Dependencies
How to list all dependencies of a CRAN/Bioconductor package?
library(pkgdepends)
prop <- new_pkg_deps("ggplot2")
prop$solve()
prop$get_solution()$data#> ✔ Updating metadata database ... done #> # A data frame: 29 × 33 #> ref type direct direc…¹ status package version license needs…² prior…³ #> <chr> <chr> <lgl> <lgl> <chr> <chr> <chr> <chr> <lgl> <chr> #> 1 cli stan… FALSE FALSE OK cli 3.4.0 MIT + … TRUE NA #> 2 colorspa… stan… FALSE FALSE OK colors… 2.0-3 BSD_3_… TRUE NA #> 3 digest stan… FALSE FALSE OK digest 0.6.29 GPL (>… TRUE NA #> 4 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … TRUE NA #> 5 farver stan… FALSE FALSE OK farver 2.1.1 MIT + … TRUE NA #> 6 ggplot2 stan… TRUE TRUE OK ggplot2 3.3.6 MIT + … FALSE NA #> 7 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … TRUE NA #> 8 gtable stan… FALSE FALSE OK gtable 0.3.1 MIT + … FALSE NA #> 9 isoband stan… FALSE FALSE OK isoband 0.2.5 MIT + … TRUE NA #> 10 labeling stan… FALSE FALSE OK labeli… 0.4.2 MIT + … FALSE NA #> # … with 19 more rows, 23 more variables: md5sum <chr>, sha256 <chr>, #> # filesize <int>, built <chr>, platform <chr>, rversion <chr>, #> # repotype <chr>, repodir <chr>, target <chr>, deps <list>, mirror <chr>, #> # sources <list>, remote <list>, error <list>, metadata <list>, extra <list>, #> # dep_types <list>, params <list>, sysreqs <chr>, cache_status <chr>, #> # lib_status <chr>, old_version <chr>, new_version <chr>, and abbreviated #> # variable names ¹directpkg, ²needscompilation, ³priority #> # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable #> names
You can also draw a dependency tree:
prop$draw()#> [31] "│ │ ├─fansi" #> #> #> [32] "│ │ ├─glue" #> #> #> [33] "│ │ ├─lifecycle" #> #> #> [34] "│ │ ├─rlang" #> #> #> [35] "│ │ ├─utf8 \033[90m1.2.2\033[39m \033[32m[new][bld][cmp][dl] \033[39m\033[ #> 90m(240.33 kB)\033[39m" #> #> [36] "│ │ └─vctrs \033[90m0.4.1\033[39m \033[32m[new][bld][cmp][dl] \033[39m\033 #> [90m(916.78 kB)\033[39m" #> #> [37] "│ │ ├─cli" #> #> #> [38] "│ │ ├─glue" #> #> #> [39] "│ │ └─rlang" #> #> #> [40] "│ ├─pkgconfig \033[90m2.0.3\033[39m \033[32m[new][bld][dl] \033[39m\033[90 #> m(6.08 kB)\033[39m" #> #> [41] "│ ├─rlang" #> #> #> [42] "│ └─vctrs" #> #> #> [43] "└─withr \033[90m2.5.0\033[39m \033[32m[new][bld]\033[39m" #> #> #> [44] "" #> #> #> [45] "Key: \033[32m[new]\033[39m new | \033[32m[old]\033[39m outdated | \033[32 #> m[dl]\033[39m download | \033[32m[bld]\033[39m build | \033[32m[cmp]\033[39m com #> pile" #> attr(,"class") #> [1] "tree" "character"
How to list all dependencies of a GitHub package?
library(pkgdepends)
prop <- new_pkg_deps("tidyverse/ggplot2")
prop$solve()
prop$get_solution()$data#> ref type direct direc…¹ status package version license needs…² prior…³ #> <chr> <chr> <lgl> <lgl> <chr> <chr> <chr> <chr> <lgl> <chr> #> 1 tidyvers… gith… TRUE TRUE OK ggplot2 3.3.6.… MIT + … TRUE NA #> 2 cli stan… FALSE FALSE OK cli 3.4.0 MIT + … TRUE NA #> 3 colorspa… stan… FALSE FALSE OK colors… 2.0-3 BSD_3_… TRUE NA #> 4 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … TRUE NA #> 5 farver stan… FALSE FALSE OK farver 2.1.1 MIT + … TRUE NA #> 6 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … TRUE NA #> 7 gtable stan… FALSE FALSE OK gtable 0.3.1 MIT + … FALSE NA #> 8 isoband stan… FALSE FALSE OK isoband 0.2.5 MIT + … TRUE NA #> 9 labeling stan… FALSE FALSE OK labeli… 0.4.2 MIT + … FALSE NA #> 10 magrittr stan… FALSE FALSE OK magrit… 2.0.3 MIT + … TRUE NA #> # … with 18 more rows, 23 more variables: md5sum <chr>, sha256 <chr>, #> # filesize <int>, built <chr>, platform <chr>, rversion <chr>, #> # repotype <chr>, repodir <chr>, target <glue>, deps <list>, mirror <chr>, #> # sources <list>, remote <list>, error <list>, metadata <list>, extra <list>, #> # dep_types <list>, params <list>, sysreqs <chr>, cache_status <chr>, #> # lib_status <chr>, old_version <chr>, new_version <chr>, and abbreviated #> # variable names ¹directpkg, ²needscompilation, ³priority #> # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable #> names
How to list all dependencies of a local package?
library(pkgdepends)
prop <- new_pkg_deps("local::.")
prop$solve()
prop$get_solution()$data#> # A data frame: 20 × 33 #> ref type direct direc…¹ status package version license needs…² prior…³ #> <chr> <chr> <lgl> <lgl> <chr> <chr> <chr> <chr> <lgl> <chr> #> 1 local::. local TRUE TRUE OK pkgdep… 0.3.2 MIT + … NA NA #> 2 callr stan… FALSE FALSE OK callr 3.7.2 MIT + … FALSE NA #> 3 cli stan… FALSE FALSE OK cli 3.4.0 MIT + … TRUE NA #> 4 crayon stan… FALSE FALSE OK crayon 1.5.1 MIT + … FALSE NA #> 5 curl stan… FALSE FALSE OK curl 4.3.2 MIT + … TRUE NA #> 6 desc stan… FALSE FALSE OK desc 1.4.2 MIT + … FALSE NA #> 7 filelock stan… FALSE FALSE OK filelo… 1.0.2 MIT + … TRUE NA #> 8 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … TRUE NA #> 9 jsonlite stan… FALSE FALSE OK jsonli… 1.8.0 MIT + … TRUE NA #> 10 lpSolve stan… FALSE FALSE OK lpSolve 5.6.16 LGPL-2 TRUE NA #> 11 pkgbuild stan… FALSE FALSE OK pkgbui… 1.3.1 MIT + … FALSE NA #> 12 pkgcache stan… FALSE FALSE OK pkgcac… 2.0.2 MIT + … TRUE NA #> 13 prettyun… stan… FALSE FALSE OK pretty… 1.1.1 MIT + … FALSE NA #> 14 processx stan… FALSE FALSE OK proces… 3.7.0 MIT + … TRUE NA #> 15 ps stan… FALSE FALSE OK ps 1.7.1 MIT + … TRUE NA #> 16 R6 stan… FALSE FALSE OK R6 2.5.1 MIT + … FALSE NA #> 17 rappdirs stan… FALSE FALSE OK rappdi… 0.3.3 MIT + … TRUE NA #> 18 rprojroot stan… FALSE FALSE OK rprojr… 2.0.3 MIT + … FALSE NA #> 19 withr stan… FALSE FALSE OK withr 2.5.0 MIT + … FALSE NA #> 20 zip stan… FALSE FALSE OK zip 2.2.1 MIT + … TRUE NA #> # … with 23 more variables: md5sum <chr>, sha256 <chr>, filesize <int>, #> # built <chr>, platform <chr>, rversion <chr>, repotype <chr>, repodir <chr>, #> # target <chr>, deps <list>, mirror <chr>, sources <list>, remote <list>, #> # error <list>, metadata <list>, extra <list>, dep_types <list>, #> # params <list>, sysreqs <chr>, cache_status <chr>, lib_status <chr>, #> # old_version <chr>, new_version <chr>, and abbreviated variable names #> # ¹directpkg, ²needscompilation, ³priority #> # ℹ Use `colnames()` to see all variable names
Downloads
How to download a package and all of its dependencies?
library(pkgdepends)
target_dir <- tempfile()
dir.create(target_dir)
prop <- new_pkg_download_proposal("ggplot2", config = list(cache_dir = target_dir))
prop$resolve()
prop$download()
prop$get_downloads()
dir(target_dir)#> ✔ Got digest 0.6.29 (source) (162.78 kB) #> ✔ Got glue 1.6.2 (source) (106.51 kB) #> ✔ Got labeling 0.4.2 (source) (10.16 kB) #> ✔ Got lifecycle 1.0.1 (source) (99.72 kB) #> ✔ Got gtable 0.3.1 (source) (92.73 kB) #> ✔ Got cli 3.4.0 (source) (526.80 kB) #> ✔ Got magrittr 2.0.3 (source) (267.07 kB) #> ✔ Got MASS 7.3-58.1 (source) (514.88 kB) #> ✔ Got munsell 0.5.0 (source) (182.65 kB) #> ✔ Got pkgconfig 2.0.3 (source) (6.08 kB) #> ✔ Got R6 2.5.1 (source) (63.42 kB) #> ✔ Got colorspace 2.0-3 (source) (2.20 MB) #> ✔ Got RColorBrewer 1.1-3 (source) (11.64 kB) #> ✔ Got nlme 3.1-159 (source) (846.86 kB) #> ✔ Got scales 1.2.1 (source) (270.61 kB) #> ✔ Got mgcv 1.8-40 (source) (1.18 MB) #> ✔ Got rlang 1.0.5 (source) (741.68 kB) #> ✔ Got pillar 1.8.1 (source) (479.98 kB) #> ✔ Got tibble 3.1.8 (source) (672.34 kB) #> ✔ Got Matrix 1.4-1 (source) (2.86 MB) #> ✔ Got utf8 1.2.2 (source) (240.33 kB) #> ✔ Got withr 2.5.0 (source) (102.09 kB) #> ✔ Got lattice 0.20-45 (source) (399.47 kB) #> ✔ Got vctrs 0.4.1 (source) (916.78 kB) #> ✔ Got MASS 7.3-58.1 (source) (514.88 kB) #> ✔ Got viridisLite 0.4.1 (source) (1.27 MB) #> ✔ Got fansi 1.0.3 (source) (481.16 kB) #> ✔ Got mgcv 1.8-40 (source) (1.18 MB) #> ✔ Got nlme 3.1-159 (source) (846.86 kB) #> ✔ Got lattice 0.20-45 (source) (399.47 kB) #> ✔ Got farver 2.1.1 (source) (1.27 MB) #> ✔ Got isoband 0.2.5 (source) (1.67 MB) #> ✔ Got ggplot2 3.3.6 (source) (3.06 MB) #> ✔ Got Matrix 1.4-1 (source) (2.86 MB) #> # A data frame: 34 × 35 #> ref type direct direc…¹ status package version license needs…² prior…³ #> <chr> <chr> <lgl> <lgl> <chr> <chr> <chr> <chr> <lgl> <chr> #> 1 cli stan… FALSE FALSE OK cli 3.4.0 MIT + … TRUE NA #> 2 colorspa… stan… FALSE FALSE OK colors… 2.0-3 BSD_3_… TRUE NA #> 3 digest stan… FALSE FALSE OK digest 0.6.29 GPL (>… TRUE NA #> 4 fansi stan… FALSE FALSE OK fansi 1.0.3 GPL-2 … TRUE NA #> 5 farver stan… FALSE FALSE OK farver 2.1.1 MIT + … TRUE NA #> 6 ggplot2 stan… TRUE TRUE OK ggplot2 3.3.6 MIT + … FALSE NA #> 7 glue stan… FALSE FALSE OK glue 1.6.2 MIT + … TRUE NA #> 8 gtable stan… FALSE FALSE OK gtable 0.3.1 MIT + … FALSE NA #> 9 isoband stan… FALSE FALSE OK isoband 0.2.5 MIT + … TRUE NA #> 10 labeling stan… FALSE FALSE OK labeli… 0.4.2 MIT + … FALSE NA #> # … with 24 more rows, 25 more variables: md5sum <chr>, sha256 <chr>, #> # filesize <int>, built <chr>, platform <chr>, rversion <chr>, #> # repotype <chr>, repodir <chr>, target <chr>, deps <list>, mirror <chr>, #> # sources <list>, remote <list>, error <list>, metadata <list>, extra <list>, #> # dep_types <list>, params <list>, sysreqs <chr>, cache_status <chr>, #> # fulltarget <chr>, fulltarget_tree <chr>, download_status <chr>, #> # download_error <list>, file_size <dbl>, and abbreviated variable names … #> # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable #> names #> [1] "src"
Installation
How to install a package into a new library?
library(pkgdepends)
dir.create(new_lib <- tempfile())
prop <- new_pkg_installation_proposal("pkgconfig", config = list(library = new_lib))
prop$solve()
prop$download()
prop$install()
lib_status(new_lib)#> ℹ No downloads are needed, 1 pkg (6.08 kB) is cached #> ℹ Building pkgconfig 2.0.3 #> ✔ Built pkgconfig 2.0.3 (1s) #> ✔ Installed pkgconfig 2.0.3 (37ms) #> ✔ Summary: 1 new in 1s #> # A data frame: 1 × 31 #> library package title version license imports sugge…¹ needs…² repos…³ built #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <lgl> <chr> <chr> #> 1 /tmp/Rtmp… pkgcon… Priv… 2.0.3 MIT + … utils covr, … FALSE CRAN R 4.… #> # … with 21 more variables: remotetype <chr>, remotepkgref <chr>, #> # remoteref <chr>, remoterepos <chr>, remotepkgplatform <chr>, #> # remotesha <chr>, depends <chr>, linkingto <chr>, enhances <chr>, #> # md5sum <chr>, platform <chr>, priority <chr>, biocviews <chr>, #> # sysreqs <chr>, ref <chr>, type <chr>, status <chr>, rversion <chr>, #> # sources <list>, repotype <chr>, deps <list>, and abbreviated variable names #> # ¹suggests, ²needscompilation, ³repository #> # ℹ Use `colnames()` to see all variable names
How to update a package?
Install an older version first.
library(pkgdepends)
dir.create(new_lib <- tempfile())
config <- list(library = new_lib)
prop <- new_pkg_installation_proposal("cran/pkgconfig@2.0.2", config = config)
prop$solve()
prop$download()
prop$install()
lib_status(new_lib)#> ℹ No downloads are needed, 1 pkg is cached #> ✔ Got pkgconfig 2.0.2 (source) (13.22 kB) #> ℹ Packaging pkgconfig 2.0.2 #> ✔ Packaged pkgconfig 2.0.2 (310ms) #> ℹ Building pkgconfig 2.0.2 #> ✔ Built pkgconfig 2.0.2 (923ms) #> ✔ Installed pkgconfig 2.0.2 (github::cran/pkgconfig@d892880) (20ms) #> ✔ Summary: 1 new in 942ms #> # A data frame: 1 × 32 #> library package title version license imports sugge…¹ needs…² repos…³ built #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <lgl> <chr> <chr> #> 1 /tmp/Rtmp… pkgcon… Priv… 2.0.2 MIT + … utils covr, … FALSE CRAN R 4.… #> # … with 22 more variables: remotetype <chr>, remotehost <chr>, #> # remoterepo <chr>, remoteusername <chr>, remotepkgref <chr>, #> # remoteref <chr>, remotesha <chr>, depends <chr>, linkingto <chr>, #> # enhances <chr>, md5sum <chr>, platform <chr>, priority <chr>, #> # biocviews <chr>, sysreqs <chr>, ref <chr>, type <chr>, status <chr>, #> # rversion <chr>, sources <list>, repotype <chr>, deps <list>, and #> # abbreviated variable names ¹suggests, ²needscompilation, ³repository #> # ℹ Use `colnames()` to see all variable names
Now update.
library(pkgdepends)
prop2 <- new_pkg_installation_proposal("pkgconfig", config = config)
prop2$set_solve_policy("upgrade")
prop2$solve()
prop2$download()
prop2$install()
lib_status(new_lib)#> ℹ No downloads are needed, 1 pkg (6.08 kB) is cached #> ℹ Building pkgconfig 2.0.3 #> ✔ Built pkgconfig 2.0.3 (961ms) #> ✔ Installed pkgconfig 2.0.3 (25ms) #> ✔ Summary: 1 updated in 985ms #> # A data frame: 1 × 31 #> library package title version license imports sugge…¹ needs…² repos…³ built #> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <lgl> <chr> <chr> #> 1 /tmp/Rtmp… pkgcon… Priv… 2.0.3 MIT + … utils covr, … FALSE CRAN R 4.… #> # … with 21 more variables: remotetype <chr>, remotepkgref <chr>, #> # remoteref <chr>, remoterepos <chr>, remotepkgplatform <chr>, #> # remotesha <chr>, depends <chr>, linkingto <chr>, enhances <chr>, #> # md5sum <chr>, platform <chr>, priority <chr>, biocviews <chr>, #> # sysreqs <chr>, ref <chr>, type <chr>, status <chr>, rversion <chr>, #> # sources <list>, repotype <chr>, deps <list>, and abbreviated variable names #> # ¹suggests, ²needscompilation, ³repository #> # ℹ Use `colnames()` to see all variable names