Replace packrat with renv
JulioV
parent
07fe3e10af
commit
f0674122ff
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@ -108,3 +108,5 @@ reports/
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.RData
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.Rhistory
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sn_profile_*/
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renv/
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10
.travis.yml
10
.travis.yml
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@ -20,9 +20,11 @@ install:
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- conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml
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- conda activate test-environment
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before_script:
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- snakemake packrat_install
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- snakemake packrat_init
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- snakemake packrat_restore
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# Install renv and library
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- snakemake renv_install
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- snakemake renv_init
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- snakemake renv_restore
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script:
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- cp -r tests/data/raw/* data/raw
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- snakemake --profile tests/settings -R sms_features
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@ -40,4 +42,4 @@ notifications:
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cache:
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directories:
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- /usr/local/lib/R
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- /usr/local/lib/R
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@ -1,5 +1,5 @@
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configfile: "config.yaml"
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include: "rules/packrat.snakefile"
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include: "rules/renv.snakefile"
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include: "rules/preprocessing.snakefile"
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include: "rules/features.snakefile"
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include: "rules/models.snakefile"
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@ -1,889 +0,0 @@
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PackratFormat: 1.4
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PackratVersion: 0.5.0
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RVersion: 4.0.0
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Repos: CRAN=http://CRAN.R-project.org
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Version: 2.62
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Hash: b4a039aae1d9b388edad2cb552a48986
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Requires: igraph
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Version: 1.72.0-3
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Package: DBI
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Version: 1.1.0
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Hash: d1075050684753e939c45775617c8f38
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Package: DEoptimR
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Version: 1.0-8
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Hash: adc74e88e85eabe6c7d73db6a86fe6cf
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Requires: Formula, acepack, base64enc, cluster, data.table, foreign,
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|
||||
"ps": {
|
||||
"Package": "ps",
|
||||
"Version": "1.3.2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"psych": {
|
||||
"Package": "psych",
|
||||
"Version": "1.9.12.31",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"purrr": {
|
||||
"Package": "purrr",
|
||||
"Version": "0.3.4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"qgraph": {
|
||||
"Package": "qgraph",
|
||||
"Version": "1.6.5",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"readr": {
|
||||
"Package": "readr",
|
||||
"Version": "1.3.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"readxl": {
|
||||
"Package": "readxl",
|
||||
"Version": "1.3.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rematch": {
|
||||
"Package": "rematch",
|
||||
"Version": "1.0.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"reprex": {
|
||||
"Package": "reprex",
|
||||
"Version": "0.3.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"reshape2": {
|
||||
"Package": "reshape2",
|
||||
"Version": "1.4.4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rjson": {
|
||||
"Package": "rjson",
|
||||
"Version": "0.2.20",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rlang": {
|
||||
"Package": "rlang",
|
||||
"Version": "0.4.5",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rmarkdown": {
|
||||
"Package": "rmarkdown",
|
||||
"Version": "2.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"robustbase": {
|
||||
"Package": "robustbase",
|
||||
"Version": "0.93-6",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rpart": {
|
||||
"Package": "rpart",
|
||||
"Version": "4.1-15",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rprojroot": {
|
||||
"Package": "rprojroot",
|
||||
"Version": "1.3-2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rstudioapi": {
|
||||
"Package": "rstudioapi",
|
||||
"Version": "0.11",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"rvest": {
|
||||
"Package": "rvest",
|
||||
"Version": "0.3.5",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"scales": {
|
||||
"Package": "scales",
|
||||
"Version": "1.1.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"selectr": {
|
||||
"Package": "selectr",
|
||||
"Version": "0.4-2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"shape": {
|
||||
"Package": "shape",
|
||||
"Version": "1.4.4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"shiny": {
|
||||
"Package": "shiny",
|
||||
"Version": "1.4.0.2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"sourcetools": {
|
||||
"Package": "sourcetools",
|
||||
"Version": "0.1.7",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"stringi": {
|
||||
"Package": "stringi",
|
||||
"Version": "1.4.6",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"stringr": {
|
||||
"Package": "stringr",
|
||||
"Version": "1.4.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"survival": {
|
||||
"Package": "survival",
|
||||
"Version": "3.1-12",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"sys": {
|
||||
"Package": "sys",
|
||||
"Version": "3.3",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"testthat": {
|
||||
"Package": "testthat",
|
||||
"Version": "2.3.2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tibble": {
|
||||
"Package": "tibble",
|
||||
"Version": "3.0.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tidygraph": {
|
||||
"Package": "tidygraph",
|
||||
"Version": "1.1.2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tidyr": {
|
||||
"Package": "tidyr",
|
||||
"Version": "1.0.2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tidyselect": {
|
||||
"Package": "tidyselect",
|
||||
"Version": "1.0.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tidyverse": {
|
||||
"Package": "tidyverse",
|
||||
"Version": "1.3.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tinytex": {
|
||||
"Package": "tinytex",
|
||||
"Version": "0.22",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"tweenr": {
|
||||
"Package": "tweenr",
|
||||
"Version": "1.0.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"utf8": {
|
||||
"Package": "utf8",
|
||||
"Version": "1.1.4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"vctrs": {
|
||||
"Package": "vctrs",
|
||||
"Version": "0.2.4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"viridis": {
|
||||
"Package": "viridis",
|
||||
"Version": "0.5.1",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"viridisLite": {
|
||||
"Package": "viridisLite",
|
||||
"Version": "0.3.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"whisker": {
|
||||
"Package": "whisker",
|
||||
"Version": "0.4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"withr": {
|
||||
"Package": "withr",
|
||||
"Version": "2.2.0",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"xfun": {
|
||||
"Package": "xfun",
|
||||
"Version": "0.13",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"xml2": {
|
||||
"Package": "xml2",
|
||||
"Version": "1.3.2",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"xtable": {
|
||||
"Package": "xtable",
|
||||
"Version": "1.8-4",
|
||||
"Source": "CRAN"
|
||||
},
|
||||
"yaml": {
|
||||
"Package": "yaml",
|
||||
"Version": "2.2.1",
|
||||
"Source": "CRAN"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
## renv_install: installs renv onto machine
|
||||
rule renv_install:
|
||||
shell:
|
||||
"R -e 'install.packages(\"renv\", repos=\"http://cran.us.r-project.org\")'"
|
||||
|
||||
## renv_install: initialize a renv environment for this project
|
||||
rule renv_init:
|
||||
shell:
|
||||
"R -e 'renv::init()'"
|
||||
|
||||
## renv_snap : Look for new R packages in files & archives them
|
||||
rule renv_snap:
|
||||
shell:
|
||||
"R -e 'renv::snapshot()'"
|
||||
|
||||
## renv_restore: Installs archived packages onto a new machine
|
||||
rule renv_restore:
|
||||
shell:
|
||||
"R -e 'renv::restore()'"
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(tidyr)
|
||||
library(dplyr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(RMySQL)
|
||||
library(stringr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(RMySQL)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
library(tidyr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library("tidyverse")
|
||||
library(readr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
library(readr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
library(stringr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library("tidyverse")
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library("tidyverse")
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
library(tidyr)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
library(entropy)
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
library(tidyr)
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
# If you want to implement extra features, source(..) a new file and duplicate the line "features <- merge(...)", then
|
||||
# swap base_sms_features(...) for your own function
|
||||
|
||||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
source("src/features/sms/sms_base.R")
|
||||
library(dplyr, warn.conflicts = FALSE)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(dplyr)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
library(tidyr)
|
||||
library(dplyr)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,8 +1,17 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(tidyr)
|
||||
library(purrr)
|
||||
library(dplyr)
|
||||
library("methods")
|
||||
library("mgm")
|
||||
library("qgraph")
|
||||
library("dplyr")
|
||||
library("scales")
|
||||
library("ggplot2")
|
||||
library("purrr")
|
||||
library("tidyr")
|
||||
library("reshape2")
|
||||
|
||||
feature_files <- snakemake@input[["feature_files"]]
|
||||
phone_valid_sensed_days <- snakemake@input[["phone_valid_sensed_days"]]
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
|
||||
library(tidyr)
|
||||
library(purrr)
|
||||
|
|
|
|||
|
|
@ -18,7 +18,7 @@ output:
|
|||
---
|
||||
|
||||
```{r include=FALSE}
|
||||
source("packrat/init.R")
|
||||
source("renv/activate.R")
|
||||
```
|
||||
|
||||
## Overall phone compliance
|
||||
|
|
|
|||
Loading…
Reference in New Issue