[Phylobase-commits] r779 - / utils

[noreply at r-forge.r-project.org]

Author: francois
Date: 2010-04-02 00:28:13 +0200 (Fri, 02 Apr 2010)
New Revision: 779

Added:
   utils/
   utils/mergeNCL.R
   utils/updateTestsOutput.R
Log:
a couple of scripts to facilitate phylobase maintenance tasks (test output and NCL merge)

Added: utils/mergeNCL.R
===================================================================
--- utils/mergeNCL.R	                        (rev 0)
+++ utils/mergeNCL.R	2010-04-01 22:28:13 UTC (rev 779)
@@ -0,0 +1,49 @@
+### Script that allows to merge automatically .cpp and .h files from NCL
+
+### IMPORTANT Notes: only works if the changes to libncl are committed (just) before the merging
+###  in other words the difference between previous revision and current revision in libncl/current
+###  represents the changes to NCL
+### IMPORTANT Notes 2: if you run the script from within Emacs, in case of conflict during the merging
+###   it's best to always choose "postpone" and do the modifications by hand.
+
+### This script does not take care of files that could be added in the future development of NCL
+
+### Procedure to follow:
+## 0. extract NCL tarball in a folder outside of phylobase
+## 1. copy the content of the folder (and overwrite) directly the content of libncl/current
+## 2. run: find libncl/current -name ._* -delete (to remove Mac's fork files)
+## 3. run: svn status | grep ^? (to identify the files that need to be added)
+## 4. add/remove files with svn add/rm to include/remove all the files with version control
+## 5. run: svn copy current 2.x.y (where 2.x.y represent the newest NCL version, to tag newest NCL version)
+## 6. commit these changes to libncl folder
+## 7. modify (to match your installation) and run the script below to merge all the files
+## 8. commit changes
+
+
+## Change this line to match your installation
+setwd("~/Work/R-dev/phylobase/")
+
+# run svn log to get latest revision number
+system("svnversion > svn.log")
+svnlog <- scan(file="svn.log", what="character")
+revNb <- unlist(strsplit(svnlog, ":"))[2]
+revNb <- gsub("[^0-9]", "", revNb)
+revNb <- as.numeric(revNb)
+
+## merge .cpp files
+setwd("pkg/src/")
+listCpp <- list.files(pattern="^nxs.+\\.cpp$")
+for (eachCpp in listCpp) {
+    cmd <- paste("svn merge -r", revNb-1, ":", revNb, " ../../libncl/current/ncl/", eachCpp, " ", eachCpp, sep="")
+    cat("\n", cmd)
+    system(cmd)
+}
+
+## merge .h files
+setwd("ncl")
+listH <- list.files(pattern="\\.h$")
+for (eachH in listH) {
+    cmd <- paste("svn merge -r", revNb-1, ":", revNb, " ../../../libncl/current/ncl/", eachH, " ", eachH, sep="")
+    cat("\n", cmd, "\n")
+    system(cmd)
+}

Added: utils/updateTestsOutput.R
===================================================================
--- utils/updateTestsOutput.R	                        (rev 0)
+++ utils/updateTestsOutput.R	2010-04-01 22:28:13 UTC (rev 779)
@@ -0,0 +1,11 @@
+### Script to recreate automatically all the output for the tests in 
+###  pkg/tests/
+
+setwd("~/Work/R-dev/phylobase/pkg/tests/")
+listTests <- list.files(pattern=".R$")
+
+for(eachTest in listTests) {
+    out <- gsub("\\.R$", "\\.Rout.save", eachTest)
+    cmd <- paste("R CMD BATCH --no-save", eachTest, out)
+    system(cmd)
+}