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Add R-update-package(s) script(s) (#20)
* Add R-update-package(s) script(s) * Improved documentation [ci skip] * Add support for private bitbucket packages
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| #!/usr/bin/env bash | ||
| # | ||
| # {{ ansible_managed }} | ||
| # | ||
| # set -x; | ||
| set -e; | ||
| set -o pipefail; | ||
| # | ||
| thisFile="$(readlink -f "${0}")"; | ||
| thisFilePath="$(dirname "${thisFile}")"; | ||
|
|
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| if [ -z "${1}" ] || [ "${1}" != '-r' ] || [ -z "${2}" ]; then | ||
| echo "Usage: ${0} -r requirements.txt"; | ||
| exit 1; | ||
| fi | ||
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| if [ ! -f "${2}" ]; then | ||
| echo "Could not open requirements file for reading"; | ||
| exit 1; | ||
| fi | ||
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| requirementsFile="${2}"; | ||
| shift 2; | ||
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| while IFS= read -r requirement; do | ||
| requirementType="$(echo "${requirement}" | awk -F'::' '{ print $1}')"; | ||
| requirementName="$(echo "${requirement}" | awk -F'::' '{ print $2}' | awk -F'@' '{ print $1}')"; | ||
| requirementVersion="$(echo "${requirement}" | awk -F'::' '{ print $2}' | awk -F'@' '{ print $2}')"; | ||
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| if [ "${requirementType}" == 'github' ]; then | ||
| installCommand="devtools::install_github(\"${requirementName}\")"; | ||
| if [ -n "${requirementVersion}" ]; then | ||
| installCommand="devtools::install_github(\"${requirementName}\", ref=\"${requirementVersion}\")"; | ||
| fi | ||
| elif [ "${requirementType}" == 'bitbucket' ]; then | ||
| installCommand="devtools::install_bitbucket(\"${requirementName}\", auth_user = Sys.getenv(\"BITBUCKET_AUTH_USER\"), password = Sys.getenv(\"BITBUCKET_AUTH_PASSWORD\"))"; | ||
| if [ -n "${requirementVersion}" ]; then | ||
| installCommand="devtools::install_bitbucket(\"${requirementName}\", ref=\"${requirementVersion}\", auth_user = Sys.getenv(\"BITBUCKET_AUTH_USER\"), password = Sys.getenv(\"BITBUCKET_AUTH_PASSWORD\"))"; | ||
| fi | ||
| else | ||
| installCommand="devtools::install_cran(\"${requirementName}\")"; | ||
| if [ -n "${requirementVersion}" ]; then | ||
| installCommand="devtools::install_version(\"${requirementName}\", version=\"${requirementVersion}\")"; | ||
| fi | ||
| fi | ||
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| Rscript -e "withCallingHandlers(${installCommand}, warning = stop)"; | ||
| done < "${requirementsFile}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| #!/usr/bin/env Rscript | ||
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| argv = commandArgs(trailingOnly = TRUE); | ||
| if (is.null(argv) | length(argv) < 1) { | ||
| cat("Usage: R-update-package package [lib] [repos]\n"); | ||
| q(status = 1); | ||
| } | ||
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| package = argv[1]; | ||
| lib = ifelse(is.na(argv[2]), '{{ r_packages_lib }}', argv[2]); | ||
| repos = ifelse(is.na(argv[3]), '{{ r_packages_repos }}', argv[3]); | ||
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| if (package %in% old.packages(lib.loc = lib)[, 'Package']) { | ||
| withCallingHandlers({ | ||
| update.packages(package, lib, repos, ask = FALSE); | ||
| cat("changed\n"); | ||
| }, warning = stop); | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| #!/usr/bin/env Rscript | ||
|
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| argv = commandArgs(trailingOnly = TRUE); | ||
| if (is.null(argv) | length(argv) < 0) { | ||
| cat("Usage: R-update-packages [lib] [repos]\n"); | ||
| q(status = 1); | ||
| } | ||
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| lib = ifelse(is.na(argv[1]), '{{ r_packages_lib }}', argv[1]); | ||
| repos = ifelse(is.na(argv[2]), '{{ r_packages_repos.rstrip('/') }}', argv[2]); | ||
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| if (!is.null(old.packages(lib.loc = lib))) { | ||
| withCallingHandlers({ | ||
| update.packages(lib, repos, ask = FALSE); | ||
| cat("changed\n"); | ||
| }, warning = stop); | ||
| } |