Truncated file upon reading a text file with 0xff characters

Hello R users,

I am having problems to read a CSV file that contains names with character ?.
In case it doesn't print correctly, it's Unicode character 00FF or LATIN SMALL
LETTER Y WITH DIAERESIS.
My computer has Windows 7 and R 3.2.4.

Initially, I configured my computer to run options(encoding="UTF-8")
in my .Rprofile,
since I prefer this encoding, for portability. Good and modern
standard, I thought.
Rather than sending a large file, here is how to reproduce my problem:

  options(encoding="UTF-8")

  f <- file("test.txt", "wb")
  writeBin(as.integer(c(65, 13, 10, 66, 255, 67, 13, 10, 68, 13, 10)),
f, size=1)
  close(f)
  read.table("test.txt", encoding="latin1")
  f <- file("test.txt", "rt")
  readLines(f, encoding="latin1")
  close(f)

I write a file with three lines, in binary to avoid any translation:
A
B\xffC
D

Upon reading I get only:

  > read.table("test.txt", encoding="latin1")
    V1
  1  A
  2  B
  Warning messages:
  1: In read.table("test.txt", encoding = "latin1") :
    invalid input found on input connection 'test.txt'
  2: In read.table("test.txt", encoding = "latin1") :
    incomplete final line found by readTableHeader on 'test.txt'
  > readLines(f, encoding="latin1")
  [1] "A" "B"
  Warning messages:
  1: In readLines(f, encoding = "latin1") :
    invalid input found on input connection 'test.txt'
  2: In readLines(f, encoding = "latin1") :
    incomplete final line found on 'test.txt'

Hence the file is truncated. However, character \xff is a valid latin1
character,
as one can check for instance at https://en.wikipedia.org/wiki/ISO/IEC_8859-1
I tried with an UTF-8 version of this file:

  f <- file("test.txt", "wb")
  writeBin(as.integer(c(65, 13, 10, 66, 195, 191, 67, 13, 10, 68, 13,
10)), f, size=1)
  close(f)
  read.table("test.txt", encoding="UTF-8")
  f <- file("test.txt", "rt")
  readLines(f, encoding="UTF-8")
  close(f)

Since this character ? is encoded as two bytes 195, 191 in UTF-8, I would expect
that I get my complete file. But I don't. Instead, I get:

  > read.table("test.txt", encoding="UTF-8")
    V1
  1  A
  2  B
  3  C
  4  D
  Warning message:
  In read.table("test.txt", encoding = "UTF-8") :
    incomplete final line found by readTableHeader on 'test.txt'

  > readLines(f, encoding="UTF-8")
  [1] "A" "B"
  Warning message:
  In readLines(f, encoding = "UTF-8") :
    incomplete final line found on 'test.txt'

I tried all the preceding but with options(encoding="latin1") at the beginning.
For the first attempt, with byte 255, I get:

  > read.table("test.txt", encoding="latin1")
    V1
  1  A
  2  B
  3  C
  4  D
  Warning message:
  In read.table("test.txt", encoding = "latin1") :
    incomplete final line found by readTableHeader on 'test.txt'
  >
  > f <- file("test.txt", "rt")
  > readLines(f, encoding="latin1")

For the other attempt, with 195, 191:

  > read.table("test.txt", encoding="UTF-8")
     V1
  1   A
  2 B?C
  3   D
  >
  > f <- file("test.txt", "rt")
  > readLines(f, encoding="UTF-8")
  [1] "A"   "B?C" "D"
  > close(f)

Thus the second one does indeed work, it seems. Just a check:

  > a <- read.table("test.txt", encoding="UTF-8")
  > Encoding(a$V1)
  [1] "unknown" "UTF-8"   "unknown"

At last, I figured out that with the default encoding in R, both attempts work,
with or without even giving the encoding as a parameter of read.table
or readLines.
However, I don't understand what happens:

  f <- file("test.txt", "wb")
  writeBin(as.integer(c(65, 13, 10, 66, 255, 67, 13, 10, 68, 13, 10)),
f, size=1)
  close(f)
  a <- read.table("test.txt", encoding="latin1")$V1
  Encoding(a)
  iconv(a[2], toRaw=T)
  a
  a <- read.table("test.txt")$V1
  Encoding(a)
  iconv(a[2], toRaw=T)
  a

This will yield:

  > a <- read.table("test.txt", encoding="latin1")$V1
  > Encoding(a)
  [1] "unknown" "latin1"  "unknown"
  > iconv(a[2], toRaw=T)
  [[1]]
  [1] 42 ff 43
  > a
  [1] "A"   "B?C" "D"
  >
  > a <- read.table("test.txt")$V1
  > Encoding(a)
  [1] "unknown" "unknown" "unknown"
  > iconv(a[2], toRaw=T)
  [[1]]
  [1] 42 ff 43
  > a
  [1] "A"   "B?C" "D"

The second line is correctly encoded, but the encoding is just not
"marked" in one case.
With the UTF-8 bytes:

  f <- file("test.txt", "wb")
  writeBin(as.integer(c(65, 13, 10, 66, 195, 191, 67, 13, 10, 68, 13,
10)), f, size=1)
  close(f)
  a <- read.table("test.txt", encoding="UTF-8")$V1
  Encoding(a)
  iconv(a[2], toRaw=T)
  a
  a <- read.table("test.txt")$V1
  Encoding(a)
  iconv(a[2], toRaw=T)
  a

This will yield: