Problem after upgrading from 1.7.9 to 1.7.10-1 - system commands not found

[Bilig Ordos <oyunbilig at gmail dot com>]

I've been happy with 1.7.9, but couldn't resist my curiosity so ran
the 1.7.10-1 setup today. During the process it complained that Cygwin
is running and offered me options to either stop the Cygwin and try
again, or continue and reboot after it is done. So I selected to
continue and then rebooted.

But when I launched the Cywin console/Mintty, I did not have most of
the system commands, such as "ls" and "which", but commands like "cd"
and "alias" are there.

I tried running the setup again (made sure all the packages I used to
have are selected) but did not help. rebooted again and it is the
same.

How can I recover from this? I hate to reinstall from scratch as doing
that will make me lose a lot of customization, such as ssh keys, etc.
Please see below for examples and logs.

My system is Win 7 Pro, 64-bit.



Thank you,

Bilig



-bash-4.1$ pwd
/usr/bin
-bash-4.1$
-bash-4.1$
-bash-4.1$ ls
-bash: ls: command not found
-bash-4.1$ which
-bash: which: command not found


Logs from the /var/log (I did not have the .full log from the failed
setup because I ran the setup again):


2012/02/24 14:32:45Starting cygwin install, version 2.764

2012/02/24 14:32:45io_stream_cygfile: fopen(/etc/setup/net-proxy-host)
failed 2 No such file ordirectory

2012/02/24 14:32:45io_stream_cygfile: fopen(/etc/setup/net-proxy-port)
failed 2 No such file ordirectory

2012/02/24 14:32:45io_stream_cygfile: fopen(/etc/setup/extrakeys)
failed 2 No such file ordirectory

2012/02/24 14:32:45io_stream_cygfile:
fopen(/etc/setup/chooser_window_settings) failed 2 No suchfile or
directory

2012/02/24 14:32:45Current Directory: C:\Users\boyun\Downloads

2012/02/24 14:32:45User has backup/restore rights

2012/02/24 14:32:45Changing gid to Administrators

2012/02/24 14:32:45Could not open service McShield for query, start
and stop. McAfee may not beinstalled, or we don't have access.

2012/02/24 14:32:47source: network install

2012/02/24 14:32:48root: C:\cygwin binary system

2012/02/24 14:32:50Selected local directory: C:\Users\boyun\Downloads

2012/02/24 14:32:51net: Direct

2012/02/24 14:32:54site: http://cygwin.mirrors.hoobly.com/

2012/02/24 14:33:37DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/_update-info-dir/_update-info-dir-01014-1.tar.bz2

2012/02/24 14:33:39DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/base-files/base-files-4.0-9.tar.bz2

2012/02/24 14:33:50DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/coreutils/coreutils-8.15-1.tar.bz2

2012/02/24 14:33:52DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/csih/csih-0.9.5-1.tar.bz2

2012/02/24 14:33:52DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/cygrunsrv/cygrunsrv-1.36-1.tar.bz2

2012/02/24 14:33:55DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/cygutils/cygutils-1.4.8-1.tar.bz2

2012/02/24 14:34:03DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/cygwin/cygwin-1.7.10-1.tar.bz2

2012/02/24 14:34:05DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/db/db4.5/libdb4.5/libdb4.5-4.5.20.2-3.tar.bz2

2012/02/24 14:34:06DownloadedC:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/pcre/libpcre0/libpcre0-8.21-2.tar.bz2

2012/02/24 14:34:07Running preremove script for _update-info-dir

2012/02/24 14:34:07Running preremove script for  base-files

2012/02/24 14:34:07running: C:\cygwin\bin\bash.exe --norc --noprofile
/etc/preremove/base-files.sh

2012/02/24 14:34:10Running preremove script for  coreutils

2012/02/24 14:34:10running: C:\cygwin\bin\bash.exe --norc --noprofile
/etc/preremove/coreutils.sh

2012/02/24 14:34:10Running preremove script for  csih

2012/02/24 14:34:10Running preremove script for  cygrunsrv

2012/02/24 14:34:10Running preremove script for  cygutils

2012/02/24 14:34:10Running preremove script for  cygwin

2012/02/24 14:34:10Running preremove script for  libdb4.5

2012/02/24 14:34:10Running preremove script for  libpcre0

2012/02/24 14:34:10Uninstalling _update-info-dir

2012/02/24 14:34:10Uninstalling base-files

2012/02/24 14:34:10Uninstalling coreutils

2012/02/24 14:34:11Uninstalling csih

2012/02/24 14:34:11Uninstalling cygrunsrv

2012/02/24 14:34:11Uninstalling cygutils

2012/02/24 14:34:11Uninstalling cygwin

2012/02/24 14:34:11Uninstalling libdb4.5

2012/02/24 14:34:11Uninstalling libpcre0

2012/02/24 14:34:11Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/_update-info-dir/_update-info-dir-01014-1.tar.bz2

2012/02/24 14:34:11Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/base-files/base-files-4.0-9.tar.bz2

2012/02/24 14:34:12Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/coreutils/coreutils-8.15-1.tar.bz2

2012/02/24 14:34:22Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/csih/csih-0.9.5-1.tar.bz2

2012/02/24 14:34:22Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/cygrunsrv/cygrunsrv-1.36-1.tar.bz2

2012/02/24 14:34:22Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/cygutils/cygutils-1.4.8-1.tar.bz2

2012/02/24 14:34:23Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/cygwin/cygwin-1.7.10-1.tar.bz2

2012/02/24 14:34:23io_stream_cygfile: fopen(/usr/bin/cygwin1.dll)
failed 13 Permission denied

2012/02/24 14:34:23Failed to open cygfile:///usr/bin/cygwin1.dll for writing.

2012/02/24 14:34:48Scheduled reboot replacement of file
C:\cygwin\bin/cygwin1.dll withC:\cygwin\bin/cygwin1.dll.new

2012/02/24 14:34:52Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/db/db4.5/libdb4.5/libdb4.5-4.5.20.2-3.tar.bz2

2012/02/24 14:34:52Extracting from
file://C:\Users\boyun\Downloads/http%3a%2f%2fcygwin.mirrors.hoobly.com%2f/release/pcre/libpcre0/libpcre0-8.21-2.tar.bz2

2012/02/24 14:34:52mbox note: In-use files have been replaced. You
need to reboot as soon aspossible to activate the new versions. Cygwin
may operate incorrectly until youreboot.

2012/02/24 14:34:59Changing gid back to original

2012/02/24 14:34:59running: C:\cygwin\bin\bash.exe --norc
--noprofile/etc/postinstall/coreutils.sh

2012/02/24 14:35:00abnormal exit: exit code=127

2012/02/24 14:35:00running: C:\cygwin\bin\bash.exe --norc
--noprofile/etc/postinstall/update-info-dir.sh

2012/02/24 14:35:10running: C:\cygwin\bin\bash.exe --norc
--noprofile/etc/postinstall/base-files-profile.sh

2012/02/24 14:35:14running: C:\cygwin\bin\bash.exe --norc
--noprofile/etc/postinstall/base-files-mketc.sh

2012/02/24 14:35:14running: C:\cygwin\bin\bash.exe --norc --noprofile
/etc/postinstall/cygutils.sh

2012/02/24 14:35:14Changing gid to Administrators

2012/02/24 14:35:34note: In-use files have been replaced. You need to
reboot as soon as possibleto activate the new versions. Cygwin may
operate incorrectly until you reboot.

2012/02/24 14:35:34Ending cygwin install

--
Bilig Oyun (Oyunbilig)
oyunbilig@gmail.com

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