just remove all "^M" from your files using vi or sed or other editors. no need using dos2unix, you can write a simple script to implement this. and name dos2linux.
#!/usr/bin/perl
# convert a dos \r\n format to unix \bn
open (FILE, $ARGV[0]);
while (<FILE>) {
# remove the stupid \r, replace with \n
# some broken editors just put \r
s/\r/\n/g;
# Remove the duplicate \n
s/\n\n/\n/g;
print;
}