From f0674122ff36fe7696511409fdb7caace7d7c48b Mon Sep 17 00:00:00 2001 From: JulioV Date: Fri, 1 May 2020 19:46:04 -0400 Subject: [PATCH] Replace packrat with renv --- .gitignore | 2 + .travis.yml | 10 +- Snakefile | 2 +- packrat/packrat.lock | 889 ------------------ packrat/packrat.opts | 19 - renv.lock | 793 ++++++++++++++++ rules/renv.snakefile | 19 + src/data/application_genres.R | 2 +- src/data/download_dataset.R | 2 +- src/data/download_participants.R | 2 +- src/data/phone_sensed_bins.R | 2 +- src/data/phone_valid_sensed_days.R | 2 +- src/data/readable_datetime.R | 2 +- src/data/resample_fused_location.R | 2 +- src/data/unify_ios_android.R | 2 +- src/features/activity_recognition_deltas.R | 2 +- src/features/battery_deltas.R | 2 +- src/features/bluetooth_features.R | 2 +- src/features/call_features.R | 2 +- src/features/location_barnett_features.R | 2 +- src/features/screen_deltas.R | 2 +- src/features/sms_features.R | 2 +- src/features/wifi_features.R | 2 +- src/models/clean_features_for_model.R | 2 +- .../merge_features_for_individual_model.R | 11 +- .../merge_features_for_population_model.R | 2 +- src/visualization/compliance_report.Rmd | 2 +- 27 files changed, 850 insertions(+), 933 deletions(-) delete mode 100644 packrat/packrat.lock delete mode 100644 packrat/packrat.opts create mode 100644 renv.lock create mode 100644 rules/renv.snakefile diff --git a/.gitignore b/.gitignore index b1e8af77..9b3345b7 100644 --- a/.gitignore +++ b/.gitignore @@ -108,3 +108,5 @@ reports/ .RData .Rhistory sn_profile_*/ +renv/ + diff --git a/.travis.yml b/.travis.yml index c0ab96c7..f9a866ec 100644 --- a/.travis.yml +++ b/.travis.yml @@ -20,9 +20,11 @@ install: - conda env create -q -n test-environment python=$TRAVIS_PYTHON_VERSION --file environment.yml - conda activate test-environment before_script: -- snakemake packrat_install -- snakemake packrat_init -- snakemake packrat_restore +# Install renv and library +- snakemake renv_install +- snakemake renv_init +- snakemake renv_restore + script: - cp -r tests/data/raw/* data/raw - snakemake --profile tests/settings -R sms_features @@ -40,4 +42,4 @@ notifications: cache: directories: - - /usr/local/lib/R + - /usr/local/lib/R diff --git a/Snakefile b/Snakefile index 28fc6427..bc1c849a 100644 --- a/Snakefile +++ b/Snakefile @@ -1,5 +1,5 @@ configfile: "config.yaml" -include: "rules/packrat.snakefile" +include: "rules/renv.snakefile" include: "rules/preprocessing.snakefile" include: "rules/features.snakefile" include: "rules/models.snakefile" diff --git a/packrat/packrat.lock b/packrat/packrat.lock deleted file mode 100644 index 633f318e..00000000 --- a/packrat/packrat.lock +++ /dev/null @@ -1,889 +0,0 @@ -PackratFormat: 1.4 -PackratVersion: 0.5.0 -RVersion: 4.0.0 -Repos: CRAN=http://CRAN.R-project.org - -Package: BDgraph -Source: CRAN -Version: 2.62 -Hash: b4a039aae1d9b388edad2cb552a48986 -Requires: igraph - -Package: BH -Source: CRAN -Version: 1.72.0-3 -Hash: 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+ "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" + } + } +} diff --git a/rules/renv.snakefile b/rules/renv.snakefile new file mode 100644 index 00000000..abd717ef --- /dev/null +++ b/rules/renv.snakefile @@ -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()'" \ No newline at end of file diff --git a/src/data/application_genres.R b/src/data/application_genres.R index 60d87f28..08944fae 100644 --- a/src/data/application_genres.R +++ b/src/data/application_genres.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(tidyr) library(dplyr) diff --git a/src/data/download_dataset.R b/src/data/download_dataset.R index 48bed63e..61b808e9 100644 --- a/src/data/download_dataset.R +++ b/src/data/download_dataset.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(RMySQL) library(stringr) diff --git a/src/data/download_participants.R b/src/data/download_participants.R index c5115e8f..d3299804 100644 --- a/src/data/download_participants.R +++ b/src/data/download_participants.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(RMySQL) diff --git a/src/data/phone_sensed_bins.R b/src/data/phone_sensed_bins.R index f0aa67e3..2d5664fa 100644 --- a/src/data/phone_sensed_bins.R +++ b/src/data/phone_sensed_bins.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) library(tidyr) diff --git a/src/data/phone_valid_sensed_days.R b/src/data/phone_valid_sensed_days.R index b3c06408..8488af76 100644 --- a/src/data/phone_valid_sensed_days.R +++ b/src/data/phone_valid_sensed_days.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) diff --git a/src/data/readable_datetime.R b/src/data/readable_datetime.R index fcd2d012..58f18f68 100644 --- a/src/data/readable_datetime.R +++ b/src/data/readable_datetime.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library("tidyverse") library(readr) diff --git a/src/data/resample_fused_location.R b/src/data/resample_fused_location.R index 3ac86f9a..8fd93906 100644 --- a/src/data/resample_fused_location.R +++ b/src/data/resample_fused_location.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) library(readr) diff --git a/src/data/unify_ios_android.R b/src/data/unify_ios_android.R index 03639f56..78bc4bdf 100644 --- a/src/data/unify_ios_android.R +++ b/src/data/unify_ios_android.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) library(stringr) diff --git a/src/features/activity_recognition_deltas.R b/src/features/activity_recognition_deltas.R index 252f9ca0..78739e16 100644 --- a/src/features/activity_recognition_deltas.R +++ b/src/features/activity_recognition_deltas.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library("tidyverse") diff --git a/src/features/battery_deltas.R b/src/features/battery_deltas.R index 8aea316e..393b1731 100644 --- a/src/features/battery_deltas.R +++ b/src/features/battery_deltas.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library("tidyverse") diff --git a/src/features/bluetooth_features.R b/src/features/bluetooth_features.R index 750dbd53..7e3cbc4d 100644 --- a/src/features/bluetooth_features.R +++ b/src/features/bluetooth_features.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) library(tidyr) diff --git a/src/features/call_features.R b/src/features/call_features.R index f4e70b75..9059bda2 100644 --- a/src/features/call_features.R +++ b/src/features/call_features.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) library(entropy) diff --git a/src/features/location_barnett_features.R b/src/features/location_barnett_features.R index 85bfbf47..bc1b315a 100644 --- a/src/features/location_barnett_features.R +++ b/src/features/location_barnett_features.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) diff --git a/src/features/screen_deltas.R b/src/features/screen_deltas.R index 47a4f1d1..d81554fc 100644 --- a/src/features/screen_deltas.R +++ b/src/features/screen_deltas.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) library(tidyr) diff --git a/src/features/sms_features.R b/src/features/sms_features.R index 2e970a8e..8c360ac4 100644 --- a/src/features/sms_features.R +++ b/src/features/sms_features.R @@ -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) diff --git a/src/features/wifi_features.R b/src/features/wifi_features.R index b2f11339..7c6e5697 100644 --- a/src/features/wifi_features.R +++ b/src/features/wifi_features.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(dplyr) diff --git a/src/models/clean_features_for_model.R b/src/models/clean_features_for_model.R index 1dd8ee9d..955ec67e 100644 --- a/src/models/clean_features_for_model.R +++ b/src/models/clean_features_for_model.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(tidyr) library(dplyr) diff --git a/src/models/merge_features_for_individual_model.R b/src/models/merge_features_for_individual_model.R index 713bea03..9c9e91d0 100644 --- a/src/models/merge_features_for_individual_model.R +++ b/src/models/merge_features_for_individual_model.R @@ -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"]] diff --git a/src/models/merge_features_for_population_model.R b/src/models/merge_features_for_population_model.R index b40218c1..abb36d6a 100644 --- a/src/models/merge_features_for_population_model.R +++ b/src/models/merge_features_for_population_model.R @@ -1,4 +1,4 @@ -source("packrat/init.R") +source("renv/activate.R") library(tidyr) library(purrr) diff --git a/src/visualization/compliance_report.Rmd b/src/visualization/compliance_report.Rmd index 928d55c8..2717875d 100644 --- a/src/visualization/compliance_report.Rmd +++ b/src/visualization/compliance_report.Rmd @@ -18,7 +18,7 @@ output: --- ```{r include=FALSE} -source("packrat/init.R") +source("renv/activate.R") ``` ## Overall phone compliance