Remove PopGenome

statgenlmu · Jan 19, 2020 · b9fca16 · b9fca16
1 parent 0edb4b4
commit b9fca16
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Showing 38 changed files with 479 additions and 416 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: coala
-Version: 0.5.3
+Version: 0.5.4
 License: MIT + file LICENSE
 Title: A Framework for Coalescent Simulation
 Authors@R: c(
@@ -31,7 +31,6 @@ Imports:
 Suggests:
     abc (>= 2.0),
     knitr,
-    PopGenome (>= 2.1.0),
     phyclust (>= 0.1-16),
     rmarkdown,
     testthat (>= 0.11.0)
@@ -55,7 +54,6 @@ Collate:
     'feature_size_change.R'
     'feature_sumstats.R'
     'feature_unphased.R'
-    'import_popgenome.R'
     'interface_abc.R'
     'locus.R'
     'model_build.R'
@@ -92,4 +90,4 @@ Collate:
     'sumstat_tajimas_d.R'
     'sumstat_trees.R'
     'tools.R'
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
diff --git a/NAMESPACE b/NAMESPACE
@@ -3,7 +3,6 @@
 S3method("+",coalmodelpart)
 S3method("[",segsites)
 S3method(as.matrix,segsites)
-S3method(as.segsites,GENOME)
 S3method(as.segsites,default)
 S3method(as.segsites,list)
 S3method(conv_to_ms_arg,default)
@@ -151,6 +150,5 @@ importFrom(scrm,scrm)
 importFrom(stats,rbinom)
 importFrom(stats,rgamma)
 importFrom(stats,simulate)
-importFrom(utils,capture.output)
 importFrom(utils,suppressForeignCheck)
 useDynLib(coala, .registration = TRUE)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+coala 0.5.4
+===========
+
+* Removes the option to import data import via PopGenome, as PopGenome is not on 
+  CRAN anymore.
+
+
+
 coala 0.5.3
 ===========
 

diff --git a/R/import_popgenome.R b/R/import_popgenome.R
diff --git a/man/as.segsites.GENOME.Rd b/man/as.segsites.GENOME.Rd
diff --git a/man/calc_sumstats_from_data.Rd b/man/calc_sumstats_from_data.Rd
diff --git a/man/coal_model.Rd b/man/coal_model.Rd
diff --git a/man/feat_growth.Rd b/man/feat_growth.Rd
diff --git a/man/feat_ignore_singletons.Rd b/man/feat_ignore_singletons.Rd
diff --git a/man/feat_migration.Rd b/man/feat_migration.Rd
diff --git a/man/feat_mutation.Rd b/man/feat_mutation.Rd
diff --git a/man/feat_outgroup.Rd b/man/feat_outgroup.Rd
diff --git a/man/feat_pop_merge.Rd b/man/feat_pop_merge.Rd
diff --git a/man/feat_recombination.Rd b/man/feat_recombination.Rd