hasINSTALL <chr>, hasLICENSE <chr>,
    ## #   Rfiles <list>, dependencyCount <chr>, Enhances <list>, dependsOnMe <list>,
    ## #   Imports <list>, importsMe <list>, suggestsMe <list>, LinkingTo <list>,
    ## #   Archs <list>, VignetteBuilder <chr>, URL <chr>, SystemRequirements <chr>,
    ## #   BugReports <chr>, Video <chr>, linksToMe <list>, OS_type <chr>,
    ## #   PackageStatus <chr>, License_restricts_use <chr>, License_is_FOSS <chr>,
    ## #   organism <chr>

As a simple example of how these columns can be used, extracting the `importsMe` column to find the packages that import the GEOquery package.

    require(dplyr)
    bpi = biocPkgList()
    bpi %>%
        filter(Package=="GEOquery") %>%
        pull(importsMe) %>%
        unlist()

    ##  [1] "bigmelon"   "ChIPXpress" "coexnet"    "crossmeta"  "EGAD"
    ##  [6] "GAPGOM"     "MACPET"     "minfi"      "MoonlightR" "phantasus"
    ## [11] "recount"    "SRAdb"

# 5 Package Explorer

For the end user of Bioconductor, an analysis often starts with finding a package or set of packages that perform required tasks or are tailored to a specific operation or data type. The `biocExplore()` function implements an interactive bubble visualization with filtering based on biocViews terms. Bubbles are sized based on download statistics. Tooltip and detail-on-click capabilities are included. To start a local session:

    biocExplore()

# 6 Dependency graphs

The Bioconductor ecosystem is built around the concept of interoperability and dependencies. These interdependencies are available as part of the `biocPkgList()` output. The `BiocPkgTools` provides some convenience functions to convert package dependencies to R graphs. A modular approach leads to the following workflow.

1. Create a `data.frame` of dependencies using `buildPkgDependencyDataFrame`.
2. Create an `igraph` object from the dependency data frame using `buildPkgDependencyIgraph`
3. Use native `igraph` functionality to perform arbitrary network operations. Convenience functions, `inducedSubgraphByPkgs` and `subgraphByDegree` are available.
4. Visualize with packages such as visNetwork.

## 6.1 Working with dependency graphs

A dependency graph for all of Bioconductor is a starting place.

    library(BiocPkgTools)
    dep_df = buildPkgDependencyDataFrame()
    g = buildPkgDependencyIgraph(dep_df)
    g

    ## IGRAPH 73e60a1 DN-- 3392 29942 --
    ## + attr: name (v/c), edgetype (e/c)
    ## + edges from 73e60a1 (vertex names):
    ##  [1] a4       ->a4Base        a4       ->a4Preproc     a4       ->a4Classif
    ##  [4] a4       ->a4Core        a4       ->a4Reporting   a4Base   ->methods
    ##  [7] a4Base   ->graphics      a4Base   ->grid          a4Base   ->Biobase
    ## [10] a4Base   ->AnnotationDbi a4Base   ->annaffy       a4Base   ->mpm
    ## [13] a4Base   ->genefilter    a4Base   ->limma         a4Base   ->multtest
    ## [16] a4Base   ->glmnet        a4Base   ->a4Preproc     a4Base   ->a4Core
    ## [19] a4Base   ->gplots        a4Classif->methods       a4Classif->a4Core
    ## [22] a4Classif->a4Preproc     a4Classif->MLInterfaces  a4Classif->ROCR
    ## + ... omitted several edges

    library(igraph)
    head(V(g))

    ## + 6/3392 vertices, named, from 73e60a1:
    ## [1] a4          a4Base      a4Classif   a4Core      a4Preproc   a4Reporting

    head(E(g))

    ## + 6/29942 edges from 73e60a1 (vertex names):
    ## [1] a4    ->a4Base      a4    ->a4Preproc   a4    ->a4Classif
    ## [4] a4    ->a4Core      a4    ->a4Reporting a4Base->methods

See `inducedSubgraphByPkgs` and `subgraphByDegree` to produce subgraphs based on a subset of packages.

See the igraph documentation for more detail on graph analytics, setting vertex and edge attributes, and advanced subsetting.

## 6.2 Graph visualization

The visNetwork package is a nice interactive visualization tool that implements graph plotting in a browser. It can be integrated into shiny applications. Interactive graphs can also be included in Rmarkdown documents (see vignette)

    igraph_network = buildPkgDependencyIgraph(buildPkgDependencyDataFrame())

The full dependency graph is really not that informative to look at, though doing so is possible. A common use case is to visualize the graph of dependencies “centered” on a package of interest. In this case, I will focus on the GEOquery package.

    igraph_geoquery_network = subgraphByDegree(igraph_network, "GEOquery")

The `subgraphByDegree()` function returns all nodes and connections within `degree` of the named package; the default `degree` is `1`.

The visNework package can plot `igraph` objects directly, but more flexibility is offered by first converting the graph to visNetwork form.

    library(visNetwork)
    data <- toVisNetworkData(igraph_geoquery_network)

The next few code chunks highlight just a few examples of the visNetwork capabilities, starting with a basic plot.

    visNetwork(nodes = data$nodes, edges = data$edges, height = "500px")

For fun, we can watch the graph stabilize during drawing, best viewed interactively.

    visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>%
        visPhysics(stabilization=FALSE)

Add arrows and colors to better capture dependencies.

    data$edges$color='lightblue'
    data$edges[data$edges$edgetype=='Imports','color']= 'red'
    data$edges[data$edges$edgetype=='Depends','color']= 'green'

    visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>%
        visEdges(arrows='from')

Add a legend.

    ledges <- data.frame(color = c("green", "lightblue", "red"),
      label = c("Depends", "Suggests", "Imports"), arrows =c("from", "from", "from"))
    visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>%
      visEdges(arrows='from') %>%
      visLegend(addEdges=ledges)

## 6.3 Integration with BiocViews

[Work in progress]

The biocViews package is a small ontology of terms describing Bioconductor packages. This is a work-in-progress section, but here is a small example of plotting the biocViews graph.

    library(biocViews)
    data(biocViewsVocab)
    biocViewsVocab

    ## A graphNEL graph with directed edges
    ## Number of Nodes = 484
    ## Number of Edges = 483

    library(igraph)
    g = igraph.from.graphNEL(biocViewsVocab)
    library(visNetwork)
    gv = toVisNetworkData(g)
    visNetwork(gv$nodes, gv$edges, width="100%") %>%
        visIgraphLayout(layout = "layout_as_tree", circular=TRUE) %>%
        visNodes(size=20) %>%
        visPhysics(stabilization=FALSE)

# 7 Dependency burden

The dependency burden of a package, namely the amount of functionality that a given package is importing, is an important parameter to take into account during package development. A package may break because one or more of its dependencies have changed the part of the API our package is importing or this part has even broken. For this reason, it may be useful for package developers to quantify the dependency burden of a given package. To do that we should first gather all dependency information using the function `buildPkgDependencyDataFrame()` but setting the arguments to work with packages in Bioconductor and CRAN and dependencies categorised as `Depends` or `Imports`, which are the ones installed by default for a given package.

    library(BiocPkgTools)

    depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"),
                                         dependencies=c("Depends", "Imports"))
    depdf

    ## # A tibble: 100,143 x 3
    ##    Package dependency    edgetype
    ##    <chr>   <chr>         <chr>
    ##  1 a4      a4Base        Depends
    ##  2 a4      a4Preproc     Depends
    ##  3 a4      a4Classif     Depends
    ##  4 a4      a4Core        Depends
    ##  5 a4      a4Reporting   Depends
    ##  6 a4Base  methods       Depends
    ##  7 a4Base  graphics      Depends
    ##  8 a4Base  grid          Depends
    ##  9 a4Base  Biobase       Depends
    ## 10 a4Base  AnnotationDbi Depends
    ## # ... with 100,133 more rows

Finally, we call the function `pkgDepMetrics()` to obtain different metrics on the dependency burden of a package we want to analyze, in the case below, the package `BiocPkgTools` itself:

    pkgDepMetrics("BiocPkgTools", depdf)

    ##               ImportedAndUsed Exported Usage DepOverlap DepGainIfExcluded
    ## utils                       1      245  0.41       0.01                 0
    ## graph                       1      116  0.86       0.09                 0
    ## rlang                       4      464  0.86       0.01                 0
    ## readr                       1      109  0.92       0.29                 3
    ## igraph                      9      782  1.15       0.13                 4
    ## RBGL                        1       77  1.30       0.10                 0
    ## htmltools                   1       67  1.49       0.06                 0
    ## xml2                        1       66  1.52       0.01                 0
    ## tidyr                       1       62  1.61       0.33                 1
    ## dplyr                       7      261  2.68       0.29                 0
    ## DT                          1       37  2.70       0.22                 4
    ## magrittr                    1       35  2.86       0.01                 0
    ## httr                        3       91  3.30       0.12                 0
    ## tidyselect                  1       25  4.00       0.12                 0
    ## tibble                      2       42  4.76       0.23                 0
    ## jsonlite                    1       17  5.88       0.01                 0
    ## rvest                       2       29  6.90       0.23                 2
    ## htmlwidgets                 1       13  7.69       0.12                 0
    ## gh                          1       10 10.00       0.23                 2
    ## stringr                     5       49 10.20       0.09                 0
    ## rex                         3       16 18.75       0.03                 1
    ## BiocManager                 1        5 20.00       0.03                 0
    ## BiocFileCache              NA       27    NA       0.51                 8
    ## biocViews                  NA       31    NA       0.21                 6
    ## rappdirs                   NA        7    NA       0.01                 0
    ## tools                      NA      119    NA       0.01                 0

In this resulting table, rows correspond to dependencies and columns provide the following information:

- `ImportedAndUsed`: number of functionality calls imported and used in the package.
- `Exported`: number of functionality calls exported by the dependency.
- `Usage`: (`ImportedAndUsed`x 100) / `Exported`. This value provides an estimate of what fraction of the functionality of the dependency is actually used in the given package.
- `DepOverlap`: Similarity between the dependency graph structure of the given package and the one of the dependency in the corresponding row, estimated as the Jaccard index between the two sets of vertices of the corresponding graphs. Its values goes between 0 and 1, where 0 indicates that no dependency is shared, while 1 indicates that the given package and the corresponding dependency depend on an identical subset of packages.
- `DepGainIfExcluded`: The ‘dependency gain’ (decrease in the total number of dependencies) that would be obtained if this package was excluded from the list of direct dependencies.

The reported information is ordered by the `Usage` column to facilitate the identification of dependencies for which the analyzed package is using a small fraction of their functionality and therefore, it could be easier remove them. To aid in that decision, the column `DepOverlap` reports the overlap of the dependency graph of each dependency with the one of the analyzed package. Here a value above, e.g., 0.5, could, albeit not necessarily, imply that removing that dependency could substantially lighten the dependency burden of the analyzed package.

An `NA` value in the `ImportedAndUsed` column indicates that the function `pkgDepMetrics()` could not identify what functionality calls in the analyzed package are made to the dependency. This may happen because `pkgDepMetrics()` has failed to identify the corresponding calls, as it happens with imported built-in constants such as `DNA_BASES` from `Biostrings`, or that although the given package is importing that dependency, none of its functionality is actually being used. In such a case, this dependency could be safely removed without any further change in the analyzed package.

We can find out what actually functionality calls are we importing as follows:

    imp <- pkgDepImports("BiocPkgTools")
    imp %>% filter(pkg == "DT")

    ## # A tibble: 1 x 2
    ##   pkg   fun
    ##   <chr> <chr>
    ## 1 DT    datatable

# 8 Provenance

    sessionInfo()

    ## R version 4.0.0 (2020-04-24)
    ## Platform: x86_64-w64-mingw32/x64 (64-bit)
    ## Running under: Windows Server 2012 R2 x64 (build 9600)
    ##
    ## Matrix products: default
    ##
    ## locale:
    ## [1] LC_COLLATE=C
    ## [2] LC_CTYPE=English_United States.1252
    ## [3] LC_MONETARY=English_United States.1252
    ## [4] LC_NUMERIC=C
    ## [5] LC_TIME=English_United States.1252
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] biocViews_1.56.0   visNetwork_2.0.9   igraph_1.2.5       dplyr_0.8.5
    ## [5] BiocPkgTools_1.6.0 htmlwidgets_1.5.1  knitr_1.28         BiocStyle_2.16.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] tidyselect_1.0.0     xfun_0.13            purrr_0.3.4
    ##  [4] vctrs_0.2.4          BiocFileCache_1.12.0 htmltools_0.4.0
    ##  [7] stats4_4.0.0         yaml_2.2.1           blob_1.2.1
    ## [10] utf8_1.1.4           RBGL_1.64.0          XML_3.99-0.3
    ## [13] rlang_0.4.5          pillar_1.4.3         DBI_1.1.0
    ## [16] glue_1.4.0           rappdirs_0.3.1       dbplyr_1.4.3
    ## [19] bit64_0.9-7          BiocGenerics_0.34.0  lifecycle_0.2.0
    ## [22] stringr_1.4.0        rvest_0.3.5          memoise_1.1.0
    ## [25] evaluate_0.14        Biobase_2.48.0       rex_1.2.0
    ## [28] RUnit_0.4.32         parallel_4.0.0       curl_4.3
    ## [31] fansi_0.4.1          Rcpp_1.0.4.6         readr_1.3.1
    ## [34] DT_0.13              BiocManager_1.30.10  graph_1.66.0
    ## [37] jsonlite_1.6.1       bit_1.1-15.2         hms_0.5.3
    ## [40] digest_0.6.25        stringi_1.4.6        bookdown_0.18
    ## [43] gh_1.1.0             cli_2.0.2            tools_4.0.0
    ## [46] bitops_1.0-6         magrittr_1.5         RSQLite_2.2.0
    ## [49] RCurl_1.98-1.2       lazyeval_0.2.2       tibble_3.0.1
    ## [52] crayon_1.3.4         tidyr_1.0.2          pkgconfig_2.0.3
    ## [55] ellipsis_0.3.0       xml2_1.3.2           assertthat_0.2.1
    ## [58] rmarkdown_2.1        httr_1.4.1           R6_2.4.1
    ## [61] compiler_4.0.0