Overview of BiocPkgTools

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

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 × 12
##   pkg    author  version git_last_commit git_last_commit_date pkgType Deprecated
##   <chr>  <chr>   <chr>   <chr>           <dttm>               <chr>   <lgl>     
## 1 ABSSeq Wentao… 1.60.0  39efc10         2024-10-29 09:51:12  bioc    FALSE     
## 2 ABSSeq Wentao… 1.60.0  39efc10         2024-10-29 09:51:12  bioc    FALSE     
## 3 ABSSeq Wentao… 1.60.0  39efc10         2024-10-29 09:51:12  bioc    FALSE     
## 4 ABSSeq Wentao… 1.60.0  39efc10         2024-10-29 09:51:12  bioc    FALSE     
## 5 ABSSeq Wentao… 1.60.0  39efc10         2024-10-29 09:51:12  bioc    FALSE     
## 6 ABSSeq Wentao… 1.60.0  39efc10         2024-10-29 09:51:12  bioc    FALSE     
## # ℹ 5 more variables: PackageStatus <chr>, node <chr>, stage <chr>,
## #   result <chr>, bioc_version <chr>

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 supplied to the authorPattern argument. The default is to report only “problem” build statuses (ERROR, WARNING).

problemPage(authorPattern = "V.*Carey")

In similar fashion, maintainers of packages that have many downstream packages that depend on them may wish to check that a change they introduced hasn’t suddenly broken a large number of these. You can use the dependsOn argument to produce the summary report of those packages that “depend on” the given package.

problemPage(dependsOn = "limma")

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.

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 × 7
##   pkgType  Package  Year Month Nb_of_distinct_IPs Nb_of_downloads Date      
##   <chr>    <chr>   <int> <chr>              <int>           <int> <date>    
## 1 software a4       2024 Jan                   75             320 2024-01-01
## 2 software a4       2024 Feb                   85             245 2024-02-01
## 3 software a4       2024 Mar                  156             296 2024-03-01
## 4 software a4       2024 Apr                  247             577 2024-04-01
## 5 software a4       2024 May                  108             510 2024-05-01
## 6 software a4       2024 Jun                   79             811 2024-06-01

The download statistics reported are for all available versions of a package. There are no separate, publicly available statistics broken down by version. The majority of Bioconductor Software packages are also available through other channels such as Anaconda, who also provided download statistics for packages installed from their repositories. Access to these counts is provided by the anacondaDownloadStats function:

head(anacondaDownloadStats())
## # A tibble: 6 × 7
##   Package Year  Month Nb_of_distinct_IPs Nb_of_downloads repo     Date      
##   <chr>   <chr> <chr>              <int>           <dbl> <chr>    <date>    
## 1 ABAData 2018  Apr                   NA               8 Anaconda 2018-04-01
## 2 ABAData 2018  Aug                   NA               5 Anaconda 2018-08-01
## 3 ABAData 2018  Dec                   NA             133 Anaconda 2018-12-01
## 4 ABAData 2018  Jul                   NA               6 Anaconda 2018-07-01
## 5 ABAData 2018  Jun                   NA              18 Anaconda 2018-06-01
## 6 ABAData 2018  Mar                   NA              13 Anaconda 2018-03-01

Note that Anaconda do not provide counts for distinct IP addresses, but this column is included for compatibility with the Bioconductor count tables.

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 included packages. The biocPkgList returns a data.frame with a row for each package. Tons of information are available, as evidenced by the column names of the results.

bpi = biocPkgList()
colnames(bpi)
##  [1] "Package"                       "Version"                      
##  [3] "Depends"                       "Imports"                      
##  [5] "Suggests"                      "License"                      
##  [7] "MD5sum"                        "NeedsCompilation"             
##  [9] "Title"                         "Description"                  
## [11] "biocViews"                     "Author"                       
## [13] "Maintainer"                    "git_url"                      
## [15] "git_branch"                    "git_last_commit"              
## [17] "git_last_commit_date"          "Date/Publication"             
## [19] "source.ver"                    "win.binary.ver"               
## [21] "mac.binary.big-sur-x86_64.ver" "mac.binary.big-sur-arm64.ver" 
## [23] "vignettes"                     "vignetteTitles"               
## [25] "hasREADME"                     "hasNEWS"                      
## [27] "hasINSTALL"                    "hasLICENSE"                   
## [29] "Rfiles"                        "importsMe"                    
## [31] "dependencyCount"               "URL"                          
## [33] "VignetteBuilder"               "Archs"                        
## [35] "suggestsMe"                    "LinkingTo"                    
## [37] "SystemRequirements"            "dependsOnMe"                  
## [39] "BugReports"                    "Enhances"                     
## [41] "Video"                         "linksToMe"                    
## [43] "License_restricts_use"         "PackageStatus"                
## [45] "License_is_FOSS"               "OS_type"                      
## [47] "organism"

Some of the variables are parsed to produce list columns.

head(bpi)
## # A tibble: 6 × 47
##   Package Version Depends Imports Suggests License MD5sum NeedsCompilation Title
##   <chr>   <chr>   <list>  <list>  <list>   <chr>   <chr>  <chr>            <chr>
## 1 ABSSeq  1.60.0  <chr>   <chr>   <chr>    GPL (>… f3c08… no               "ABS…
## 2 ABarray 1.74.0  <chr>   <chr>   <chr>    GPL     429b9… no               "Mic…
## 3 ACE     1.24.0  <chr>   <chr>   <chr>    GPL-2   046bd… no               "Abs…
## 4 ACME    2.62.0  <chr>   <chr>   <chr>    GPL (>… daf93… yes              "Alg…
## 5 ADAM    1.22.0  <chr>   <chr>   <chr>    GPL (>… 7f115… yes              "ADA…
## 6 ADAMgui 1.22.0  <chr>   <chr>   <chr>    GPL (>… a136c… no               "Act…
## # ℹ 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.big-sur-x86_64.ver` <chr>,
## #   `mac.binary.big-sur-arm64.ver` <chr>, vignettes <list>,
## #   vignetteTitles <list>, hasREADME <chr>, hasNEWS <chr>, hasINSTALL <chr>,
## #   hasLICENSE <chr>, Rfiles <list>, importsMe <list>, dependencyCount <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] "ChIPXpress"                       "DExMA"                           
##  [3] "EGAD"                             "GEOexplorer"                     
##  [5] "Moonlight2R"                      "MoonlightR"                      
##  [7] "bigmelon"                         "minfi"                           
##  [9] "phantasus"                        "recount"                         
## [11] "BeadArrayUseCases"                "BioPlex"                         
## [13] "GSE13015"                         "healthyControlsPresenceChecker"  
## [15] "easyDifferentialGeneCoexpression" "geneExpressionFromGEO"           
## [17] "seeker"

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()

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.

Working with dependency graphs

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

dep_df = buildPkgDependencyDataFrame()
g = buildPkgDependencyIgraph(dep_df)
g
## IGRAPH bf59ac3 DN-- 3628 29099 -- 
## + attr: name (v/c), edgetype (e/c)
## + edges from bf59ac3 (vertex names):
##  [1] ABSSeq  ->methods       ACME    ->Biobase       ACME    ->methods      
##  [4] ACME    ->BiocGenerics  ADAM    ->stats         ADAM    ->utils        
##  [7] ADAM    ->methods       ADAMgui ->stats         ADAMgui ->utils        
## [10] ADAMgui ->methods       ADAMgui ->ADAM          ADaCGH2 ->parallel     
## [13] ADaCGH2 ->ff            ADaCGH2 ->GLAD          AGDEX   ->Biobase      
## [16] AGDEX   ->GSEABase      AIMS    ->e1071         AIMS    ->Biobase      
## [19] ALDEx2  ->methods       ALDEx2  ->stats         ALDEx2  ->zCompositions
## [22] ALDEx2  ->lattice       ALDEx2  ->latticeExtra  AMARETTO->impute       
## + ... omitted several edges
library(igraph)
head(V(g))
## + 6/3628 vertices, named, from bf59ac3:
## [1] ABSSeq  ACME    ADAM    ADAMgui ADaCGH2 AGDEX
head(E(g))
## + 6/29099 edges from bf59ac3 (vertex names):
## [1] ABSSeq->methods      ACME  ->Biobase      ACME  ->methods     
## [4] ACME  ->BiocGenerics ADAM  ->stats        ADAM  ->utils

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.

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)

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 = 497 
## Number of Edges = 496
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)

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.

depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"),
                                     dependencies=c("Depends", "Imports"))
dim(depdf)
## [1] 146154      3
head(depdf)  # too big to show all
##   Package   dependency edgetype
## 1  ABSSeq      methods  Depends
## 2    ACME      Biobase  Depends
## 3    ACME      methods  Depends
## 4    ACME BiocGenerics  Depends
## 5    ADAM        stats  Depends
## 6    ADAM        utils  Depends

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
## stats                       1      453  0.22       0.01                 0
## graph                       1      116  0.86       0.06                 0
## utils                       2      228  0.88       0.01                 0
## rlang                       4      438  0.91       0.02                 0
## igraph                      9      809  1.11       0.14                 4
## RBGL                        1       77  1.30       0.07                 0
## htmltools                   1       77  1.30       0.07                 0
## xml2                        1       67  1.49       0.04                 0
## tools                       2      122  1.64       0.01                 0
## stringr                     1       59  1.69       0.11                 0
## tibble                      1       45  2.22       0.12                 0
## DT                          1       42  2.38       0.38                 6
## rvest                       1       42  2.38       0.27                 2
## magrittr                    1       42  2.38       0.01                 0
## dplyr                       8      292  2.74       0.18                 0
## rorcid                      1       32  3.12       0.31                 8
## httr                        5       91  5.49       0.09                 0
## htmlwidgets                 1       14  7.14       0.30                 0
## jsonlite                    2       23  8.70       0.01                 0
## gh                          1       11  9.09       0.20                 4
## BiocFileCache               4       29 13.79       0.41                 8
## BiocManager                 3        6 50.00       0.02                 0
## biocViews                  NA       32    NA       0.14                 6
## readr                      NA      115    NA       0.25                 6

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: (ImportedAndUsedx 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 × 2
##   pkg   fun      
##   <chr> <chr>    
## 1 DT    datatable

Identities of maintainers

It is important to be able to identify the maintainer of a package in a reliable way. The DESCRIPTION file for a package can include an Authors@R field. This field can capture metadata about maintainers and contributors in a programmatically accessible way. Each element of the role field of a person (see ?person) in the Authors@R field comes from a subset of the relations vocabulary of the Library of Congress.

Metadata about maintainers can be extracted from DESCRIPTION in various ways. As of October 2022, we focus on the use of the ORCID field which is an optional comment component in a person element. For example, in the DESCRIPTION for the AnVIL package we have

Authors@R:
    c(person(
        "Martin", "Morgan", role = c("aut", "cre"),
        email = "[email protected]",
        comment = c(ORCID = "0000-0002-5874-8148")
     ),

This convention is used for a fair number of Bioconductor and CRAN packages.

We’ll demonstrate the use of get_cre_orcids with some packages.

inst = rownames(installed.packages())
cands = c("devtools", "evaluate", "ggplot2", "GEOquery", "gert", "utils")
totry = intersect(cands, inst)
oids = get_cre_orcids(totry)
oids
##              evaluate                  gert                 utils 
##                    NA "0000-0002-4035-0289"                    NA

We use the ORCID API to tabulate metadata about the holders of these IDs. We’ll avoid evaluating this because a token must be refreshed for the query to succeed.

orcid_table(oids)

In October 2022 the result is

> orcid_table(.Last.value)
                        name                                            org
devtools      Jennifer Bryan                                        RStudio
evaluate           Yihui Xie                                  RStudio, Inc.
ggplot2  Thomas Lin Pedersen                                        RStudio
GEOquery          Sean Davis University of Colorado Anschutz Medical Campus
gert             Jeroen Ooms            Berkeley Institute for Data Science
utils                   <NA>                                           <NA>
               city   region country               orcid
devtools     Boston       MA      US 0000-0002-6983-2759
evaluate    Elkhorn       NE      US 0000-0003-0645-5666
ggplot2  Copenhagen     <NA>      DK 0000-0002-5147-4711
GEOquery     Aurora Colorado      US 0000-0002-8991-6458
gert       Berkeley       CA      US 0000-0002-4035-0289
utils          <NA>     <NA>    <NA>                <NA>

Provenance

sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] biocViews_1.75.0    visNetwork_2.1.2    igraph_2.1.1       
## [4] dplyr_1.1.4         BiocPkgTools_1.23.1 htmlwidgets_1.6.4  
## [7] knitr_1.48          BiocStyle_2.35.0   
## 
## loaded via a namespace (and not attached):
##  [1] xfun_0.49            bslib_0.8.0          gh_1.4.1            
##  [4] Biobase_2.67.0       tzdb_0.4.0           vctrs_0.6.5         
##  [7] tools_4.4.1          bitops_1.0-9         generics_0.1.3      
## [10] stats4_4.4.1         curl_5.2.3           RUnit_0.4.33        
## [13] tibble_3.2.1         fansi_1.0.6          RSQLite_2.3.7       
## [16] blob_1.2.4           pkgconfig_2.0.3      dbplyr_2.5.0        
## [19] graph_1.85.0         lifecycle_1.0.4      stringr_1.5.1       
## [22] compiler_4.4.1       htmltools_0.5.8.1    sys_3.4.3           
## [25] buildtools_1.0.0     sass_0.4.9           RCurl_1.98-1.16     
## [28] yaml_2.3.10          pillar_1.9.0         jquerylib_0.1.4     
## [31] whisker_0.4.1        DT_0.33              cachem_1.1.0        
## [34] rvest_1.0.4          tidyselect_1.2.1     digest_0.6.37       
## [37] stringi_1.8.4        purrr_1.0.2          maketools_1.3.1     
## [40] fastmap_1.2.0        cli_3.6.3            magrittr_2.0.3      
## [43] RBGL_1.83.0          XML_3.99-0.17        crul_1.5.0          
## [46] utf8_1.2.4           withr_3.0.2          readr_2.1.5         
## [49] filelock_1.0.3       bit64_4.5.2          rmarkdown_2.28      
## [52] httr_1.4.7           bit_4.5.0            hms_1.1.3           
## [55] memoise_2.0.1        evaluate_1.0.1       BiocFileCache_2.15.0
## [58] rlang_1.1.4          glue_1.8.0           DBI_1.2.3           
## [61] httpcode_0.3.0       BiocManager_1.30.25  xml2_1.3.6          
## [64] fauxpas_0.5.2        BiocGenerics_0.53.1  rorcid_0.7.0        
## [67] jsonlite_1.8.9       R6_2.5.1