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Read more:
How to install cygwin
How to add packages after install Cygwin

Installation:

apt-cyg install automake

cygwin install automake

Result:

$ apt-cyg install automake
Installing automake
--2016-08-20 21:53:40--  http://cygwin.mirror.constant.com//noarch/release/automake/automake-9-1.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3043 (3,0K) [application/octet-stream]
Saving to: ‘automake-9-1.tar.bz2’

automake-9-1.tar.bz 100%[===================>]   2,97K  --.-KB/s    in 0s

2016-08-20 21:53:41 (82,3 MB/s) - ‘automake-9-1.tar.bz2’ saved [3043/3043]

automake-9-1.tar.bz2: OK
Unpacking...
Package automake requires the following packages, installing:
automake1.10 automake1.11 automake1.12 automake1.13 automake1.14 automake1.15 automake1.4 automake1.5 automake1.6 automake1.7 automake1.8 automake1.9 bash gawk
Installing automake1.10
--2016-08-20 21:53:46--  http://cygwin.mirror.constant.com//noarch/release/automake1.10/automake1.10-1.10.3-2.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 730203 (713K) [application/octet-stream]
Saving to: ‘automake1.10-1.10.3-2.tar.bz2’

automake1.10-1.10.3 100%[===================>] 713,09K  48,6KB/s    in 18s

2016-08-20 21:54:05 (39,1 KB/s) - ‘automake1.10-1.10.3-2.tar.bz2’ saved [730203/730203]

automake1.10-1.10.3-2.tar.bz2: OK
Unpacking...
Package automake1.10 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo xz
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Installing texinfo
--2016-08-20 21:54:14--  http://cygwin.mirror.constant.com//x86_64/release/texinfo/texinfo-6.1-2.tar.xz
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 918040 (897K) [application/octet-stream]
Saving to: ‘texinfo-6.1-2.tar.xz’

texinfo-6.1-2.tar.x 100%[===================>] 896,52K  79,9KB/s    in 13s

2016-08-20 21:54:29 (66,8 KB/s) - ‘texinfo-6.1-2.tar.xz’ saved [918040/918040]

texinfo-6.1-2.tar.xz: OK
Unpacking...
Package texinfo requires the following packages, installing:
cygwin info perl perl-Pod-Simple perl-Unicode-Normalize perl_base
Package cygwin is already installed, skipping
Package info is already installed, skipping
Package perl is already installed, skipping
Installing perl-Pod-Simple
--2016-08-20 21:54:37--  http://cygwin.mirror.constant.com//x86_64/release/perl-Pod-Simple/perl-Pod-Simple-3.32-1.tar.xz
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 187996 (184K) [application/octet-stream]
Saving to: ‘perl-Pod-Simple-3.32-1.tar.xz’

perl-Pod-Simple-3.3 100%[===================>] 183,59K  72,0KB/s    in 2,6s

2016-08-20 21:54:41 (72,0 KB/s) - ‘perl-Pod-Simple-3.32-1.tar.xz’ saved [187996/187996]

perl-Pod-Simple-3.32-1.tar.xz: OK
Unpacking...
Package perl-Pod-Simple requires the following packages, installing:
perl perl_base
Package perl is already installed, skipping
Package perl_base is already installed, skipping
Installing perl-Unicode-Normalize
--2016-08-20 21:54:48--  http://cygwin.mirror.constant.com//x86_64/release/perl-Unicode-Normalize/perl-Unicode-Normalize-1.25-1.tar.xz
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 54760 (53K) [application/octet-stream]
Saving to: ‘perl-Unicode-Normalize-1.25-1.tar.xz’

perl-Unicode-Normal 100%[===================>]  53,48K  57,7KB/s    in 0,9s

2016-08-20 21:54:49 (57,7 KB/s) - ‘perl-Unicode-Normalize-1.25-1.tar.xz’ saved [54760/54760]

perl-Unicode-Normalize-1.25-1.tar.xz: OK
Unpacking...
Package perl-Unicode-Normalize requires the following packages, installing:
cygwin libssp0 perl perl_base
Package cygwin is already installed, skipping
Package libssp0 is already installed, skipping
Package perl is already installed, skipping
Package perl_base is already installed, skipping
Package perl_base is already installed, skipping
Package xz is already installed, skipping
Installing automake1.11
--2016-08-20 21:54:56--  http://cygwin.mirror.constant.com//noarch/release/automake1.11/automake1.11-1.11.6-2.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 879836 (859K) [application/octet-stream]
Saving to: ‘automake1.11-1.11.6-2.tar.bz2’

automake1.11-1.11.6 100%[===================>] 859,21K  72,2KB/s    in 15s

2016-08-20 21:55:12 (56,8 KB/s) - ‘automake1.11-1.11.6-2.tar.bz2’ saved [879836/879836]

automake1.11-1.11.6-2.tar.bz2: OK
Unpacking...
Package automake1.11 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo xz
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Package xz is already installed, skipping
Installing automake1.12
--2016-08-20 21:55:20--  http://cygwin.mirror.constant.com//noarch/release/automake1.12/automake1.12-1.12.6-2.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 750462 (733K) [application/octet-stream]
Saving to: ‘automake1.12-1.12.6-2.tar.bz2’

automake1.12-1.12.6 100%[===================>] 732,87K  55,6KB/s    in 15s

2016-08-20 21:55:36 (50,4 KB/s) - ‘automake1.12-1.12.6-2.tar.bz2’ saved [750462/750462]

automake1.12-1.12.6-2.tar.bz2: OK
Unpacking...
Package automake1.12 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo xz
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Package xz is already installed, skipping
Installing automake1.13
--2016-08-20 21:55:44--  http://cygwin.mirror.constant.com//noarch/release/automake1.13/automake1.13-1.13.4-1.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 797813 (779K) [application/octet-stream]
Saving to: ‘automake1.13-1.13.4-1.tar.bz2’

automake1.13-1.13.4 100%[===================>] 779,11K  46,3KB/s    in 17s

2016-08-20 21:56:01 (45,9 KB/s) - ‘automake1.13-1.13.4-1.tar.bz2’ saved [797813/797813]

automake1.13-1.13.4-1.tar.bz2: OK
Unpacking...
Package automake1.13 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo xz
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Package xz is already installed, skipping
Installing automake1.14
--2016-08-20 21:56:08--  http://cygwin.mirror.constant.com//noarch/release/automake1.14/automake1.14-1.14.1-2.tar.xz
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 594916 (581K) [application/octet-stream]
Saving to: ‘automake1.14-1.14.1-2.tar.xz’

automake1.14-1.14.1 100%[===================>] 580,97K  44,9KB/s    in 13s

2016-08-20 21:56:22 (45,7 KB/s) - ‘automake1.14-1.14.1-2.tar.xz’ saved [594916/594916]

automake1.14-1.14.1-2.tar.xz: OK
Unpacking...
Package automake1.14 requires the following packages, installing:
autoconf autoconf2.5 bash coreutils m4 perl perl-Carp perl_base texinfo xz
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Installing perl-Carp
--2016-08-20 21:56:29--  http://cygwin.mirror.constant.com//x86_64/release/perl-Carp/perl-Carp-1.38-1.tar.xz
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 17492 (17K) [application/octet-stream]
Saving to: ‘perl-Carp-1.38-1.tar.xz’

perl-Carp-1.38-1.ta 100%[===================>]  17,08K  59,0KB/s    in 0,3s

2016-08-20 21:56:30 (59,0 KB/s) - ‘perl-Carp-1.38-1.tar.xz’ saved [17492/17492]

perl-Carp-1.38-1.tar.xz: OK
Unpacking...
Package perl-Carp requires the following packages, installing:
perl_base
Package perl_base is already installed, skipping
Package perl_base is already installed, skipping
Package texinfo is already installed, skipping
Package xz is already installed, skipping
Installing automake1.15
--2016-08-20 21:56:37--  http://cygwin.mirror.constant.com//noarch/release/automake1.15/automake1.15-1.15-1.tar.xz
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 799284 (781K) [application/octet-stream]
Saving to: ‘automake1.15-1.15-1.tar.xz’

automake1.15-1.15-1 100%[===================>] 780,55K   122KB/s    in 7,3s

2016-08-20 21:56:45 (107 KB/s) - ‘automake1.15-1.15-1.tar.xz’ saved [799284/799284]

automake1.15-1.15-1.tar.xz: OK
Unpacking...
Package automake1.15 requires the following packages, installing:
autoconf autoconf2.5 bash coreutils m4 perl-Carp perl_base texinfo xz
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl-Carp is already installed, skipping
Package perl_base is already installed, skipping
Package texinfo is already installed, skipping
Package xz is already installed, skipping
Installing automake1.4
--2016-08-20 21:56:53--  http://cygwin.mirror.constant.com//noarch/release/automake1.4/automake1.4-1.4p6-11.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 253595 (248K) [application/octet-stream]
Saving to: ‘automake1.4-1.4p6-11.tar.bz2’

automake1.4-1.4p6-1 100%[===================>] 247,65K  84,1KB/s    in 2,9s

2016-08-20 21:56:57 (84,1 KB/s) - ‘automake1.4-1.4p6-11.tar.bz2’ saved [253595/253595]

automake1.4-1.4p6-11.tar.bz2: OK
Unpacking...
Package automake1.4 requires the following packages, installing:
alternatives autoconf autoconf2.1 bash coreutils m4 perl texinfo
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.1 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Installing automake1.5
--2016-08-20 21:57:04--  http://cygwin.mirror.constant.com//noarch/release/automake1.5/automake1.5-1.5-11.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 339540 (332K) [application/octet-stream]
Saving to: ‘automake1.5-1.5-11.tar.bz2’

automake1.5-1.5-11. 100%[===================>] 331,58K  88,6KB/s    in 3,7s

2016-08-20 21:57:08 (88,6 KB/s) - ‘automake1.5-1.5-11.tar.bz2’ saved [339540/339540]

automake1.5-1.5-11.tar.bz2: OK
Unpacking...
Package automake1.5 requires the following packages, installing:
alternatives autoconf autoconf2.1 bash coreutils m4 perl texinfo
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.1 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Installing automake1.6
--2016-08-20 21:57:15--  http://cygwin.mirror.constant.com//noarch/release/automake1.6/automake1.6-1.6.3-12.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 373724 (365K) [application/octet-stream]
Saving to: ‘automake1.6-1.6.3-12.tar.bz2’

automake1.6-1.6.3-1 100%[===================>] 364,96K  63,2KB/s    in 5,8s

2016-08-20 21:57:22 (63,2 KB/s) - ‘automake1.6-1.6.3-12.tar.bz2’ saved [373724/373724]

automake1.6-1.6.3-12.tar.bz2: OK
Unpacking...
Package automake1.6 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Installing automake1.7
--2016-08-20 21:57:29--  http://cygwin.mirror.constant.com//noarch/release/automake1.7/automake1.7-1.7.9-11.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 435994 (426K) [application/octet-stream]
Saving to: ‘automake1.7-1.7.9-11.tar.bz2’

automake1.7-1.7.9-1 100%[===================>] 425,78K  76,7KB/s    in 5,6s

2016-08-20 21:57:35 (76,7 KB/s) - ‘automake1.7-1.7.9-11.tar.bz2’ saved [435994/435994]

automake1.7-1.7.9-11.tar.bz2: OK
Unpacking...
Package automake1.7 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Installing automake1.8
--2016-08-20 21:57:43--  http://cygwin.mirror.constant.com//noarch/release/automake1.8/automake1.8-1.8.5-11.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 510652 (499K) [application/octet-stream]
Saving to: ‘automake1.8-1.8.5-11.tar.bz2’

automake1.8-1.8.5-1 100%[===================>] 498,68K  60,9KB/s    in 8,1s

2016-08-20 21:57:52 (61,6 KB/s) - ‘automake1.8-1.8.5-11.tar.bz2’ saved [510652/510652]

automake1.8-1.8.5-11.tar.bz2: OK
Unpacking...
Package automake1.8 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Installing automake1.9
--2016-08-20 21:58:00--  http://cygwin.mirror.constant.com//noarch/release/automake1.9/automake1.9-1.9.6-11.tar.bz2
Resolving cygwin.mirror.constant.com (cygwin.mirror.constant.com)... 108.61.5.83
Connecting to cygwin.mirror.constant.com (cygwin.mirror.constant.com)|108.61.5.83|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 569347 (556K) [application/octet-stream]
Saving to: ‘automake1.9-1.9.6-11.tar.bz2’

automake1.9-1.9.6-1 100%[===================>] 556,00K  62,6KB/s    in 9,4s

2016-08-20 21:58:10 (58,8 KB/s) - ‘automake1.9-1.9.6-11.tar.bz2’ saved [569347/569347]

automake1.9-1.9.6-11.tar.bz2: OK
Unpacking...
Package automake1.9 requires the following packages, installing:
alternatives autoconf autoconf2.5 bash coreutils m4 perl texinfo
Package alternatives is already installed, skipping
Package autoconf is already installed, skipping
Package autoconf2.5 is already installed, skipping
Package bash is already installed, skipping
Package coreutils is already installed, skipping
Package m4 is already installed, skipping
Package perl is already installed, skipping
Package texinfo is already installed, skipping
Package bash is already installed, skipping
Package gawk is already installed, skipping
Running /etc/postinstall/automake.sh
Running /etc/postinstall/automake1.10.sh
Running /etc/postinstall/automake1.11.sh
Running /etc/postinstall/automake1.12.sh
Running /etc/postinstall/automake1.13.sh
Running /etc/postinstall/automake1.4.sh
Running /etc/postinstall/automake1.5.sh
Running /etc/postinstall/automake1.6.sh
Running /etc/postinstall/automake1.7.sh
Running /etc/postinstall/automake1.8.sh
Running /etc/postinstall/automake1.9.sh
Package automake installed

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