Pretty much as the title says; it would be nice to see an option in pkgDepTools to capture relationships in the LinkingTo field. For example:

library(pkgDepTools)
library(BiocInstaller)
biocUrl <- biocinstallRepos()["BioCsoft"]
biocDeps <- makeDepGraph(biocUrl, type="source", dosize=FALSE)
stuff <- dijkstra.sp(biocDeps, start="scran")$distance
"Rhdf5lib" %in% stuff[is.finite(stuff)] # FALSE

... because Rhdf5lib only resides in the LinkingTo: field of scran (see https://bioconductor.org/packages/scran for details). The current result is correct in a sense, as the function only aims to pull down Depends/Imports; but one might want to capture the LinkingTo relationships as well, especially as the linked packages represent a "hard" dependency.

It seems like a simple modification to makeDepGraph would be sufficient:

                deps <- cleanPkgField(pMat[p, "Depends"])
                deps <- c(deps, cleanPkgField(pMat[p, "Imports"]))
                deps <- c(deps, cleanPkgField(pMat[p, "LinkingTo"])) # new line

Session information:

R version 3.4.2 Patched (2017-10-30 r73642)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/cri.camres.org/lun01/Software/R/R-3-4-branch_release/lib/libRblas.so
LAPACK: /home/cri.camres.org/lun01/Software/R/R-3-4-branch_release/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] BiocInstaller_1.28.0 pkgDepTools_1.44.0   RCurl_1.95-4.10     
[4] bitops_1.0-6         RBGL_1.54.0          graph_1.56.0        
[7] BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
[1] compiler_3.4.2 tools_3.4.2    stats4_3.4.2

Thanks; fixed in 1.45.1. For future issues, I create a github repository for this package.