Merge pull request #36 from 4dn-dcic/v0.3.7

rebuilt package for 0.3.7
4dn-dcic · Apr 12, 2019 · e083a66 · e083a66
2 parents 08dd7fd + 3995551
commit e083a66
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Showing 5 changed files with 18 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Rpairix
 Title: Rpairix
-Version: 0.3.6
+Version: 0.3.7
 Authors@R: person("Soo", "Lee", email = "duplexa@gmail.com", role = c("aut", "cre"))
 Description: R binder for pairix, tool for querying a pair of genomic ranges in a pairs file (pairix-indexed bgzipped text file)
 Depends:
@@ -11,7 +11,6 @@ Imports:
 License: MIT
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Suggests:
     testthat
-
diff --git a/README.md b/README.md
@@ -55,7 +55,7 @@ R --no-site-file --no-environ --no-save --no-restore CMD INSTALL --install-tests
 To install a specific version,
 ```r
 library(devtools)
-install_url("https://github.com/4dn-dcic/Rpairix/archive/0.3.6.zip")
+install_url("https://github.com/4dn-dcic/Rpairix/archive/0.3.7.zip")
 ```
 
 
@@ -316,7 +316,12 @@ px_get_linecount(filename)
 ## For developers
 When you modify the repo, rebuild the R package before your commit/push:
 ```
-library(devtools)
+# dependencies
+install.packages("BiocManager")
+BiocManager::install("GenomicRanges")
+BiocManager::install("InteractionSet")
+# build
+library(devtools)  # use 1.13.5 (2.0.2 does not work)
 setwd("Rpairix")
 document()
 ```
@@ -325,6 +330,9 @@ Individual R functions are written and documented in `R/`. The `src/rpairixlib.c
 ***
 
 ## Version history
+### 0.3.7
+* Fixed issue where autoflip causes segmentation fault or returns an empty result on some systems. This affects the `px_query()` function with the `autoflip=TRUE` option.
+
 ### 0.3.6
 * Index structure is consistent with pairix/pypairix 0.3.6. This new structure resolves integer overflow issues for linecount. the older indices can be read and used otherwise. (backward-compatible)
 

diff --git a/Rpairix.Rproj b/Rpairix.Rproj
@@ -1,4 +1,4 @@
-Version: 0.3.5
+Version: 0.3.7
 
 RestoreWorkspace: No
 SaveWorkspace: No

diff --git a/man/px_build_index.Rd b/man/px_build_index.Rd
diff --git a/src/pairix.h b/src/pairix.h
@@ -28,7 +28,7 @@
 #ifndef __TABIDX_H
 #define __TABIDX_H
 
-#define PACKAGE_VERSION "0.3.6"
+#define PACKAGE_VERSION "0.3.7"
 
 #include <stdint.h>
 #include "kstring.h"