Pre CRAN v0.2.3.4 2nd submission

.Rbuildignore

@@ -19,5 +19,9 @@
 ^vignettes/Introduction\.tex$
 ^vignettes/Introduction\.aux$
 ^vignettes/Introduction\.out$
+^vignettes/Introduction\.log$
 ^PGRdup\.pdf$
-^inst/extdata/PGRdup v2\.png$
+^vignettes/Introduction\.html$
+^Introduction\.aux$
+^Introduction\.out$
+^Introduction\.log$

.gitignore

@@ -7,4 +7,7 @@ src/fdouble_metaphone.o
 src/register.o
 Release.R
 docs/articles/Introduction.pdf
-desktop.ini
+desktop.ini
+vignettes/Introduction.log
+vignettes/Introduction.tex
+vignettes/Introduction.out

DESCRIPTION

@@ -59,13 +59,13 @@ Suggests:
     XML,
     knitr,
     rmarkdown,
-	pander
+	  pander
 Copyright: 2014-2018, ICAR-NBPGR
 License: GPL-2 | GPL-3
 Encoding: latin1
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 URL: https://cran.r-project.org/package=PGRdup,
     https://github.com/aravind-j/PGRdup,
     https://doi.org/10.5281/zenodo.841963,

NEWS.md

@@ -1,7 +1,9 @@
 # PGRdup 0.2.3.4
 
 ## UPDATED FUNCTIONS:
+* `MergeKW` - Updated regular expressions to be PCRE2 compliant.
 * `read.genesys` - Updated for reading of doi field.
+* `DoubleMetaphone` - Fixed issue with underlying `C` code with ‘strncpy’. Changed all specified bound depending on the length of the source argument to that of destination argument.
 
 ***
 # PGRdup 0.2.3.3

R/MergeKW.R

@@ -103,7 +103,7 @@ MergeKW <- function(x, y, delim = c("space", "dash", "period")) {
   # Escape all Regex special characters in y
   y <- lapply(y, function(x) gsub(pattern = "([.|()\\^{}+$*?]|\\[|\\])",
                                   replacement = "\\\\\\1", x))
-  options <- c("\\s", "-", ".")
+  options <- c("\\s", "\\-", ".")
   options2 <- logical(length = 3)
   if (is.element("space", delim)) {
     options2[1] <- TRUE
@@ -143,7 +143,7 @@ MergePrefix <- function(x, y, delim = c("space", "dash", "period")) {
   y <- unique(toupper(y))
   y <- gsub(pattern = "([.|()\\^{}+$*?]|\\[|\\])",
             replacement = "\\\\\\1", y)
-  options <- c("\\s", "-", ".")
+  options <- c("\\s", "\\-", ".")
   options2 <- logical(length = 3)
   if (is.element("space", delim)) {
     options2[1] <- TRUE
@@ -181,7 +181,7 @@ MergeSuffix <- function(x, y, delim = c("space", "dash", "period")) {
   y <- unique(toupper(y))
   y <- gsub(pattern = "([.|()\\^{}+$*?]|\\[|\\])",
             replacement = "\\\\\\1", y)
-  options <- c("\\s", "-", ".")
+  options <- c("\\s", "\\-", ".")
   options2 <- logical(length = 3)
   if (is.element("space", delim)) {
     options2[1] <- TRUE

cran-comments.md

@@ -1,3 +1,22 @@
+# Version 0.2.3.4 - Second submission
+
+* Fixed issue with missing vignette files in 'inst/doc' leading to failure of CRAN pre-tests.
+
+### Test environments
+* local Windows 10 Home v1809, R-release (R 3.6.1) & R-devel (R 3.7.0 Pre-release).
+* local Ubuntu 16.04, R-release (R 3.6.1) & R-devel (R 3.7.0 Pre-release).
+* win-builder, R-release (R 3.6.1) & R-devel (R 3.7.0 Pre-release).
+
+# Version 0.2.3.4 - First submission
+
+* Updated regular expressions to be PCRE2 compliant.
+* Fixed issue with underlying `C` code with ‘strncpy’. Changed all specified bound depending on the length of the source argument to that of destination argument.
+
+### Test environments
+* local Windows 10 Home v1809, R-release (R 3.6.1) & R-devel (R 3.7.0 Pre-release).
+* local Ubuntu 16.04, R-release (R 3.6.1) & R-devel (R 3.7.0 Pre-release).
+* win-builder, R-release (R 3.6.1) & R-devel (R 3.7.0 Pre-release).
+
 # Version 0.2.3.3 - First submission
 
 * Use of packages in Suggests such as microbenchmark made conditional to avoid problems when they are not available for an OS.