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Test results vary depending on your host system and your Cygwin configuration. If a test can pass in some Cygwin setup, it is always attempted and explainable test failures are documented. It is possible for Perl to pass all the tests, but it is more...
File Permissions
UNIX file permissions are based on sets of mode bits for {read,write,execute} for each {user,group,other}. By default Cygwin only tracks the Win32 read-only attribute represented as the UNIX file user write bit (files are always readable, files are e...
  Failed Test           List of failed
  ------------------------------------
  io/fs.t               5, 7, 9-10
  lib/anydbm.t          2
  lib/db-btree.t        20
  lib/db-hash.t         16
  lib/db-recno.t        18
  lib/gdbm.t            2
  lib/ndbm.t            2
  lib/odbm.t            2
  lib/sdbm.t            2
  op/stat.t             9, 20 (.tmp not an executable extension)
Hard Links
FAT partitions do not support hard links (whereas NTFS does), in which case Cygwin implements link() by copying the file. On remote (network) drives Cygwin's stat() always sets st_nlink to 1, so the link count for remote directories and files is not ...
  Failed Test           List of failed
  ------------------------------------
  io/fs.t               4
  op/stat.t             3
Filetime Granularity
On FAT partitions the filetime granularity is 2 seconds. The following test will fail:
  Failed Test           List of failed
  ------------------------------------
  io/fs.t               18
Tainting Checks
When Perl is running in taint mode, $ENV{PATH} is considered tainted and not used, so DLLs not in the default system directories will not be found. While the tests are running you will see warnings popup from the system with messages like:
  Win9x
    Error Starting Program
    A required .DLL file, CYGWIN1.DLL, was not found
  WinNT
    perl.exe - Unable to Locate DLL
    The dynamic link library cygwin1.dll could not be found in the
      specified path ...
Just click OK and ignore them. When running `make test', 2 popups occur. During `./perl harness', 4 popups occur. Also, these tests will fail:
  Failed Test           List of failed
  ------------------------------------
  op/taint.t            1, 3, 31, 37
Alternatively, you can copy cygwin1.dll into the directory where the tests run:
  cp /bin/cygwin1.dll t
or one of the Windows system directories (although, this is not recommended).
/etc/group
Cygwin does not require /etc/group, in which case the op/grent.t test will be skipped. The check performed by op/grent.t expects to see entries that use the members field, otherwise this test will fail:
  Failed Test           List of failed
  ------------------------------------
  op/grent.t            1
Script Portability
Cygwin does an outstanding job of providing UNIX-like semantics on top of Win32 systems. However, in addition to the items noted above, there are some differences that you should know about. This is a very brief guide to portability, more information...
Pathnames
Cygwin pathnames can be separated by forward (/) or backward (\) slashes. They may also begin with drive letters (C:) or Universal Naming Codes (//UNC). DOS device names (aux, con, prn, com*, lpt?, nul) are invalid as base filenames. However, they ca...
  : * ? " < > |
File names are case insensitive, but case preserving. A pathname that contains a backslash or drive letter is a Win32 pathname (and not subject to the translations applied to POSIX style pathnames).
Text/Binary
When a file is opened it is in either text or binary mode. In text mode a file is subject to CR/LF/Ctrl-Z translations. With Cygwin, the default mode for an open() is determined by the mode of the mount that underlies the file. Perl provides a binmod...
    sysopen(FOO, "bar", O_WRONLY|O_CREAT|O_TEXT)
lseek(), tell() and sysseek() only work with files opened in binary mode.
The text/binary issue is covered at length in the Cygwin documentation.
.exe
The Cygwin stat(), lstat() and readlink() functions make the .exe extension transparent by looking for foo.exe when you ask for foo (unless a foo also exists). Cygwin does not require a .exe extension, but gcc adds it automatically when building a pr...
chown()
On WinNT chown() can change a file's user and group IDs. On Win9x chown() is a no-op, although this is appropriate since there is no security model.
Miscellaneous
File locking using the F_GETLK command to fcntl() is a stub that returns ENOSYS.
Win9x can not rename() an open file (although WinNT can).
The Cygwin chroot() implementation has holes (it can not restrict file access by native Win32 programs).
INSTALL
This will install Perl, including man pages.
  make install | tee log.make-install
NOTE: If STDERR is redirected `make install' will not prompt you to install perl into /usr/bin.
You may need to be Administrator to run `make install'. If you are not, you must have write access to the directories in question.
Information on installing the Perl documentation in HTML format can be found in the INSTALL document.
MANIFEST
These are the files in the Perl release that contain references to Cygwin. These very brief notes attempt to explain the reason for all conditional code. Hopefully, keeping this up to date will allow the Cygwin port to be kept as clean as possible.
Documentation
  INSTALL README.cygwin README.win32 MANIFEST
  Changes Changes5.005 Changes5.004 Changes5.6
  pod/perl.pod pod/perlport.pod pod/perlfaq3.pod
  pod/perldelta.pod pod/perl5004delta.pod pod/perl56delta.pod
  pod/perlhist.pod pod/perlmodlib.pod pod/buildtoc.PL pod/perltoc.pod
Build, Configure, Make, Install
  cygwin/Makefile.SHs
  cygwin/ld2.in
  cygwin/perlld.in
  ext/IPC/SysV/hints/cygwin.pl
  ext/NDBM_File/hints/cygwin.pl
  ext/ODBM_File/hints/cygwin.pl
  hints/cygwin.sh
  Configure             - help finding hints from uname,
                          shared libperl required for dynamic loading
  Makefile.SH           - linklibperl
  Porting/patchls       - cygwin in port list
  installman            - man pages with :: translated to .
  installperl           - install dll/ld2/perlld, install to pods
  makedepend.SH         - uwinfix
Tests
  t/io/tell.t           - binmode
  t/lib/b.t             - ignore Cwd from os_extras
  t/lib/glob-basic.t    - Win32 directory list access differs from read mode
  t/op/magic.t          - $^X/symlink WORKAROUND, s/.exe//
  t/op/stat.t           - no /dev, skip Win32 ftCreationTime quirk
                          (cache manager sometimes preserves ctime of file
                          previously created and deleted), no -u (setuid)
Compiled Perl Source
  EXTERN.h              - __declspec(dllimport)
  XSUB.h                - __declspec(dllexport)
  cygwin/cygwin.c       - os_extras (getcwd, spawn)
  perl.c                - os_extras
  perl.h                - binmode
  doio.c                - win9x can not rename a file when it is open
  pp_sys.c              - do not define h_errno, pp_system with spawn
  util.c                - use setenv
Compiled Module Source
  ext/POSIX/POSIX.xs    - tzname defined externally
  ext/SDBM_File/sdbm/pair.c
                        - EXTCONST needs to be redefined from EXTERN.h
  ext/SDBM_File/sdbm/sdbm.c
                        - binary open
Perl Modules/Scripts
  lib/Cwd.pm            - hook to internal Cwd::cwd
  lib/ExtUtils/MakeMaker.pm
                        - require MM_Cygwin.pm