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R 2.15.1-1 sub() function produces unexpected output


Hi,

The sub() function in R 2.15.1-1 produces unexpected output.  Here is a minimal piece of R code:

unlist(R.Version())
genos <- c("6_7", "6_6", NA, "5_5")
genos
sub("5", "4", genos)

Based on the documentation for the sub function, see e.g. http://stat.ethz.ch/R-manual/R-patched/library/base/html/grep.html, I would expect the sub function to convert the first "5" character to a "4", and this is the output I get running R on several other systems.  The behaviour of this function is not expected to differ between R versions.  In my opinion this is a serious bug.  I cannot say for sure whether it is a bug in this R version, or a bug introduced by packaging R for Cygwin.

Output from R 2.15.1-1 under Cygwin, unexpected result:

> unlist(R.Version())
                       platform                            arch
               "i686-pc-cygwin"                          "i686"
                             os                          system
                       "cygwin"                  "i686, cygwin"
                         status                           major
                             ""                             "2"
                          minor                            year
                         "15.1"                          "2012"
                          month                             day
                           "06"                            "22"
                        svn rev                        language
                        "59600"                             "R"
                 version.string                        nickname
"R version 2.15.1 (2012-06-22)"          "Roasted Marshmallows"
> genos <- c("6_7", "6_6", NA, "5_5")
> genos
[1] "6_7" "6_6" NA    "5_5"
> sub("5", "4", genos)
[1] "6_7" "6_6" NA    "4"
>

Output from R 2.14.0 under GNU/Linux, expected result:

> unlist(R.Version())
                       platform                            arch
     "x86_64-unknown-linux-gnu"                        "x86_64"
                             os                          system
                    "linux-gnu"             "x86_64, linux-gnu"
                         status                           major
                             ""                             "2"
                          minor                            year
                         "14.0"                          "2011"
                          month                             day
                           "10"                            "31"
                        svn rev                        language
                        "57496"                             "R"
                 version.string
"R version 2.14.0 (2011-10-31)"
> genos <- c("6_7", "6_6", NA, "5_5")
> genos
[1] "6_7" "6_6" NA    "5_5"
> sub("5", "4", genos)
[1] "6_7" "6_6" NA    "4_5"
>

I attach the product of cygcheck -s -v -r > cygcheck.out


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Attachment: cygcheck.out
Description: cygcheck.out

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