diff --git a/renv.lock b/renv.lock index 971800d01..c3efbeadc 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.1.0", + "Version": "4.2.2", "Repositories": [ { "Name": "CRAN", @@ -123,7 +123,7 @@ }, "cli": { "Package": "cli", - "Version": "2.5.0", + "Version": "3.6.0", "Source": "Repository", "Repository": "CRAN", "Hash": "a94ba44cee3ea571e813721e64184172" @@ -172,10 +172,10 @@ }, "curl": { "Package": "curl", - "Version": "4.3", + "Version": "5.0.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "2b7d10581cc730804e9ed178c8374bd6" + "Hash": "e4f97056611e8e6b8b852d13b7400cf1" }, "data.table": { "Package": "data.table", @@ -289,7 +289,7 @@ }, "git2r": { "Package": "git2r", - "Version": "0.29.0", + "Version": "0.30.1", "Source": "Repository", "Repository": "CRAN", "Hash": "b114135c4749076bd5ef74a5827b6f62" @@ -303,7 +303,7 @@ }, "glue": { "Package": "glue", - "Version": "1.4.2", + "Version": "1.6.2", "Source": "Repository", "Repository": "CRAN", "Hash": "6efd734b14c6471cfe443345f3e35e29" @@ -345,10 +345,10 @@ }, "igraph": { "Package": "igraph", - "Version": "1.2.11", + "Version": "1.4.0", "Source": "Repository", "Repository": "CRAN", - "Hash": "1d10cd31c2979f9c819ffe4d16b9dc2b" + "Hash": "14734eae03f062b55e794b07784aeddc" }, "ini": { "Package": "ini", @@ -394,7 +394,7 @@ }, "lifecycle": { "Package": "lifecycle", - "Version": "1.0.0", + "Version": "1.0.3", "Source": "Repository", "Repository": "CRAN", "Hash": "3471fb65971f1a7b2d4ae7848cf2db8d" @@ -436,10 +436,10 @@ }, "openssl": { "Package": "openssl", - "Version": "1.4.3", + "Version": "2.0.5", "Source": "Repository", "Repository": "CRAN", - "Hash": "a399e4773075fc2375b71f45fca186c4" + "Hash": "b04c27110bf367b4daa93f34f3d58e75" }, "pillar": { "Package": "pillar", @@ -520,7 +520,7 @@ }, "readr": { "Package": "readr", - "Version": "1.4.0", + "Version": "2.1.4", "Source": "Repository", "Repository": "CRAN", "Hash": "2639976851f71f330264a9c9c3d43a61" @@ -555,7 +555,7 @@ }, "rlang": { "Package": "rlang", - "Version": "0.4.11", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", "Hash": "515f341d3affe0de9e4a7f762efb0456" @@ -569,7 +569,7 @@ }, "roxygen2": { "Package": "roxygen2", - "Version": "7.1.1", + "Version": "7.2.3", "Source": "Repository", "Repository": "CRAN", "Hash": "fcd94e00cc409b25d07ca50f7bf339f5" @@ -723,7 +723,7 @@ }, "xml2": { "Package": "xml2", - "Version": "1.3.2", + "Version": "1.3.3", "Source": "Repository", "Repository": "CRAN", "Hash": "d4d71a75dd3ea9eb5fa28cc21f9585e2" diff --git a/vignettes/driverdrake_vignette.Rmd b/vignettes/driverdrake_vignette.Rmd index 350c18fc4..03bafbd71 100644 --- a/vignettes/driverdrake_vignette.Rmd +++ b/vignettes/driverdrake_vignette.Rmd @@ -247,14 +247,14 @@ When running `driver_drake()` with parallelism, the following arguments to `make ### The `clustermq` backend -See the `clustermq` [installation guide](https://cran.r-project.org/web/packages/clustermq/vignettes/userguide.html) for installation instructions and options. `clustermq` requires `R version 3.5` or greater. Note, on Mac and Windows a simple `install.packages("clustermq") is sufficient. - +See the `clustermq` [installation guide](https://cran.r-project.org/web/packages/clustermq/vignettes/userguide.html) for installation instructions and options. `clustermq` requires `R version 3.5` or greater. Note, on Mac and Windows a simple `install.packages("clustermq")` is sufficient. For using `clustermq` on PIC (PNNL Institutional Computing) we have already installed the full set of required R packages in a shared space as successfully compiling `clustermq` was not straightforward due to compiler version issues. To use `drake` + `clustermq` in PIC a user can: - * Get necessary libraries with: `export R_LIBS=/pic/projects/GCAM/GCAM-libraries/R/x86_64-pc-linux-gnu-library/3.5` - * Load the `zeromq` library with: `module load zeromq/4.1.4` - * Open `R 3.5.1` with: `module load R/3.5.1` - * Open an `R` session and set the global option below - * Run `driver_drake()` with the arguments such as below + +* Get necessary libraries with: `export R_LIBS=/pic/projects/GCAM/GCAM-libraries/R/x86_64-pc-linux-gnu-library/3.5` +* Load the `zeromq` library with: `module load zeromq/4.1.4` +* Open `R 3.5.1` with: `module load R/3.5.1` +* Open an `R` session and set the global option below +* Run `driver_drake()` with the arguments such as below ```r @@ -390,8 +390,9 @@ vis_drake_graph(plan, from = make.names("L210.RenewRsrc")) See the `drake` documentation for other features. Some that may be useful with `gcamdata` include - * `outdated(plan)`: lists all of the targets that are outdated - * `predict_runtime(plan)`: `drake` records the time it takes to build each target and uses this to predict the runtime of the next `make()` + +* `outdated(plan)`: lists all of the targets that are outdated +* `predict_runtime(plan)`: `drake` records the time it takes to build each target and uses this to predict the runtime of the next `make()` diff --git a/vignettes/driverdrake_vignette.Rmd.orig b/vignettes/driverdrake_vignette.Rmd.orig index 94d416e18..d22a17423 100644 --- a/vignettes/driverdrake_vignette.Rmd.orig +++ b/vignettes/driverdrake_vignette.Rmd.orig @@ -147,14 +147,14 @@ When running `driver_drake()` with parallelism, the following arguments to `make ### The `clustermq` backend -See the `clustermq` [installation guide](https://cran.r-project.org/web/packages/clustermq/vignettes/userguide.html) for installation instructions and options. `clustermq` requires `R version 3.5` or greater. Note, on Mac and Windows a simple `install.packages("clustermq") is sufficient. - +See the `clustermq` [installation guide](https://cran.r-project.org/web/packages/clustermq/vignettes/userguide.html) for installation instructions and options. `clustermq` requires `R version 3.5` or greater. Note, on Mac and Windows a simple `install.packages("clustermq")` is sufficient. For using `clustermq` on PIC (PNNL Institutional Computing) we have already installed the full set of required R packages in a shared space as successfully compiling `clustermq` was not straightforward due to compiler version issues. To use `drake` + `clustermq` in PIC a user can: - * Get necessary libraries with: `export R_LIBS=/pic/projects/GCAM/GCAM-libraries/R/x86_64-pc-linux-gnu-library/3.5` - * Load the `zeromq` library with: `module load zeromq/4.1.4` - * Open `R 3.5.1` with: `module load R/3.5.1` - * Open an `R` session and set the global option below - * Run `driver_drake()` with the arguments such as below + +* Get necessary libraries with: `export R_LIBS=/pic/projects/GCAM/GCAM-libraries/R/x86_64-pc-linux-gnu-library/3.5` +* Load the `zeromq` library with: `module load zeromq/4.1.4` +* Open `R 3.5.1` with: `module load R/3.5.1` +* Open an `R` session and set the global option below +* Run `driver_drake()` with the arguments such as below ```{r eval = FALSE} # Load clustermq and set type to multicore @@ -233,8 +233,9 @@ vis_drake_graph(plan, from = make.names("L210.RenewRsrc")) See the `drake` documentation for other features. Some that may be useful with `gcamdata` include - * `outdated(plan)`: lists all of the targets that are outdated - * `predict_runtime(plan)`: `drake` records the time it takes to build each target and uses this to predict the runtime of the next `make()` + +* `outdated(plan)`: lists all of the targets that are outdated +* `predict_runtime(plan)`: `drake` records the time it takes to build each target and uses this to predict the runtime of the next `make()`