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Interference with Astex and Scilab

I just installed cygwin 1.3.2 under NT4.0 using setup.exe. Everything
went OK, and the install log seems OK too.

I click on the Cygwin icon and type "ls".
Surprise, three files which have nothing to do  with Cygwin are listed:

Scilab.hist, site-lisp, and SITE-LIS.
The first is used by Scilab, a Matlab clone written at INRIA, Paris.
The two others are part of Astex, a french TEX distribution.

I then type "pwd" and read: cygwin/c/ast/astex/emacs. I also discover
that no "home" directory has been created by setup.exe.

Exiting cygwin, I find that a cygwin/c/ast/astex/emacs has indeed just
been created in my Astex directory. If I rename it and reenter cygwin,
this same directory is created anew.

I have tested cygwin software in a very limited fashion (vim and gcc,
mostly) and find that they perform satisfactorily.

My guess is that cygwin uses the HOME environment variable, which I had
previously defined in order to use a WIN port of Emacs along with Astex.

This seems to be confirmed by the cygcheck file which is appended. This
file also contains references to Borland C directory and files.

So my question is: how can I resolve this conflict betwwen two programs
that use the same environment variable ?

Cygnus Win95/NT Configuration Diagnostics
Current System Time: Mon Aug 20 09:10:32 2001

WinNT Ver 4.0 build 1381 Service Pack 6

Path:	/usr/local/bin

SysDir: C:\WINNT\System32
WinDir: C:\WINNT

PWD = `/cygdrive/c/AST/ASTEX/EMACS'
USER = `grivet'
MAKE_MODE = `unix'
HOME = `/cygdrive/c/AST/ASTEX/EMACS'

OS2LIBPATH = `C:\WINNT\system32\os2\dll;'
COMSPEC = `C:\WINNT\system32\cmd.exe'
!C: = `C:\WINNT\Profiles\grivet\Bureau'
ASTEXDIR = `C:\AST\astex'
!E: = `E:\cygwin\bin'
USERPROFILE = `C:\WINNT\Profiles\grivet'
PS1 = `\[\033]0;\w\007
\033[32m\]\u@\h \[\033[33m\w\033[0m\]
$ '
MACHTYPE = `i686-pc-cygwin'
PROCESSOR_IDENTIFIER = `x86 Family 5 Model 2 Stepping 12, GenuineIntel'
OS = `Windows_NT'
OLDPWD = `/usr/bin'
TEMP = `/cygdrive/c/TEMP'
SHLVL = `1'
USERNAME = `grivet'
SHELL = `/bin/bash'
HOSTTYPE = `i686'
OSTYPE = `cygwin'
TERM = `cygwin'
_ = `/usr/bin/cygcheck'

HKEY_CURRENT_USER\Software\Cygnus Solutions
HKEY_CURRENT_USER\Software\Cygnus Solutions\Cygwin
HKEY_CURRENT_USER\Software\Cygnus Solutions\Cygwin\mounts v2
  (default) = `/cygdrive'
  cygdrive flags = 0x00000020
HKEY_CURRENT_USER\Software\Cygnus Solutions\Cygwin\Program Options
HKEY_LOCAL_MACHINE\SOFTWARE\Cygnus Solutions\Cygwin\mounts v2
HKEY_LOCAL_MACHINE\SOFTWARE\Cygnus Solutions\Cygwin\mounts v2\/
  (default) = `E:/cygwin'
  flags = 0x00000008
HKEY_LOCAL_MACHINE\SOFTWARE\Cygnus Solutions\Cygwin\mounts v2\/usr/bin
  (default) = `E:/cygwin/bin'
  flags = 0x00000008
HKEY_LOCAL_MACHINE\SOFTWARE\Cygnus Solutions\Cygwin\mounts v2\/usr/lib
  (default) = `E:/cygwin/lib'
  flags = 0x00000008
HKEY_LOCAL_MACHINE\SOFTWARE\Cygnus Solutions\Cygwin\Program Options

a:  fd           N/A    N/A                    
c:  hd  NTFS    2000Mb  40% CP CS UN PA FC     
d:  hd  NTFS    2996Mb   8% CP CS UN PA FC     
e:  hd  NTFS    3223Mb  21% CP CS UN PA FC     
f:  cd  CDFS     643Mb 100%    CS UN           ASTEX_31C

E:\cygwin\bin  /usr/bin  system  textmode
E:\cygwin\lib  /usr/lib  system  textmode
E:\cygwin  /        system  textmode
c:    /cygdrive/c  user    textmode,noumount
d:    /cygdrive/d  user    textmode,noumount
e:    /cygdrive/e  user    textmode,noumount
f:    /cygdrive/f  user    textmode,noumount

Found: E:\cygwin\bin\bash.exe
Found: E:\cygwin\bin\cat.exe
Found: E:\cygwin\bin\cpp.exe
Found: e:\BC5\BIN\cpp.exe
Warning: E:\cygwin\bin\cpp.exe hides e:\BC5\BIN\cpp.exe
Found: E:\cygwin\bin\find.exe
Found: E:\cygwin\bin\gcc.exe
Found: E:\cygwin\bin\gdb.exe
Found: E:\cygwin\bin\ld.exe
Found: E:\cygwin\bin\ls.exe
Found: E:\cygwin\bin\make.exe
Found: e:\BC5\BIN\make.exe
Warning: E:\cygwin\bin\make.exe hides e:\BC5\BIN\make.exe
Found: E:\cygwin\bin\sh.exe

   56k 2000/12/03 E:\cygwin\bin\cygbz21.0.dll - os=4.0 img=1.0 sys=4.0
                  "cygbz21.0.dll" v0.0 ts=2000/11/20 23:53
   45k 2001/04/25 E:\cygwin\bin\cygform5.dll - os=4.0 img=1.0 sys=4.0
                  "cygform5.dll" v0.0 ts=2001/4/25 5:28
   18k 2000/10/23 E:\cygwin\bin\cyggdbm.dll - os=4.0 img=1.0 sys=4.0
                  "cyggdbm.dll" v0.0 ts=2000/10/23 2:26
   17k 2001/06/28 E:\cygwin\bin\cyghistory4.dll - os=4.0 img=1.0 sys=4.0
                  "cyghistory4.dll" v0.0 ts=2001/1/7 4:34
   21k 2001/06/28 E:\cygwin\bin\cyghistory5.dll - os=4.0 img=1.0 sys=4.0
                  "cyghistory5.dll" v0.0 ts=2001/6/28 2:27
   21k 2001/06/20 E:\cygwin\bin\cygintl.dll - os=4.0 img=1.0 sys=4.0
                  "cygintl.dll" v0.0 ts=2001/6/20 17:09
   81k 2000/12/05 E:\cygwin\bin\cygitcl30.dll - os=4.0 img=1.0 sys=4.0
                  "cygitcl30.dll" v0.0 ts=2000/11/26 1:43
   35k 2000/12/05 E:\cygwin\bin\cygitk30.dll - os=4.0 img=1.0 sys=4.0
                  "cygitk30.dll" v0.0 ts=2000/11/26 1:43
   45k 2001/07/04 E:\cygwin\bin\cygjbig1.dll - os=4.0 img=1.0 sys=4.0
                  "cygjbig1.dll" v0.0 ts=2001/7/4 3:25
  119k 2001/06/06 E:\cygwin\bin\cygjpeg6b.dll - os=4.0 img=1.0 sys=4.0
                  "cygjpeg6b.dll" v0.0 ts=2001/6/6 4:27
   26k 2001/04/25 E:\cygwin\bin\cygmenu5.dll - os=4.0 img=1.0 sys=4.0
                  "cygmenu5.dll" v0.0 ts=2001/4/25 5:27
  156k 2001/04/25 E:\cygwin\bin\cygncurses++5.dll - os=4.0 img=1.0 sys=4.0
                  "cygncurses++5.dll" v0.0 ts=2001/4/25 5:29
  226k 2001/04/25 E:\cygwin\bin\cygncurses5.dll - os=4.0 img=1.0 sys=4.0
                  "cygncurses5.dll" v0.0 ts=2001/4/25 5:17
   15k 2001/04/25 E:\cygwin\bin\cygpanel5.dll - os=4.0 img=1.0 sys=4.0
                  "cygpanel5.dll" v0.0 ts=2001/4/25 5:27
  163k 2001/05/06 E:\cygwin\bin\cygpng2.dll - os=4.0 img=1.0 sys=4.0
                  "cygpng2.dll" v0.0 ts=2001/5/6 4:05
  108k 2001/06/28 E:\cygwin\bin\cygreadline4.dll - os=4.0 img=1.0 sys=4.0
                  "cygreadline4.dll" v0.0 ts=2001/1/7 4:34
  135k 2001/06/28 E:\cygwin\bin\cygreadline5.dll - os=4.0 img=1.0 sys=4.0
                  "cygreadline5.dll" v0.0 ts=2001/6/28 2:27
  390k 2000/12/05 E:\cygwin\bin\cygtcl80.dll - os=4.0 img=1.0 sys=4.0
                  "cygtcl80.dll" v0.0 ts=2000/11/26 1:39
    5k 2000/12/05 E:\cygwin\bin\cygtclpip80.dll - os=4.0 img=1.0 sys=4.0
   10k 2000/12/05 E:\cygwin\bin\cygtclreg80.dll - os=4.0 img=1.0 sys=4.0
                  "cygtclreg80.dll" v0.0 ts=2000/11/26 1:39
  245k 2001/06/12 E:\cygwin\bin\cygtiff3.dll - os=4.0 img=1.0 sys=4.0
                  "cygtiff3.dll" v0.0 ts=2001/6/12 17:25
  623k 2000/12/05 E:\cygwin\bin\cygtk80.dll - os=4.0 img=1.0 sys=4.0
                  "cygtk80.dll" v0.0 ts=2000/11/26 1:43
   41k 2001/07/04 E:\cygwin\bin\cygXpm-noX4.dll - os=4.0 img=1.0 sys=4.0
                  "cygXpm-noX4.dll" v0.0 ts=2001/7/4 1:21
   45k 2001/07/04 E:\cygwin\bin\cygXpm-X4.dll - os=4.0 img=1.0 sys=4.0
                  "cygXpm-X4.dll" v0.0 ts=2000/11/20 2:45
   49k 2001/02/03 E:\cygwin\bin\cygz.dll - os=4.0 img=1.0 sys=4.0
                  "cygz.dll" v0.0 ts=2001/2/3 20:35
  678k 2001/05/21 E:\cygwin\bin\cygwin1.dll - os=4.0 img=1.0 sys=4.0
                  "cygwin1.dll" v0.0 ts=2001/5/21 3:28
    Cygwin DLL version info:
        dll major: 1003
        dll minor: 2
        dll epoch: 19
        dll bad signal mask: 19005
        dll old termios: 5
        dll malloc env: 28
        api major: 0
        api minor: 39
        shared data: 3
        dll identifier: cygwin1
        mount registry: 2
        cygnus registry name: Cygnus Solutions
        cygwin registry name: Cygwin
        program options name: Program Options
        cygwin mount registry name: mounts v2
        cygdrive flags: cygdrive flags
        cygdrive prefix: cygdrive prefix
        cygdrive default prefix: 
        build date: Sun May 20 23:28:17 EDT 2001
        shared id: cygwin1S3

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