Why is my cygwin installation missing so many fundamental commands (e.g., ls, cp, mv, etc.)?

Question

I installed Cygwin. However, many fundamental commands are missing. Can anyone advise me where to look to solve this?

From cygcheck:

• Not Found: ls
• Not Found: make
• Not Found: mv
• Not Found: patch
• Not Found: perl
• Not Found: rm

The PATH variable is set properly (see below). Here's the full output from cygcheck:

Cygwin Configuration Diagnostics
Current System Time: Tue Aug 05 16:45:00 2014

Windows 7 Enterprise Ver 6.1 Build 7601 Service Pack 1

Path:
C:\cygwin64\bin
C:\Program Files (x86)\Intel\iCLS Client
C:\Program Files\Intel\iCLS Client
C:\Windows\system32
C:\Windows
C:\Windows\System32\Wbem
C:\Windows\System32\WindowsPowerShell\v1.0
C:\Program Files\ThinkPad\Bluetooth Software
C:\Program Files\ThinkPad\Bluetooth Software\syswow64
C:\Program Files\Intel\WiFi\bin
C:\Program Files\Common Files\Intel\WirelessCommon
C:\Program Files\Intel\Intel(R) Management Engine Components\DAL
C:\Program Files\Intel\Intel(R) Management Engine Components\IPT
C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL
C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT
C:\windows\corpam
C:\Program Files (x86)\Google\Cert Installer
C:\python_27_amd64\files
C:\Windows\ccmsetup
C:\windows\corpam
C:\windows\corpam
C:\Program Files (x86)\Google\Cert Installer
C:\Windows\mrmagoo
C:\Program Files (x86)\Lenovo\Access Connections
C:\Program Files (x86)\Intel\OpenCL SDK\3.0\bin\x86
C:\Program Files (x86)\Intel\OpenCL SDK\3.0\bin\x64

SysDir: C:\Windows\system32
WinDir: C:\Windows

PWD = '/home'
HOME = '/home/sugupta'

HOMEPATH = '\Users\sugupta'
APPDATA = 'C:\Users\sugupta\AppData\Roaming'
ProgramW6432 = 'C:\Program Files'
TERM = 'xterm'
PROCESSOR_IDENTIFIER = 'Intel64 Family 6 Model 58 Stepping 9, GenuineIntel'
WINDIR = 'C:\Windows'
TVT = 'C:\Program Files (x86)\Lenovo'
PUBLIC = 'C:\Users\Public'
USERDOMAIN = 'GOOGLE'
COMMPath = 'C:\Program Files\Lenovo\Communications Utility'
CommonProgramFiles(x86) = 'C:\Program Files (x86)\Common Files'
ACPath = 'C:\Program Files (x86)\Lenovo\Access Connections\'
UATDATA = 'C:\Windows\CCM\UATData\D9F8C395-CAB8-491d-B8AC-179A1FE1BE77'
OS = 'Windows_NT'
ALLUSERSPROFILE = 'C:\ProgramData'
windows_tracing_flags = '3'
windows_tracing_logfile = 'C:\BVTBin\Tests\installpackage\csilogfile.log'
TEMP = '/cygdrive/c/Users/sugupta/AppData/Local/Temp'
COMMONPROGRAMFILES = 'C:\Program Files\Common Files'
USERNAME = 'sugupta'
PROCESSOR_LEVEL = '6'
ProgramFiles(x86) = 'C:\Program Files (x86)'
PSModulePath = 'C:\Windows\system32\WindowsPowerShell\v1.0\Modules\;c:\Program Files\Microsoft Security Client\MpProvider\'
FP_NO_HOST_CHECK = 'NO'
SYSTEMDRIVE = 'C:'
USERPROFILE = 'C:\Users\sugupta'
TFS_DIR = 'C:\Program Files\ThinkVantage Fingerprint Software\'
LOGONSERVER = '\\HOT-DC-5'
CommonProgramW6432 = 'C:\Program Files\Common Files'
PROCESSOR_ARCHITECTURE = 'AMD64'
LOCALAPPDATA = 'C:\Users\sugupta\AppData\Local'
ProgramData = 'C:\ProgramData'
SHLVL = '1'
USERDNSDOMAIN = 'AD.CORP.GOOGLE.COM'
PATHEXT = '.COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH;.MSC'
HOMEDRIVE = 'C:'
COMSPEC = 'C:\Windows\system32\cmd.exe'
TMP = '/cygdrive/c/Users/sugupta/AppData/Local/Temp'
SYSTEMROOT = 'C:\Windows'
PROCESSOR_REVISION = '3a09'
PROGRAMFILES = 'C:\Program Files'
NUMBER_OF_PROCESSORS = '4'
SESSIONNAME = 'Console'
COMPUTERNAME = 'SUGUPTA3-W'
CYGWIN_HOME = 'C:\cygwin64'
OLDPWD = '/'
_ = '/usr/bin/cygcheck'

HKEY_CURRENT_USER\Software\Cygwin
HKEY_CURRENT_USER\Software\Cygwin\Installations
  (default) = '\??\C:\cygwin64'
HKEY_CURRENT_USER\Software\Cygwin\Program Options
HKEY_CURRENT_USER\Software\Cygwin\setup
HKEY_LOCAL_MACHINE\SOFTWARE\Cygwin
HKEY_LOCAL_MACHINE\SOFTWARE\Cygwin\Installations
  (default) = '\??\C:\cygwin64'
HKEY_LOCAL_MACHINE\SOFTWARE\Cygwin\Program Options
HKEY_LOCAL_MACHINE\SOFTWARE\Cygwin\setup
  (default) = 'C:\cygwin64'

obcaseinsensitive set to 1

Cygwin installations found in the registry:
  System: Key: e022582115c10879 Path: C:\cygwin64
  User:   Key: e022582115c10879 Path: C:\cygwin64

c:  hd  NTFS    121751Mb  64% CP CS UN PA FC     

C:\cygwin64      /          system  binary,auto
C:\cygwin64\bin  /usr/bin   system  binary,auto
C:\cygwin64\lib  /usr/lib   system  binary,auto
cygdrive prefix  /cygdrive  user    binary,auto

Found: C:\cygwin64\bin\awk
 -> C:\cygwin64\bin\gawk.exe
Found: C:\cygwin64\bin\bash.exe
Not Found: cat
Not Found: cp
Not Found: cpp (good!)
Not Found: crontab
Found: C:\cygwin64\bin\find.exe
Found: C:\Windows\system32\find.exe
Warning: C:\cygwin64\bin\find.exe hides C:\Windows\system32\find.exe
Not Found: gcc
Not Found: gdb
Found: C:\cygwin64\bin\grep.exe
Found: C:\cygwin64\bin\kill.exe
Not Found: ld
Not Found: ls
Not Found: make
Not Found: mv
Not Found: patch
Not Found: perl
Not Found: rm
Found: C:\cygwin64\bin\sed.exe
Not Found: ssh
Found: C:\cygwin64\bin\sh.exe
Found: C:\cygwin64\bin\tar.exe
Not Found: test
Found: C:\cygwin64\bin\vi.exe
Not Found: vim

   38k 2013/07/19 C:\cygwin64\bin\cygargp-0.dll - os=4.0 img=0.0 sys=5.2
                  "cygargp-0.dll" v0.0 ts=2013-07-19 10:07
  172k 2014/07/09 C:\cygwin64\bin\cygblkid-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygblkid-1.dll" v0.0 ts=1969-12-31 19:00
   64k 2013/03/07 C:\cygwin64\bin\cygbz2-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygbz2-1.dll" v0.0 ts=2013-03-06 21:54
   12k 2014/06/09 C:\cygwin64\bin\cygcom_err-2.dll - os=4.0 img=0.0 sys=5.2
                  "cygcom_err-2.dll" v0.0 ts=1969-12-31 19:00
    9k 2013/03/07 C:\cygwin64\bin\cygcrypt-0.dll - os=4.0 img=0.0 sys=5.2
                  "cygcrypt-0.dll" v0.0 ts=2013-03-07 04:29
 1748k 2014/06/06 C:\cygwin64\bin\cygcrypto-1.0.0.dll - os=4.0 img=0.0 sys=5.2
                  "cygcrypto-1.0.0.dll" v0.0 ts=1969-12-31 19:00
  413k 2014/05/23 C:\cygwin64\bin\cygcurl-4.dll - os=4.0 img=0.0 sys=5.2
                  "cygcurl-4.dll" v0.0 ts=1969-12-31 19:00
 1526k 2013/03/08 C:\cygwin64\bin\cygdb-5.3.dll - os=4.0 img=0.0 sys=5.2
                  "cygdb-5.3.dll" v0.0 ts=2013-03-08 02:55
  111k 2013/03/08 C:\cygwin64\bin\cygdb_cxx-5.3.dll - os=4.0 img=0.0 sys=5.2
                  "cygdb_cxx-5.3.dll" v0.0 ts=2013-03-08 02:56
  472k 2013/03/08 C:\cygwin64\bin\cygdb_sql-5.3.dll - os=4.0 img=0.0 sys=5.2
                  "cygdb_sql-5.3.dll" v0.0 ts=2013-03-08 02:58
  147k 2013/07/31 C:\cygwin64\bin\cygexpat-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygexpat-1.dll" v0.0 ts=2013-07-31 17:53
   22k 2013/05/12 C:\cygwin64\bin\cygffi-6.dll - os=4.0 img=0.0 sys=5.2
                  "cygffi-6.dll" v0.0 ts=2013-05-12 17:53
   56k 2014/05/26 C:\cygwin64\bin\cygformw-10.dll - os=4.0 img=0.0 sys=5.2
                  "cygformw-10.dll" v0.0 ts=1969-12-31 19:00
   67k 2014/06/01 C:\cygwin64\bin\cyggcc_s-seh-1.dll - os=4.0 img=0.0 sys=5.2
                  "cyggcc_s-seh-1.dll" v0.0 ts=1969-12-31 19:00
   40k 2014/05/27 C:\cygwin64\bin\cyggdbm-4.dll - os=4.0 img=0.0 sys=5.2
                  "cyggdbm-4.dll" v0.0 ts=1969-12-31 19:00
   13k 2014/05/27 C:\cygwin64\bin\cyggdbm_compat-4.dll - os=4.0 img=0.0 sys=5.2
                  "cyggdbm_compat-4.dll" v0.0 ts=1969-12-31 19:00
  516k 2014/04/05 C:\cygwin64\bin\cyggmp-10.dll - os=4.0 img=0.0 sys=5.2
                  "cyggmp-10.dll" v0.0 ts=1969-12-31 19:00
  251k 2014/05/23 C:\cygwin64\bin\cyggssapi_krb5-2.dll - os=4.0 img=0.0 sys=5.2
                  "cyggssapi_krb5-2.dll" v0.0 ts=1969-12-31 19:00
   29k 2013/03/14 C:\cygwin64\bin\cyghistory7.dll - os=4.0 img=0.0 sys=5.2
                  "cyghistory7.dll" v0.0 ts=2013-03-14 06:14
  998k 2013/03/07 C:\cygwin64\bin\cygiconv-2.dll - os=4.0 img=0.0 sys=5.2
                  "cygiconv-2.dll" v0.0 ts=2013-03-06 22:03
  195k 2013/04/05 C:\cygwin64\bin\cygidn-11.dll - os=4.0 img=0.0 sys=5.2
                  "cygidn-11.dll" v0.0 ts=2013-04-05 04:58
   38k 2014/06/16 C:\cygwin64\bin\cygintl-8.dll - os=4.0 img=0.0 sys=5.2
                  "cygintl-8.dll" v0.0 ts=1969-12-31 19:00
  181k 2014/05/23 C:\cygwin64\bin\cygk5crypto-3.dll - os=4.0 img=0.0 sys=5.2
                  "cygk5crypto-3.dll" v0.0 ts=1969-12-31 19:00
  700k 2014/05/23 C:\cygwin64\bin\cygkrb5-3.dll - os=4.0 img=0.0 sys=5.2
                  "cygkrb5-3.dll" v0.0 ts=1969-12-31 19:00
   36k 2014/05/23 C:\cygwin64\bin\cygkrb5support-0.dll - os=4.0 img=0.0 sys=5.2
                  "cygkrb5support-0.dll" v0.0 ts=1969-12-31 19:00
   44k 2013/06/18 C:\cygwin64\bin\cyglber-2-4-2.dll - os=4.0 img=0.0 sys=5.2
                  "cyglber-2-4-2.dll" v0.0 ts=2013-06-17 16:00
  243k 2013/06/18 C:\cygwin64\bin\cygldap-2-4-2.dll - os=4.0 img=0.0 sys=5.2
                  "cygldap-2-4-2.dll" v0.0 ts=2013-06-17 16:00
  260k 2013/06/18 C:\cygwin64\bin\cygldap_r-2-4-2.dll - os=4.0 img=0.0 sys=5.2
                  "cygldap_r-2-4-2.dll" v0.0 ts=2013-06-17 16:01
    6k 2014/07/25 C:\cygwin64\bin\cyglsa64.dll - os=4.0 img=0.0 sys=5.2
                  "cyglsa64.dll" v0.0 ts=2014-07-25 05:25
  129k 2014/05/29 C:\cygwin64\bin\cyglzma-5.dll - os=4.0 img=0.0 sys=5.2
                  "cyglzma-5.dll" v0.0 ts=1969-12-31 19:00
  106k 2014/07/01 C:\cygwin64\bin\cygmagic-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygmagic-1.dll" v0.0 ts=1969-12-31 19:00
  158k 2014/06/04 C:\cygwin64\bin\cygman-2-6-7.dll - os=4.0 img=0.0 sys=5.2
                  "cygman-2-6-7.dll" v0.0 ts=1969-12-31 19:00
   30k 2014/05/26 C:\cygwin64\bin\cygmenuw-10.dll - os=4.0 img=0.0 sys=5.2
                  "cygmenuw-10.dll" v0.0 ts=1969-12-31 19:00
   42k 2013/08/12 C:\cygwin64\bin\cygmetalink-3.dll - os=4.0 img=0.0 sys=5.2
                  "cygmetalink-3.dll" v0.0 ts=2013-08-12 19:02
  319k 2013/05/05 C:\cygwin64\bin\cygmpfr-4.dll - os=4.0 img=0.0 sys=5.2
                  "cygmpfr-4.dll" v0.0 ts=2013-05-05 08:40
   53k 2014/05/26 C:\cygwin64\bin\cygncurses++w-10.dll - os=4.0 img=0.0 sys=5.2
                  "cygncurses++w-10.dll" v0.0 ts=1969-12-31 19:00
  299k 2014/05/26 C:\cygwin64\bin\cygncursesw-10.dll - os=4.0 img=0.0 sys=5.2
                  "cygncursesw-10.dll" v0.0 ts=1969-12-31 19:00
  207k 2014/03/13 C:\cygwin64\bin\cygp11-kit-0.dll - os=4.0 img=0.0 sys=5.2
                  "cygp11-kit-0.dll" v0.0 ts=2014-03-12 22:35
   15k 2014/05/26 C:\cygwin64\bin\cygpanelw-10.dll - os=4.0 img=0.0 sys=5.2
                  "cygpanelw-10.dll" v0.0 ts=1969-12-31 19:00
  271k 2014/03/12 C:\cygwin64\bin\cygpcre-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygpcre-1.dll" v0.0 ts=2014-03-11 21:35
   38k 2014/05/12 C:\cygwin64\bin\cygpipeline-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygpipeline-1.dll" v0.0 ts=1969-12-31 19:00
   41k 2013/10/21 C:\cygwin64\bin\cygpopt-0.dll - os=4.0 img=0.0 sys=5.2
                  "cygpopt-0.dll" v0.0 ts=2013-10-21 16:52
  193k 2013/03/14 C:\cygwin64\bin\cygreadline7.dll - os=4.0 img=0.0 sys=5.2
                  "cygreadline7.dll" v0.0 ts=2013-03-14 06:14
   97k 2014/05/26 C:\cygwin64\bin\cygsasl2-3.dll - os=4.0 img=0.0 sys=5.2
                  "cygsasl2-3.dll" v0.0 ts=1969-12-31 19:00
  141k 2013/03/11 C:\cygwin64\bin\cygssh2-1.dll - os=4.0 img=0.0 sys=5.2
                  "cygssh2-1.dll" v0.0 ts=2013-03-11 06:42
  377k 2014/06/06 C:\cygwin64\bin\cygssl-1.0.0.dll - os=4.0 img=0.0 sys=5.2
                  "cygssl-1.0.0.dll" v0.0 ts=1969-12-31 19:00
  892k 2014/06/01 C:\cygwin64\bin\cygstdc++-6.dll - os=4.0 img=0.0 sys=5.2
                  "cygstdc++-6.dll" v0.0 ts=1969-12-31 19:00
   69k 2013/04/22 C:\cygwin64\bin\cygtasn1-6.dll - os=4.0 img=0.0 sys=5.2
                  "cygtasn1-6.dll" v0.0 ts=2013-04-21 20:25
   53k 2014/05/26 C:\cygwin64\bin\cygticw-10.dll - os=4.0 img=0.0 sys=5.2
                  "cygticw-10.dll" v0.0 ts=1969-12-31 19:00
   14k 2014/07/09 C:\cygwin64\bin\cyguuid-1.dll - os=4.0 img=0.0 sys=5.2
                  "cyguuid-1.dll" v0.0 ts=1969-12-31 19:00
   79k 2013/05/09 C:\cygwin64\bin\cygz.dll - os=4.0 img=0.0 sys=5.2
                  "cygz.dll" v0.0 ts=2013-05-09 17:20
 3081k 2014/07/25 C:\cygwin64\bin\cygwin1.dll - os=4.0 img=0.0 sys=5.2
                  "cygwin1.dll" v0.0 ts=1969-12-31 19:00
    Cygwin DLL version info:
        DLL version: 1.7.31
        DLL epoch: 19
        DLL old termios: 5
        DLL malloc env: 28
        Cygwin conv: 181
        API major: 0
        API minor: 272
        Shared data: 5
        DLL identifier: cygwin1
        Mount registry: 3
        Cygwin registry name: Cygwin
        Program options name: Program Options
        Installations name: Installations
        Cygdrive default prefix: 
        Build date: 
        Shared id: cygwin1S5


Can't find the cygrunsrv utility, skipping services check.


Cygwin Package Information
Last downloaded files to: C:\cygwin64\Installation files
Last downloaded files from: ftp://mirrors-usa.go-parts.com/cygwin/

Package                  Version            Status
_autorebase              000186-1           OK
_update-info-dir         00299-1            OK
alternatives             1.3.30c-10         OK
base-cygwin              3.3-1              OK
base-files               4.2-3              OK
bash                     4.1.11-2           OK
bzip2                    1.0.6-2            OK
ca-certificates          1.97-1             OK
curl                     7.37.0-1           OK
cygutils                 1.4.14-1           OK
cygwin                   1.7.31-3           OK
dash                     0.5.7-4            OK
editrights               1.02-1             OK
file                     5.19-1             OK
findutils                4.5.12-1           OK
gawk                     4.1.1-1            OK
getent                   2.18.90-2          OK
grep                     2.16-1             OK
groff                    1.22.2-2           OK
gzip                     1.4-1              OK
hostname                 3.13-1             OK
ipc-utils                1.0-2              OK
less                     458-1              OK
libargp                  20110921-2         OK
libblkid1                2.24.2-1           OK
libbz2_1                 1.0.6-2            OK
libcom_err2              1.42.10-1          OK
libcrypt0                1.1-1              OK
libcurl4                 7.37.0-1           OK
libdb5.3                 5.3.21-1           OK
libexpat1                2.1.0-3            OK
libffi6                  3.0.13-1           OK
libgcc1                  4.8.3-2            OK
libgdbm4                 1.11-1             OK
libgmp10                 6.0.0a-1           OK
libgssapi_krb5_2         1.12.1-2           OK
libiconv2                1.14-1             OK
libidn11                 1.26-1             OK
libintl8                 0.18.3.2-2         OK
libk5crypto3             1.12.1-2           OK
libkrb5_3                1.12.1-2           OK
libkrb5support0          1.12.1-2           OK
liblzma5                 5.0.5-1            OK
libmetalink3             0.1.2-1            OK
libmpfr4                 3.1.2-1            OK
libncursesw10            5.9-20140524-1     OK
libopenldap2_4_2         2.4.35-1           OK
libopenssl100            1.0.1h-1           OK
libp11-kit0              0.20.2-1           OK
libpcre1                 8.34-1             OK
libpipeline1             1.3.0-3            OK
Empty package libpopt0
libpopt0                 1.16-1             OK
libreadline7             6.2-1              OK
libsasl2_3               2.1.26-7           OK
libssh2_1                1.4.2-1            OK
libstdc++6               4.8.3-2            OK
libtasn1_6               3.3-1              OK
libuuid1                 2.24.2-1           OK
login                    1.10-10            OK
lynx                     2.8.7-2            OK
man-db                   2.6.7-1            OK
mintty                   1.2-beta1-1        OK
ncurses                  5.9-20140524-1     OK
p11-kit                  0.20.2-1           OK
p11-kit-trust            0.20.2-1           OK
popt                     1.16-1             OK
rebase                   4.4.1-1            OK
run                      1.3.1-1            OK
sed                      4.2.2-3            OK
tar                      1.27.1-1           OK
terminfo                 5.9-20140524-1     OK
texinfo                  5.2-1              OK
tzcode                   2013c-1            OK
util-linux               2.24.2-1           OK
vim-minimal              7.4.335-1          OK
which                    2.20-2             OK
windows-default-manifest 6.3-1              OK
xz                       5.0.5-1            OK
zlib0                    1.2.8-1            OK
Use -h to see help about each section

Answer 1

Perhaps (re)installing coreutils package might help. That package is not present on provided cygcheck log. It holds ls, cp, mv, etc. (as listed here http://en.wikipedia.org/wiki/GNU_Core_Utilities). If that's the case, then you must also download proper packages for make and perl. This is all done through Cygwin Setup, using search on "Select Packages" screen.