rbbt-util 5.26.4 → 5.26.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9e4dda2ba8718e44af7064ac562b5535cb4271bf
-  data.tar.gz: 87e7d84660913247bae2b99da8728c9b22edba12
+  metadata.gz: ca8e3fcd160d5743a6ea4486713dcf07eeecab91
+  data.tar.gz: 8531b92294b52a849a1eee3699800612f9a462b2
 SHA512:
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+  metadata.gz: c500a6bc24bfecde13f14345139e6761f2d7f3f75a8f7d833b13155780807d64d46e9d648dd0541021c10386f2d173fe1cba3e2c2959874ea5f7d0a958570e57
+  data.tar.gz: d7c1d77b55d08790449d4ebfcaee94da1a6fc8dd70568de84b634abd2d5d4987a617b9d63840d1c4b72d5b0e259e4e7e129c1e21efb464d902b26a2c28af50a8

data/lib/rbbt/workflow/definition.rb

@@ -71,9 +71,10 @@ module Workflow
       set_info :result_type, dep.info[:result_type]
       forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
       if forget
-        Open.cp dep.path, self.path
         self.dependencies = self.dependencies - [dep]
         self.set_info :dependency, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
+        FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist? dep.files_dir
+        Open.cp dep.path, self.tmp_path
       else
         Open.link dep.path, self.path
       end

data/share/Rlib/util.R

@@ -733,22 +733,28 @@ rbbt.plot.text_scatter <- function(formula, data) {
 rbbt.install.CRAN <- function(pkg){
     cat("Try CRAN install:", pkg, "\n")
     res = FALSE
-    tryCatch({ install.packages(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
-    cat("CRAN", res)
+    tryCatch({ install.packages(pkg); library(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
     return(res)
 }
 
 rbbt.install.bioc <-function(pkg){
     cat("Try BIOC install:", pkg, "\n")
     res = FALSE
-    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 })
+    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 })
+    return(res)
+}
+
+rbbt.install.biocManager <-function(pkg, ...){
+    cat("Try BiocManager install:", pkg, "\n")
+    res = FALSE
+    tryCatch({ BiocManager::install(pkg, ...) }, error = function(e){ warning(paste("Could not install BiocManager ", pkg, "\n")); res = FALSE })
     return(res)
 }
 
 rbbt.install.github <- function(pkg, ...){
     cat("Try GITHUB install:", pkg, "\n")
     res = FALSE
-    tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg)); res = FALSE })
+    tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg, "\n")); res = FALSE })
     return(res)
 }
 
@@ -767,7 +773,9 @@ rbbt.require <- function(pkg, ...){
         if (!rbbt.install.github(pkg, ...)){
             if (!rbbt.install.CRAN(pkg, ...)){
                 if (!rbbt.install.bioc(pkg, ...)){
-                    stop("Error!", pkg)
+                    if (!rbbt.install.biocManager(pkg, ...)){
+                        stop("Error!", pkg)
+                    }
                 }
             }
         }

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.4
+  version: 5.26.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-04-26 00:00:00.000000000 Z
+date: 2019-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake