Merge branch 'release-v0_0_4' into dev

Author: itsrainingdata

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ccdrAlgorithm
 Title: CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks
 Version: 0.0.4
-Date: 2017-03-09
+Date: 2017-09-09
 Authors@R: c(
     person("Bryon", "Aragam", email = "sparsebn@gmail.com", role = c("aut", "cre")),
     person("Dacheng", "Zhang", role = c("aut"))
@@ -11,7 +11,7 @@ Description: Implementation of the CCDr (Concave penalized Coordinate Descent wi
 Depends:
     R (>= 3.2.3)
 Imports:
-    sparsebnUtils (>= 0.0.4),
+    sparsebnUtils (>= 0.0.5),
     Rcpp (>= 0.11.0),
     stats,
     utils
@@ -20,7 +20,6 @@ Suggests:
     testthat,
     graph,
     igraph
-Remotes: itsrainingdata/sparsebnUtils@dev
 URL: https://github.com/itsrainingdata/ccdrAlgorithm
 BugReports: https://github.com/itsrainingdata/ccdrAlgorithm/issues
 License: GPL (>= 2)

NEWS.md

@@ -2,8 +2,12 @@
 
 ## Features
 
-* `ccdr.run` now supports black lists and white lists
-* Users can now use prior knowledge of variances via the new `sigmas` argument to `ccdr.run`
+* `ccdr.run` now supports black lists and white lists (sparsebn #6)
+* Users can now use prior knowledge of variances via the new `sigmas` argument to `ccdr.run` (sparsebn #12)
+
+## Bug fixes
+
+* `ivn.rand = FALSE` not handled correctly (#4)
 
 # ccdrAlgorithm 0.0.3
 

cran-comments.md

@@ -1,8 +1,8 @@
 ## Test environments
-* local OS X install, R 3.3.3
+* local OS X install, R 3.4.1
 * ubuntu 12.04.5 (travis-ci: oldrel, devel, and release)
 * win-builder (devel and release)
-* r-hub (oldrel, devel, and release)
+* r-hub (devel)
 
 ## R CMD check results
 There were no ERRORs, WARNINGs, or NOTEs.
@@ -11,37 +11,14 @@ There were no ERRORs, WARNINGs, or NOTEs.
 
 From https://cran.rstudio.com/web/checks/check_results_ccdrAlgorithm.html
 
-Version: 0.0.2
-Check: compiled code
+Version: 0.0.3
+Check: package dependencies
 Result: NOTE
-    File ‘ccdrAlgorithm/libs/ccdrAlgorithm.so’:
-     Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
-    
-    It is good practice to register native routines and to disable symbol
-    search.
-    
-    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. 
+    Package suggested but not available for checking: ‘graph’
+Flavor: r-release-osx-x86_64
 
 This has been fixed.
 
-Version: 0.0.2
-Flags: --no-stop-on-test-error
-Check: tests
-Result: ERROR
-     Running ‘testthat.R’
-    Running the tests in ‘tests/testthat.R’ failed.
-    Complete output:
-     > library(testthat)
-     > library(ccdrAlgorithm)
-     >
-     > test_check("ccdrAlgorithm")
-     Error: 'cor_vector' is not an exported object from 'namespace:sparsebnUtils'
-     testthat results ================================================================
-     OK: 0 SKIPPED: 0 FAILED: 0
-     Execution halted 
-     
-This is an issue caused by a recent update to the dependency `sparsebnUtils`, and is fixed in this update to `ccdrAlgorithm`.
-
 ## Dependencies
 
 CHECK has been run on all dependencies and passed.

revdep/README.md

@@ -4,35 +4,32 @@
 
 |setting  |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.3.3 (2017-03-06) |
-|system   |x86_64, darwin13.4.0         |
-|ui       |RStudio (1.0.44)             |
+|version  |R version 3.4.1 (2017-06-30) |
+|system   |x86_64, darwin15.6.0         |
+|ui       |RStudio (1.0.153)            |
 |language |(EN)                         |
 |collate  |en_US.UTF-8                  |
 |tz       |America/New_York             |
-|date     |2017-03-09                   |
+|date     |2017-09-09                   |
 
 ## Packages
 
-|package       |*  |version |date       |source                                  |
-|:-------------|:--|:-------|:----------|:---------------------------------------|
-|ccdrAlgorithm |   |0.0.3   |2017-03-09 |local (itsrainingdata/ccdrAlgorithm@NA) |
+|package       |*  |version |date       |source                                        |
+|:-------------|:--|:-------|:----------|:---------------------------------------------|
+|ccdrAlgorithm |*  |0.0.4   |2017-09-09 |local (itsrainingdata/ccdrAlgorithm@NA)       |
+|sparsebnUtils |*  |0.0.5   |2017-09-09 |Github (itsrainingdata/sparsebnUtils@7a12b41) |
 
 # Check results
+
 1 packages
 
-## sparsebn (0.0.2)
+|package  |version | errors| warnings| notes|
+|:--------|:-------|------:|--------:|-----:|
+|sparsebn |0.0.4   |      0|        0|     0|
+
+## sparsebn (0.0.4)
 Maintainer: Bryon Aragam <sparsebn@gmail.com>  
 Bug reports: https://github.com/itsrainingdata/sparsebn/issues
 
-0 errors | 1 warning  | 0 notes
-
-```
-checking Rd cross-references ... WARNING
-Missing link or links in documentation object 'estimate.dag.Rd':
-  ‘[discretecdAlgorithm]{cd.run}’
-
-See section 'Cross-references' in the 'Writing R Extensions' manual.
-
-```
+0 errors | 0 warnings | 0 notes
 

revdep/checks.rds

@@ -4,35 +4,25 @@
 
 |setting  |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.3.3 (2017-03-06) |
-|system   |x86_64, darwin13.4.0         |
-|ui       |RStudio (1.0.44)             |
+|version  |R version 3.4.1 (2017-06-30) |
+|system   |x86_64, darwin15.6.0         |
+|ui       |RStudio (1.0.153)            |
 |language |(EN)                         |
 |collate  |en_US.UTF-8                  |
 |tz       |America/New_York             |
-|date     |2017-03-09                   |
+|date     |2017-09-09                   |
 
 ## Packages
 
-|package       |*  |version |date       |source                                  |
-|:-------------|:--|:-------|:----------|:---------------------------------------|
-|ccdrAlgorithm |   |0.0.3   |2017-03-09 |local (itsrainingdata/ccdrAlgorithm@NA) |
+|package       |*  |version |date       |source                                        |
+|:-------------|:--|:-------|:----------|:---------------------------------------------|
+|ccdrAlgorithm |*  |0.0.4   |2017-09-09 |local (itsrainingdata/ccdrAlgorithm@NA)       |
+|sparsebnUtils |*  |0.0.5   |2017-09-09 |Github (itsrainingdata/sparsebnUtils@7a12b41) |
 
 # Check results
-1 packages with problems
 
-## sparsebn (0.0.2)
-Maintainer: Bryon Aragam <sparsebn@gmail.com>  
-Bug reports: https://github.com/itsrainingdata/sparsebn/issues
+0 packages with problems
 
-0 errors | 1 warning  | 0 notes
 
-```
-checking Rd cross-references ... WARNING
-Missing link or links in documentation object 'estimate.dag.Rd':
-  ‘[discretecdAlgorithm]{cd.run}’
 
-See section 'Cross-references' in the 'Writing R Extensions' manual.
-
-```
 

revdep/problems.md

@@ -0,0 +1,7 @@
+# Check times
+
+|package  |version | check_time|
+|:--------|:-------|----------:|
+|sparsebn |0.0.4   |       40.7|
+
+