Dependency analysis on package <%=pkg$package%>

General information

<% if(grepl("bioconductor", pkg$repository)) { %> <% } else { %> <% } %> <% m = co_heaviness(pkg) diag(m) = -Inf if(nrow(m) >= 2) { if(max(m) > 0) { ind = which(m == max(m), arr.ind = TRUE) rn = rownames(m) %> <% } } %>

Bioconductor link	link
CRAN link	link
Package version	<%= pkg$version%>
Number of strong dependencies	<%= pkg$n_by_strong %>
Number of all dependencies	<%= pkg$n_by_all %>
Number of parent packages	<%= sum(pkg$which_required) %>
Max heaviness from parent packages	<%= if(any(pkg$which_required)) max(pkg$heaviness[pkg$which_required]) else 0 %>
Total heaviness from parent packages	<%= if(any(pkg$which_required)) sum(pkg$heaviness[pkg$which_required]) else 0 %>
Number of parent packages (including Suggests and Enhances)	<%= length(pkg$heaviness) %>
Max co-heaviness from parent packages ("<%=rn[ind[1, 1]]%>" and "<%=rn[ind[1, 2]]%>")	<%= max(m) %>

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of <%=pkg$package%> and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on <%=pkg$package%>.

<% file.remove(tmp_file) %>

Dependency table

<% if(n_total > 0) { %> <% if(grepl("(bioc|books|annotation|experiment|workflow)", pkg$repository)) { namespace_link = paste0("https://code.bioconductor.org/browse/", pkg$package, "/blob/master/NAMESPACE") } else if(pkg$package %in% BASE_PKGS) { namespace_link = paste0("https://github.com/wch/r-source/blob/trunk/src/library/", pkg$package, "/NAMESPACE") } else { namespace_link = paste0("https://github.com/cran/", pkg$package, "/blob/master/NAMESPACE") } %>

"Import" information is from the NAMESPACE file of <%=pkg$package%>.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on <%=pkg$package%>: number of required packages that can be reduced if moving parent package to Suggests of <%=pkg$package%>.

<% if(pkgndep_opt$add_link) { tb[, 1] = qq("@{tb[, 1]}", collapse = FALSE) } else { tb[, 1] = qq("@{tb[, 1]}", collapse = FALSE) } html_tb = as.character(knitr::kable(tb, format = "html", row.names = FALSE, escape = FALSE, col.names = c("Parent package", "Field", "imports", "importMethods", "importClasses", "Required packages", qq("Heaviness from parent on @{pkg$package}")), table.attr = "class='table table-striped' id='parent-dependency'", align = c("l", rep("r", ncol(tb) - 1)))) html_tb = gsub("(]*?> Suggests \\s+)]*?> 0 \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1No object is imported into the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> Enhances \\s+)]*?> 0 \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1No object is imported into the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> Depends \\s+)]*?> 0 \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1The whole set of functions/methods/classes from parent package is imported to the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> Depends \\s+)]*?> -(\\d+) \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1The whole set of functions/methods/classes from parent package excluding \\2 objects is imported to the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> Depends \\s+)]*?> -Inf \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1Parent package is listed in Depends of @{pkg$package} but no object from parent package is imported.\n"), html_tb) html_tb = gsub("(]*?> Imports \\s+)]*?> 0 \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1The whole set of functions/methods/classes from parent package is imported to the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> Imports \\s+)]*?> -(\\d+) \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1The whole set of functions/methods/classes from parent package excluding \\2 objects is imported to the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> Imports \\s+)]*?> -Inf \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1Parent package is listed in Imports of @{pkg$package} but no object from parent package is imported.\n"), html_tb) html_tb = gsub("(]*?> LinkingTo \\s+)]*?> 0 \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1No object is imported into the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> LinkingTo \\s+)]*?> -(\\d+) \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1The whole set of functions/methods/classes from parent package excluding \\2 objects is imported to the namespace of @{pkg$package}.\n"), html_tb) html_tb = gsub("(]*?> LinkingTo \\s+)]*?> -Inf \\s+]*?> 0 \\s+]*?> 0 \\s+", qq("\\1Parent package is listed in LinkingTo of @{pkg$package} but no object from parent package is imported.\n"), html_tb) %> <%= html_tb %> <% m = co_heaviness(pkg) if(nrow(m) > 1) { if(attr(m, "max") > 10) { m2 = co_heaviness(pkg, jaccard = TRUE) pair1 = NULL pair2 = NULL hv1 = NULL hv2 = NULL nr = nrow(m) for(i in 1:(nr-1)) { for(j in (i+1):nr) { if(m[i, j] > 10) { pair1 = c(pair1, rownames(m)[i]) pair2 = c(pair2, rownames(m)[j]) hv1 = c(hv1, m[i, j]) hv2 = c(hv2, m2[i, j]) } } } co_tb = data.frame(pair1 = pair1, pair2 = pair2, heaviness = hv1, jaccard = round(hv2, 3)) co_tb = co_tb[order(co_tb$heaviness, decreasing = TRUE), , drop = FALSE] if(pkgndep_opt$add_link) { co_tb[, 1] = qq("@{co_tb[, 1]}", collapse = FALSE) co_tb[, 2] = qq("@{co_tb[, 2]}", collapse = FALSE) } else { co_tb[, 1] = qq("@{co_tb[, 1]}", collapse = FALSE) co_tb[, 2] = qq("@{co_tb[, 2]}", collapse = FALSE) } %>

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

<%= as.character(knitr::kable(co_tb, format = "html", row.names = FALSE, escape = FALSE, col.names = c("Parent 1", "Parent 2", qq("Co-heaviness on @{pkg$package}"), "Co-heaviness as Jaccard coeffcient"), table.attr = "class='table table-striped' style='width:900px'" )) %> <% } } %> <% } else { %>

No dependency found.

<% } %>

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Analysis was done with pkgndep.