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 CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA1:
3
- metadata.gz: 9e4dda2ba8718e44af7064ac562b5535cb4271bf
4
- data.tar.gz: 87e7d84660913247bae2b99da8728c9b22edba12
3
+ metadata.gz: ca8e3fcd160d5743a6ea4486713dcf07eeecab91
4
+ data.tar.gz: 8531b92294b52a849a1eee3699800612f9a462b2
5
5
  SHA512:
6
- metadata.gz: e7439eb5f1aab09428f79bca41ce43545e18c52ff5361ef43d35ae3394d6cc4655d3761dc6223c4e03617236927f2588a8e5e02d661a30959cbdc6e8fb88027f
7
- data.tar.gz: 31c6f48ab66ac09fd20c6ba164623f2a33cab3ee7a0b968ec3fc26f9349706bbbd3824945b8021eebd4a60d02d216b6a3c8d11e8f9c450e9b8f56d0a49c3b347
6
+ metadata.gz: c500a6bc24bfecde13f14345139e6761f2d7f3f75a8f7d833b13155780807d64d46e9d648dd0541021c10386f2d173fe1cba3e2c2959874ea5f7d0a958570e57
7
+ data.tar.gz: d7c1d77b55d08790449d4ebfcaee94da1a6fc8dd70568de84b634abd2d5d4987a617b9d63840d1c4b72d5b0e259e4e7e129c1e21efb464d902b26a2c28af50a8
@@ -71,9 +71,10 @@ module Workflow
71
71
  set_info :result_type, dep.info[:result_type]
72
72
  forget = config :forget_dep_tasks, :forget_dep_tasks, :default => FORGET_DEP_TASKS
73
73
  if forget
74
- Open.cp dep.path, self.path
75
74
  self.dependencies = self.dependencies - [dep]
76
75
  self.set_info :dependency, dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]}
76
+ FileUtils.cp_r dep.files_dir, self.files_dir if Open.exist? dep.files_dir
77
+ Open.cp dep.path, self.tmp_path
77
78
  else
78
79
  Open.link dep.path, self.path
79
80
  end
data/share/Rlib/util.R CHANGED
@@ -733,22 +733,28 @@ rbbt.plot.text_scatter <- function(formula, data) {
733
733
  rbbt.install.CRAN <- function(pkg){
734
734
  cat("Try CRAN install:", pkg, "\n")
735
735
  res = FALSE
736
- tryCatch({ install.packages(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
737
- cat("CRAN", res)
736
+ tryCatch({ install.packages(pkg); library(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
738
737
  return(res)
739
738
  }
740
739
 
741
740
  rbbt.install.bioc <-function(pkg){
742
741
  cat("Try BIOC install:", pkg, "\n")
743
742
  res = FALSE
744
- 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 })
743
+ 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 })
744
+ return(res)
745
+ }
746
+
747
+ rbbt.install.biocManager <-function(pkg, ...){
748
+ cat("Try BiocManager install:", pkg, "\n")
749
+ res = FALSE
750
+ tryCatch({ BiocManager::install(pkg, ...) }, error = function(e){ warning(paste("Could not install BiocManager ", pkg, "\n")); res = FALSE })
745
751
  return(res)
746
752
  }
747
753
 
748
754
  rbbt.install.github <- function(pkg, ...){
749
755
  cat("Try GITHUB install:", pkg, "\n")
750
756
  res = FALSE
751
- tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg)); res = FALSE })
757
+ tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg, "\n")); res = FALSE })
752
758
  return(res)
753
759
  }
754
760
 
@@ -767,7 +773,9 @@ rbbt.require <- function(pkg, ...){
767
773
  if (!rbbt.install.github(pkg, ...)){
768
774
  if (!rbbt.install.CRAN(pkg, ...)){
769
775
  if (!rbbt.install.bioc(pkg, ...)){
770
- stop("Error!", pkg)
776
+ if (!rbbt.install.biocManager(pkg, ...)){
777
+ stop("Error!", pkg)
778
+ }
771
779
  }
772
780
  }
773
781
  }
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-util
3
3
  version: !ruby/object:Gem::Version
4
- version: 5.26.4
4
+ version: 5.26.5
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2019-04-26 00:00:00.000000000 Z
11
+ date: 2019-04-29 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rake