rbbt-util 5.26.4 → 5.26.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/workflow/definition.rb +2 -1
- data/share/Rlib/util.R +13 -5
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: ca8e3fcd160d5743a6ea4486713dcf07eeecab91
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data.tar.gz: 8531b92294b52a849a1eee3699800612f9a462b2
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c500a6bc24bfecde13f14345139e6761f2d7f3f75a8f7d833b13155780807d64d46e9d648dd0541021c10386f2d173fe1cba3e2c2959874ea5f7d0a958570e57
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data.tar.gz: d7c1d77b55d08790449d4ebfcaee94da1a6fc8dd70568de84b634abd2d5d4987a617b9d63840d1c4b72d5b0e259e4e7e129c1e21efb464d902b26a2c28af50a8
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@@ -71,9 +71,10 @@ module Workflow
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set_info :result_type, dep.info[:result_type]
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forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
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if forget
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-
Open.cp dep.path, self.path
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self.dependencies = self.dependencies - [dep]
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self.set_info :dependency, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
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FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist? dep.files_dir
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Open.cp dep.path, self.tmp_path
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else
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Open.link dep.path, self.path
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end
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data/share/Rlib/util.R
CHANGED
@@ -733,22 +733,28 @@ rbbt.plot.text_scatter <- function(formula, data) {
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rbbt.install.CRAN <- function(pkg){
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cat("Try CRAN install:", pkg, "\n")
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res = FALSE
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tryCatch({ install.packages(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
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cat("CRAN", res)
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tryCatch({ install.packages(pkg); library(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
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return(res)
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}
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rbbt.install.bioc <-function(pkg){
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cat("Try BIOC install:", pkg, "\n")
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res = FALSE
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tryCatch({ source("http://bioconductor.org/biocLite.R"); biocLite(pkg, ask=FALSE, suppressUpdates = TRUE); res = TRUE }, error = function(e){ warning(paste("Could not install Bioconductor ", pkg)); res = FALSE })
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tryCatch({ source("http://bioconductor.org/biocLite.R"); biocLite(pkg, ask=FALSE, suppressUpdates = TRUE); res = TRUE }, error = function(e){ warning(paste("Could not install Bioconductor ", pkg, "\n")); res = FALSE })
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return(res)
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}
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rbbt.install.biocManager <-function(pkg, ...){
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cat("Try BiocManager install:", pkg, "\n")
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res = FALSE
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tryCatch({ BiocManager::install(pkg, ...) }, error = function(e){ warning(paste("Could not install BiocManager ", pkg, "\n")); res = FALSE })
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return(res)
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}
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rbbt.install.github <- function(pkg, ...){
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cat("Try GITHUB install:", pkg, "\n")
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res = FALSE
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tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg)); res = FALSE })
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tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg, "\n")); res = FALSE })
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return(res)
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}
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@@ -767,7 +773,9 @@ rbbt.require <- function(pkg, ...){
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if (!rbbt.install.github(pkg, ...)){
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if (!rbbt.install.CRAN(pkg, ...)){
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if (!rbbt.install.bioc(pkg, ...)){
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-
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if (!rbbt.install.biocManager(pkg, ...)){
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stop("Error!", pkg)
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}
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}
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}
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}
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metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: rbbt-util
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version: !ruby/object:Gem::Version
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version: 5.26.
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version: 5.26.5
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2019-04-
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date: 2019-04-29 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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