printf '

' | fink --no-use-binary-dist --yes  --build-as-nobody rebuild tcoffee 2>&1
The package 'tcoffee' will be built without being installed.
Reading build dependency for tcoffee-9.03.r1318-202...
Reading dependency for tcoffee-9.03.r1318-202...
Reading build conflict for tcoffee-9.03.r1318-202...

fink needs help picking an alternative to satisfy a virtual dependency. The
candidates:

(1)	soap-lite-ssl-pm5162: Simple Object Access Protocol (SOAP) modules
(2)	soap-lite-pm5162: Simple Object Access Protocol (SOAP) modules

Pick one: [1] (assuming default)
The package 'gcc49-compiler' will be installed.
Reading dependency for gcc49-compiler-4.9.1-1000...
Reading runtime dependency for gcc49-compiler-4.9.1-1000...
The package 'gcc49-shlibs' will be installed.
Reading dependency for gcc49-shlibs-4.9.1-1000...
Reading runtime dependency for gcc49-shlibs-4.9.1-1000...
The package 'libwww-pm5162' will be installed.
Reading dependency for libwww-pm5162-6.07-1...
Reading runtime dependency for libwww-pm5162-6.07-1...
The package 'soap-lite-ssl-pm5162' will be installed.
Reading dependency for soap-lite-ssl-pm5162-0.712-6...
Reading runtime dependency for soap-lite-ssl-pm5162-0.712-6...
The package 'xml-simple-pm5162' will be installed.
Reading dependency for xml-simple-pm5162-2.20-1...
Reading runtime dependency for xml-simple-pm5162-2.20-1...
The package 'gmp5-shlibs' will be installed.
Reading dependency for gmp5-shlibs-6.0.0a-1...
Reading runtime dependency for gmp5-shlibs-6.0.0a-1...
The package 'libgmpxx5-shlibs' will be installed.
Reading dependency for libgmpxx5-shlibs-6.0.0a-1...
Reading runtime dependency for libgmpxx5-shlibs-6.0.0a-1...
The package 'libmpfr4-shlibs' will be installed.
Reading dependency for libmpfr4-shlibs-3.1.2-1...
Reading runtime dependency for libmpfr4-shlibs-3.1.2-1...
The package 'cloog-org2-shlibs' will be installed.
Reading dependency for cloog-org2-shlibs-0.18.2-1...
Reading runtime dependency for cloog-org2-shlibs-0.18.2-1...
The package 'isl-shlibs' will be installed.
Reading dependency for isl-shlibs-0.12.2-2...
Reading runtime dependency for isl-shlibs-0.12.2-2...
The package 'libmpc3-shlibs' will be installed.
Reading dependency for libmpc3-shlibs-1.0.2-1...
Reading runtime dependency for libmpc3-shlibs-1.0.2-1...
The package 'authen-ntlm-pm5162' will be installed.
Reading dependency for authen-ntlm-pm5162-1.09-1...
Reading runtime dependency for authen-ntlm-pm5162-1.09-1...
The package 'encode-locale-pm5162' will be installed.
Reading dependency for encode-locale-pm5162-1.03-1...
Reading runtime dependency for encode-locale-pm5162-1.03-1...
The package 'encode-pm5162' will be installed.
Reading dependency for encode-pm5162-2.60-1...
Reading runtime dependency for encode-pm5162-2.60-1...
The package 'file-listing-pm5162' will be installed.
Reading dependency for file-listing-pm5162-6.04-1...
Reading runtime dependency for file-listing-pm5162-6.04-1...
The package 'html-parser-pm5162' will be installed.
Reading dependency for html-parser-pm5162-3.71-1...
Reading runtime dependency for html-parser-pm5162-3.71-1...
The package 'http-cookies-pm5162' will be installed.
Reading dependency for http-cookies-pm5162-6.01-1...
Reading runtime dependency for http-cookies-pm5162-6.01-1...
The package 'http-daemon-pm5162' will be installed.
Reading dependency for http-daemon-pm5162-6.01-1...
Reading runtime dependency for http-daemon-pm5162-6.01-1...
The package 'http-date-pm5162' will be installed.
Reading dependency for http-date-pm5162-6.02-1...
Reading runtime dependency for http-date-pm5162-6.02-1...
The package 'http-message-pm5162' will be installed.
Reading dependency for http-message-pm5162-6.06-1...
Reading runtime dependency for http-message-pm5162-6.06-1...
The package 'http-negotiate-pm5162' will be installed.
Reading dependency for http-negotiate-pm5162-6.01-1...
Reading runtime dependency for http-negotiate-pm5162-6.01-1...
The package 'lwp-mediatypes-pm5162' will be installed.
Reading dependency for lwp-mediatypes-pm5162-6.02-1...
Reading runtime dependency for lwp-mediatypes-pm5162-6.02-1...
The package 'net-http-pm5162' will be installed.
Reading dependency for net-http-pm5162-6.06-1...
Reading runtime dependency for net-http-pm5162-6.06-1...
The package 'uri-pm5162' will be installed.
Reading dependency for uri-pm5162-1.64-1...
Reading runtime dependency for uri-pm5162-1.64-1...
The package 'www-robotrules-pm5162' will be installed.
Reading dependency for www-robotrules-pm5162-6.02-1...
Reading runtime dependency for www-robotrules-pm5162-6.02-1...
The package 'crypt-ssleay-pm5162' will be installed.
Reading dependency for crypt-ssleay-pm5162-0.72-1...
Reading runtime dependency for crypt-ssleay-pm5162-0.72-1...
The package 'io-socket-ssl-pm5162' will be installed.
Reading dependency for io-socket-ssl-pm5162-1.997-1...
Reading runtime dependency for io-socket-ssl-pm5162-1.997-1...
The package 'class-inspector-pm5162' will be installed.
Reading dependency for class-inspector-pm5162-1.28-1...
Reading runtime dependency for class-inspector-pm5162-1.28-1...
The package 'constant-pm' will be installed.
Reading dependency for constant-pm-1.27-1...
Reading runtime dependency for constant-pm-1.27-1...
The package 'data-uuid-pm5162' will be installed.
Reading dependency for data-uuid-pm5162-1.219-1...
Reading runtime dependency for data-uuid-pm5162-1.219-1...
The package 'dime-tools-pm5162' will be installed.
Reading dependency for dime-tools-pm5162-0.03-1...
Reading runtime dependency for dime-tools-pm5162-0.03-1...
The package 'fcgi-pm5162' will be installed.
Reading dependency for fcgi-pm5162-0.74-1...
Reading runtime dependency for fcgi-pm5162-0.74-1...
The package 'io-compress-pm5162' will be installed.
Reading dependency for io-compress-pm5162-2.063-1...
Reading runtime dependency for io-compress-pm5162-2.063-1...
The package 'io-stringy-pm' will be installed.
Reading dependency for io-stringy-pm-2.110-1022...
Reading runtime dependency for io-stringy-pm-2.110-1022...
The package 'mime-lite-pm5162' will be installed.
Reading dependency for mime-lite-pm5162-3.030-2...
Reading runtime dependency for mime-lite-pm5162-3.030-2...
The package 'mime-tools-pm5162' will be installed.
Reading dependency for mime-tools-pm5162-5.505-1...
Reading runtime dependency for mime-tools-pm5162-5.505-1...
The package 'task-weaken-pm5162' will be installed.
Reading dependency for task-weaken-pm5162-1.04-1...
Reading runtime dependency for task-weaken-pm5162-1.04-1...
The package 'version-pm5162' will be installed.
Reading dependency for version-pm5162-0.99.08-1...
Reading runtime dependency for version-pm5162-0.99.08-1...
The package 'xml-parser-pm5162' will be installed.
Reading dependency for xml-parser-pm5162-2.41-2...
Reading runtime dependency for xml-parser-pm5162-2.41-2...
The package 'xml-namespacesupport-pm' will be installed.
Reading dependency for xml-namespacesupport-pm-1.11-1...
Reading runtime dependency for xml-namespacesupport-pm-1.11-1...
The package 'xml-sax-pm5162' will be installed.
Reading dependency for xml-sax-pm5162-0.99-3...
Reading runtime dependency for xml-sax-pm5162-0.99-3...
The package 'xml-sax-expat-pm5162' will be installed.
Reading dependency for xml-sax-expat-pm5162-0.51-1...
Reading runtime dependency for xml-sax-expat-pm5162-0.51-1...
The package 'digest-hmac-pm' will be installed.
Reading dependency for digest-hmac-pm-1.03-1...
Reading runtime dependency for digest-hmac-pm-1.03-1...
The package 'html-tagset-pm' will be installed.
Reading dependency for html-tagset-pm-3.20-1...
Reading runtime dependency for html-tagset-pm-3.20-1...
The package 'time-date-pm' will be installed.
Reading dependency for time-date-pm-1.16-1...
Reading runtime dependency for time-date-pm-1.16-1...
The package 'io-html-pm5162' will be installed.
Reading dependency for io-html-pm5162-1.001-1...
Reading runtime dependency for io-html-pm5162-1.001-1...
The package 'net-ssleay-pm5162' will be installed.
Reading dependency for net-ssleay-pm5162-1.65-1...
Reading runtime dependency for net-ssleay-pm5162-1.65-1...
The package 'net-idn-encode-pm5162' will be installed.
Reading dependency for net-idn-encode-pm5162-2.004-1...
Reading runtime dependency for net-idn-encode-pm5162-2.004-1...
The package 'mozilla-ca-pm' will be installed.
Reading dependency for mozilla-ca-pm-20130114-1...
Reading runtime dependency for mozilla-ca-pm-20130114-1...
The package 'compress-raw-bzip2-pm5162' will be installed.
Reading dependency for compress-raw-bzip2-pm5162-2.063-1...
Reading runtime dependency for compress-raw-bzip2-pm5162-2.063-1...
The package 'compress-raw-zlib-pm5162' will be installed.
Reading dependency for compress-raw-zlib-pm5162-2.063-1...
Reading runtime dependency for compress-raw-zlib-pm5162-2.063-1...
The package 'email-date-format-pm' will be installed.
Reading dependency for email-date-format-pm-1.004-1...
Reading runtime dependency for email-date-format-pm-1.004-1...
The package 'mailtools-pm5162' will be installed.
Reading dependency for mailtools-pm5162-2.13-1...
Reading runtime dependency for mailtools-pm5162-2.13-1...
The package 'mime-types-pm' will be installed.
Reading dependency for mime-types-pm-2.04-2...
Reading runtime dependency for mime-types-pm-2.04-2...
The package 'unicode-string-pm5162' will be installed.
Reading dependency for unicode-string-pm5162-2.09-11...
Reading runtime dependency for unicode-string-pm5162-2.09-11...
The package 'unicode-map-pm5162' will be installed.
Reading dependency for unicode-map-pm5162-0.112-16...
Reading runtime dependency for unicode-map-pm5162-0.112-16...
The package 'scalar-list-utils-pm5162' will be installed.
Reading dependency for scalar-list-utils-pm5162-1.35-1...
Reading runtime dependency for scalar-list-utils-pm5162-1.35-1...
The package 'expat1-shlibs' will be installed.
Reading dependency for expat1-shlibs-2.1.0-1...
Reading runtime dependency for expat1-shlibs-2.1.0-1...
The package 'xml-sax-base-pm' will be installed.
Reading dependency for xml-sax-base-pm-1.08-1...
Reading runtime dependency for xml-sax-base-pm-1.08-1...
The package 'openssl100-shlibs' will be installed.
Reading dependency for openssl100-shlibs-1.0.1h-1...
Reading runtime dependency for openssl100-shlibs-1.0.1h-1...
The package 'unicode-normalize-pm5162' will be installed.
Reading dependency for unicode-normalize-pm5162-1.18-1...
Reading runtime dependency for unicode-normalize-pm5162-1.18-1...
The following package will be rebuilt:
 tcoffee
The following 61 additional packages will be installed:
 authen-ntlm-pm5162 class-inspector-pm5162 cloog-org2-shlibs
 compress-raw-bzip2-pm5162 compress-raw-zlib-pm5162 constant-pm
 crypt-ssleay-pm5162 data-uuid-pm5162 digest-hmac-pm dime-tools-pm5162
 email-date-format-pm encode-locale-pm5162 encode-pm5162 expat1-shlibs
 fcgi-pm5162 file-listing-pm5162 gcc49-compiler gcc49-shlibs gmp5-shlibs
 html-parser-pm5162 html-tagset-pm http-cookies-pm5162 http-daemon-pm5162
 http-date-pm5162 http-message-pm5162 http-negotiate-pm5162
 io-compress-pm5162 io-html-pm5162 io-socket-ssl-pm5162 io-stringy-pm
 isl-shlibs libgmpxx5-shlibs libmpc3-shlibs libmpfr4-shlibs libwww-pm5162
 lwp-mediatypes-pm5162 mailtools-pm5162 mime-lite-pm5162 mime-tools-pm5162
 mime-types-pm mozilla-ca-pm net-http-pm5162 net-idn-encode-pm5162
 net-ssleay-pm5162 openssl100-shlibs scalar-list-utils-pm5162
 soap-lite-ssl-pm5162 task-weaken-pm5162 time-date-pm unicode-map-pm5162
 unicode-normalize-pm5162 unicode-string-pm5162 uri-pm5162 version-pm5162
 www-robotrules-pm5162 xml-namespacesupport-pm xml-parser-pm5162
 xml-sax-base-pm xml-sax-expat-pm5162 xml-sax-pm5162 xml-simple-pm5162
Do you want to continue? [Y/n] (assuming default)
curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/T-COFFEE_distribution_Version_9.03.r1318.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 3374k    0 12788    0     0  51742      0  0:01:06 --:--:--  0:01:06 51564
 11 3374k   11  387k    0     0   193k      0  0:00:17  0:00:01  0:00:16  193k
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 50 3374k   50 1699k    0     0   281k      0  0:00:11  0:00:06  0:00:05  291k
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 90 3374k   90 3038k    0     0   270k      0  0:00:12  0:00:11  0:00:01  317k
100 3374k  100 3374k    0     0   284k      0  0:00:11  0:00:11 --:--:--  396k
Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/class-inspector-pm5162_1.28-1_darwin-x86_64.deb
Selecting previously deselected package class-inspector-pm5162.
(Reading database ... 4296 files and directories currently installed.)
Unpacking class-inspector-pm5162 (from .../class-inspector-pm5162_1.28-1_darwin-x86_64.deb) ...
Setting up class-inspector-pm5162 (1.28-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/compress-raw-bzip2-pm5162_2.063-1_darwin-x86_64.deb
Selecting previously deselected package compress-raw-bzip2-pm5162.
(Reading database ... 4315 files and directories currently installed.)
Unpacking compress-raw-bzip2-pm5162 (from .../compress-raw-bzip2-pm5162_2.063-1_darwin-x86_64.deb) ...
Setting up compress-raw-bzip2-pm5162 (2.063-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/compress-raw-zlib-pm5162_2.063-1_darwin-x86_64.deb
Selecting previously deselected package compress-raw-zlib-pm5162.
(Reading database ... 4329 files and directories currently installed.)
Unpacking compress-raw-zlib-pm5162 (from .../compress-raw-zlib-pm5162_2.063-1_darwin-x86_64.deb) ...
Setting up compress-raw-zlib-pm5162 (2.063-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/constant-pm_1.27-1_darwin-x86_64.deb
Selecting previously deselected package constant-pm.
(Reading database ... 4339 files and directories currently installed.)
Unpacking constant-pm (from .../constant-pm_1.27-1_darwin-x86_64.deb) ...
Setting up constant-pm (1.27-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/crypt-ssleay-pm5162_0.72-1_darwin-x86_64.deb
Selecting previously deselected package crypt-ssleay-pm5162.
(Reading database ... 4349 files and directories currently installed.)
Unpacking crypt-ssleay-pm5162 (from .../crypt-ssleay-pm5162_0.72-1_darwin-x86_64.deb) ...
Setting up crypt-ssleay-pm5162 (0.72-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/data-uuid-pm5162_1.219-1_darwin-x86_64.deb
Selecting previously deselected package data-uuid-pm5162.
(Reading database ... 4373 files and directories currently installed.)
Unpacking data-uuid-pm5162 (from .../data-uuid-pm5162_1.219-1_darwin-x86_64.deb) ...
Setting up data-uuid-pm5162 (1.219-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/digest-hmac-pm_1.03-1_darwin-x86_64.deb
Selecting previously deselected package digest-hmac-pm.
(Reading database ... 4387 files and directories currently installed.)
Unpacking digest-hmac-pm (from .../digest-hmac-pm_1.03-1_darwin-x86_64.deb) ...
Setting up digest-hmac-pm (1.03-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/email-date-format-pm_1.004-1_darwin-x86_64.deb
Selecting previously deselected package email-date-format-pm.
(Reading database ... 4401 files and directories currently installed.)
Unpacking email-date-format-pm (from .../email-date-format-pm_1.004-1_darwin-x86_64.deb) ...
Setting up email-date-format-pm (1.004-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/encode-pm5162_2.60-1_darwin-x86_64.deb
Selecting previously deselected package encode-pm5162.
(Reading database ... 4414 files and directories currently installed.)
Unpacking encode-pm5162 (from .../encode-pm5162_2.60-1_darwin-x86_64.deb) ...
Setting up encode-pm5162 (2.60-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/expat1-shlibs_2.1.0-1_darwin-x86_64.deb
Selecting previously deselected package expat1-shlibs.
(Reading database ... 4512 files and directories currently installed.)
Unpacking expat1-shlibs (from .../expat1-shlibs_2.1.0-1_darwin-x86_64.deb) ...
Setting up expat1-shlibs (2.1.0-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/fcgi-pm5162_0.74-1_darwin-x86_64.deb
Selecting previously deselected package fcgi-pm5162.
(Reading database ... 4517 files and directories currently installed.)
Unpacking fcgi-pm5162 (from .../fcgi-pm5162_0.74-1_darwin-x86_64.deb) ...
Setting up fcgi-pm5162 (0.74-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/html-tagset-pm_3.20-1_darwin-x86_64.deb
Selecting previously deselected package html-tagset-pm.
(Reading database ... 4528 files and directories currently installed.)
Unpacking html-tagset-pm (from .../html-tagset-pm_3.20-1_darwin-x86_64.deb) ...
Setting up html-tagset-pm (3.20-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/io-compress-pm5162_2.063-1_darwin-x86_64.deb
Selecting previously deselected package io-compress-pm5162.
(Reading database ... 4538 files and directories currently installed.)
Unpacking io-compress-pm5162 (from .../io-compress-pm5162_2.063-1_darwin-x86_64.deb) ...
Setting up io-compress-pm5162 (2.063-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/io-stringy-pm_2.110-1022_darwin-x86_64.deb
Selecting previously deselected package io-stringy-pm.
(Reading database ... 4603 files and directories currently installed.)
Unpacking io-stringy-pm (from .../io-stringy-pm_2.110-1022_darwin-x86_64.deb) ...
Setting up io-stringy-pm (2.110-1022) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb
Selecting previously deselected package libgmpxx5-shlibs.
(Reading database ... 4628 files and directories currently installed.)
Unpacking libgmpxx5-shlibs (from .../libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb) ...
Selecting previously deselected package gmp5-shlibs.
Unpacking gmp5-shlibs (from .../gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb) ...
Setting up gmp5-shlibs (6.0.0a-1) ...

Setting up libgmpxx5-shlibs (6.0.0a-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb
Selecting previously deselected package libmpfr4-shlibs.
(Reading database ... 4657 files and directories currently installed.)
Unpacking libmpfr4-shlibs (from .../libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb) ...
Setting up libmpfr4-shlibs (3.1.2-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/lwp-mediatypes-pm5162_6.02-1_darwin-x86_64.deb
Selecting previously deselected package lwp-mediatypes-pm5162.
(Reading database ... 4670 files and directories currently installed.)
Unpacking lwp-mediatypes-pm5162 (from .../lwp-mediatypes-pm5162_6.02-1_darwin-x86_64.deb) ...
Setting up lwp-mediatypes-pm5162 (6.02-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/mime-types-pm_2.04-2_darwin-x86_64.deb
Selecting previously deselected package mime-types-pm.
(Reading database ... 4681 files and directories currently installed.)
Unpacking mime-types-pm (from .../mime-types-pm_2.04-2_darwin-x86_64.deb) ...
Setting up mime-types-pm (2.04-2) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/debs/mozilla-ca-pm_20130114-1_darwin-x86_64.deb
Selecting previously deselected package mozilla-ca-pm.
(Reading database ... 4696 files and directories currently installed.)
Unpacking mozilla-ca-pm (from .../mozilla-ca-pm_20130114-1_darwin-x86_64.deb) ...
Setting up mozilla-ca-pm (20130114-1) ...

Reading buildlock packages...
	All buildlocks accounted for.
/sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb
Selecting previously deselected package openssl100-shlibs.
(Reading database ... 4708 files and directories currently installed.)
Unpacking openssl100-shlibs (from .../openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb) ...
Setting up openssl100-shlibs (1.0.1h-1) ...

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/sw/bin/dpkg-lockwait -i /sw/fink/debs/unicode-map-pm5162_0.112-16_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/unicode-normalize-pm5162_1.18-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/version-pm5162_0.99.08-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/www-robotrules-pm5162_6.02-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/xml-namespacesupport-pm_1.11-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/xml-sax-base-pm_1.08-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/xml-sax-pm5162_0.99-3_darwin-x86_64.deb
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Creating config files in /sw/etc/perl5/5.16.2/XML/SAX...
Setting up xml-sax-pm5162 (0.99-3) ...
update-perl5162-sax-parsers: adding Perl SAX parser module info file of XML::SAX::PurePerl...
update-perl5162-sax-parsers: updating overall Perl SAX parser modules info file...

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/sw/bin/dpkg-lockwait -i /sw/fink/debs/authen-ntlm-pm5162_1.09-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/dime-tools-pm5162_0.03-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/encode-locale-pm5162_1.03-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/html-parser-pm5162_3.71-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/http-date-pm5162_6.02-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/io-html-pm5162_1.001-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/isl-shlibs_0.12.2-2_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/mime-lite-pm5162_3.030-2_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/mime-tools-pm5162_5.505-1_darwin-x86_64.deb
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Setting up xml-sax-expat-pm5162 (0.51-1) ...
update-perl5162-sax-parsers: adding Perl SAX parser module info file of XML::SAX::Expat...
update-perl5162-sax-parsers: updating overall Perl SAX parser modules info file...

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Clearing dependency_libs of .la files being installed

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/sw/bin/dpkg-lockwait -i /sw/fink/debs/http-negotiate-pm5162_6.01-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/io-socket-ssl-pm5162_1.997-1_darwin-x86_64.deb
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Selecting previously deselected package net-http-pm5162.
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/http-cookies-pm5162_6.01-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/http-daemon-pm5162_6.01-1_darwin-x86_64.deb
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/sw/bin/dpkg-lockwait -i /sw/fink/debs/soap-lite-ssl-pm5162_0.712-6_darwin-x86_64.deb
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Setting up soap-lite-ssl-pm5162 (0.712-6) ...

Setting runtime build-lock...
dpkg-deb -b /sw/build.build/root-fink-buildlock-tcoffee-9.03.r1318-202 /sw/build.build
dpkg-deb: building package `fink-buildlock-tcoffee-9.03.r1318-202' in `/sw/build.build/fink-buildlock-tcoffee-9.03.r1318-202_2014.07.30-19.24.39_darwin-x86_64.deb'.
Installing build-lock package...
/sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-tcoffee-9.03.r1318-202_2014.07.30-19.24.39_darwin-x86_64.deb
Selecting previously deselected package fink-buildlock-tcoffee-9.03.r1318-202.
(Reading database ... 11302 files and directories currently installed.)
Unpacking fink-buildlock-tcoffee-9.03.r1318-202 (from .../fink-buildlock-tcoffee-9.03.r1318-202_2014.07.30-19.24.39_darwin-x86_64.deb) ...
Setting up fink-buildlock-tcoffee-9.03.r1318-202 (2014.07.30-19.24.39) ...

sudo -u fink-bld [ENV] sh -c /tmp/fink.ujr8H
env LANG=C LC_ALL=C /sw/bin/tar  --no-same-owner --no-same-permissions -xvf /sw/src/T-COFFEE_distribution_Version_9.03.r1318.tar.gz
T-COFFEE_distribution_Version_9.03.r1318/
T-COFFEE_distribution_Version_9.03.r1318/bin/
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_100_exp_220000
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/BLOSUM.scr
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_matrix.scr
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_250_exp_110000
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/blosum80.mat
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/BLOSUM75.scr
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/hmmtop.psv
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/hmmtop.arch
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/BLOSUM90.scr
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_150_exp_110000
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/New_KS.267.obs
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/BLOSUM75.diag_prob_t2
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_100_exp_550000
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_100_exp_110000
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_100_exp_330000
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/BLOSUM.diag_prob_t10
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/blosum80_trunc.mat
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/New_KS.267.seq
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/mix80.mod
T-COFFEE_distribution_Version_9.03.r1318/mcoffee/dna_diag_prob_200_exp_110000
T-COFFEE_distribution_Version_9.03.r1318/reference_test/
T-COFFEE_distribution_Version_9.03.r1318/license.txt
T-COFFEE_distribution_Version_9.03.r1318/tclinkdb.txt
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/aln_compare.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_fasta_nw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev3.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/pavie_dp.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/evaluate.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dps.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/define_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/fsa_dp.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/t_coffee.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_ssec_pwaln.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/aln_convertion_util.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev4_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/CUSTOM_evaluate_for_struc.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/evaluate_dirichlet.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/fastal_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/Vector.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_domain_dp.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/hsearch.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_make_tree.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_domain_constraints_list.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/iteration.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/scoring.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/km_coffee.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/reformat_struc.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_aln_analyze.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_gotoh_nw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/perl_header_lib.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_sim.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/fastal_opt_parsing.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/reformat.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_suboptimal_nw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/t_coffee.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/Stack.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/parttree.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/matrices.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/io_func.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/tree_util.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/random.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_constraints_list.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_graph_maln.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_est.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/fastal.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev4.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/io_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_fasta_sw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/classes.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_declare.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/header_list
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/source_list
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_gotoh_sw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dp_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/TMalign.f
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_drivers.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/fast_tree_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev2.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/kmeans.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev3_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/evaluate_for_struc.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_cdna_fasta_nw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/km_util.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev1.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_analyse_constraints_list.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev2_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/evaluate_for_domain.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/dev1_lib_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/diagonal.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/showpair.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_domain_dp_drivers.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_mm_nw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/tree.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/pb_util_read_sequence.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/makefile
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/km_coffee_header.h
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_generic_fasta_nw.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/pb_util_read_seq_util.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_dp_clean_maln.c
T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source/util_job_handling.c
T-COFFEE_distribution_Version_9.03.r1318/example/
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.template_file
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln6.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.cw_aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq6.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/3d_sample5.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/1SG1-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/marna.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/1JMA-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large_muscle_trim.aln
T-COFFEE_distribution_Version_9.03.r1318/example/three_pdb_two_seq.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_profile1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.b62_aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_dnaseq1.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln2.msf
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases1_small.aln
T-COFFEE_distribution_Version_9.03.r1318/example/1XU2-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/struc2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq4.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq1.score_ascii
T-COFFEE_distribution_Version_9.03.r1318/example/combined_aln.aln.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.cons.stk
T-COFFEE_distribution_Version_9.03.r1318/example/template_file.template
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln4.aln
T-COFFEE_distribution_Version_9.03.r1318/example/1SG1-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.g0.cw_aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.tc_aln
T-COFFEE_distribution_Version_9.03.r1318/example/struc1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/2HEY-4.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/new_profile1_pdb1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln1_2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/three_pdb_two_seq.aln
T-COFFEE_distribution_Version_9.03.r1318/example/three_pdb_two_seq.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sample_lib4.tc_lib02
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.aln
T-COFFEE_distribution_Version_9.03.r1318/example/tlara_tRNA_aln50.output
T-COFFEE_distribution_Version_9.03.r1318/example/sv.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases2_small.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sv.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/test.lib
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.muscle
T-COFFEE_distribution_Version_9.03.r1318/example/2seqs.fas
T-COFFEE_distribution_Version_9.03.r1318/example/sample1.score_ascii
T-COFFEE_distribution_Version_9.03.r1318/example/struc3.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.g10.score_ascii
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.cw_aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq1.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.cw.stk
T-COFFEE_distribution_Version_9.03.r1318/example/sample_lib3.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/struc7.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/struc6.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/block1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/command_line.txt
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln1.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_oneseq.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases.small
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.mafft
T-COFFEE_distribution_Version_9.03.r1318/example/profile2_pdb2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/1D4V-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.ph
T-COFFEE_distribution_Version_9.03.r1318/example/charge_relay_lib.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases.small.blosum62mt.sim_file
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln7.cache_aln
T-COFFEE_distribution_Version_9.03.r1318/example/3d.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq7.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq1.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_tree.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.g0.aln
T-COFFEE_distribution_Version_9.03.r1318/example/block2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.probcons
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/three_pdb.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln2.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_lib5.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/prf1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/tlara_tRNA_aln51.output
T-COFFEE_distribution_Version_9.03.r1318/example/sv.maln
T-COFFEE_distribution_Version_9.03.r1318/example/cache
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_chain.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq1.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq5.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/1OQE-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/1EXT-3.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_lib1.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/1EXT-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln6.cache
T-COFFEE_distribution_Version_9.03.r1318/example/test_lib.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/sample_tree3.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/1XU1-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases1_small.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/combined_aln.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases1_small.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/template_file7.template
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.tcoffee.stk
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.expresso
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large.code_name
T-COFFEE_distribution_Version_9.03.r1318/example/3d.aln
T-COFFEE_distribution_Version_9.03.r1318/example/prf3.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/test.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/1D4V-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/profile1_pdb1_1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/2UWI-3.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq3.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/template_file6.template
T-COFFEE_distribution_Version_9.03.r1318/example/3d_sample5.template_list
T-COFFEE_distribution_Version_9.03.r1318/example/3d.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/profile2_pdb2.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/tlara_tRNA_aln10.output
T-COFFEE_distribution_Version_9.03.r1318/example/g15.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases2_small.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.alifold
T-COFFEE_distribution_Version_9.03.r1318/example/1EXT-4.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq2.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/struc8.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/2HEY-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln5.aln
T-COFFEE_distribution_Version_9.03.r1318/example/g10.aln
T-COFFEE_distribution_Version_9.03.r1318/example/two_profiles.template_file
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln3.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/g5.aln
T-COFFEE_distribution_Version_9.03.r1318/example/p120.aln
T-COFFEE_distribution_Version_9.03.r1318/example/g0.aln
T-COFFEE_distribution_Version_9.03.r1318/example/prf1.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/3d_sample3.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.tc_aln.aln
T-COFFEE_distribution_Version_9.03.r1318/example/prf2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/1D4V-3.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_pair.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/seq.fas
T-COFFEE_distribution_Version_9.03.r1318/example/sample_lib1.mocca_lib
T-COFFEE_distribution_Version_9.03.r1318/example/profile2_pdb2.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_tree2.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sample_lib2.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln7.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln1_1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases2_small.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large.aln
T-COFFEE_distribution_Version_9.03.r1318/example/three_cdna.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln1.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small_dna.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sample_profile2.aln
T-COFFEE_distribution_Version_9.03.r1318/example/3d_sample4.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/p350.aln
T-COFFEE_distribution_Version_9.03.r1318/example/three_pdb.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/struc5.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/b30.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sample_rnaseq2.stk
T-COFFEE_distribution_Version_9.03.r1318/example/kinases.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large.muscle
T-COFFEE_distribution_Version_9.03.r1318/example/1SG1-4.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/t_coffee.log
T-COFFEE_distribution_Version_9.03.r1318/example/prf2.dnd
T-COFFEE_distribution_Version_9.03.r1318/example/sv.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/three_pdb.aln
T-COFFEE_distribution_Version_9.03.r1318/example/error_report.T-COFFEE
T-COFFEE_distribution_Version_9.03.r1318/example/sample_param_file.param
T-COFFEE_distribution_Version_9.03.r1318/example/profile1_pdb1.aln
T-COFFEE_distribution_Version_9.03.r1318/example/2HEY-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_aln1.tc_lib
T-COFFEE_distribution_Version_9.03.r1318/example/prf1.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/prf3.aln
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_large.coded.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/1SG1-3.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/newprf.aln
T-COFFEE_distribution_Version_9.03.r1318/example/profile1_pdb1.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.mcoffee
T-COFFEE_distribution_Version_9.03.r1318/example/3d_sample2.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.g10.cw_aln
T-COFFEE_distribution_Version_9.03.r1318/example/2UWI-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/struc4.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/1JMA-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.score_ascii
T-COFFEE_distribution_Version_9.03.r1318/example/sample_seq8.seq
T-COFFEE_distribution_Version_9.03.r1318/example/prf2.fasta
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.g15.cw_aln
T-COFFEE_distribution_Version_9.03.r1318/example/2UWI-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/sample_list1.lib_list
T-COFFEE_distribution_Version_9.03.r1318/example/1EXT-2.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/2RPJ-1.pdb
T-COFFEE_distribution_Version_9.03.r1318/example/p250
T-COFFEE_distribution_Version_9.03.r1318/example/x
T-COFFEE_distribution_Version_9.03.r1318/example/sproteases_small.score_html
T-COFFEE_distribution_Version_9.03.r1318/doc/
T-COFFEE_distribution_Version_9.03.r1318/install
sudo -u fink-bld [ENV] sh -c /tmp/fink.70188
[ -r /sw/fink/dists/stable/main/finkinfo/sci/tcoffee.patch ]
sudo -u fink-bld [ENV] sh -c /tmp/fink.KNza8
patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/tcoffee.patch
patching file install
perl -pi -e 's|f77|/sw/lib/gcc4.9/bin/gfortran-fsf-4.9|g' install
perl -pi -e 's|=\"gcc\"|=\"/sw/lib/gcc4.9/bin/gcc-fsf-4.9\"|g' install
perl -pi -e 's|/usr/local/bin|/sw/bin|g ' install
perl -pi -e 's|"perl |"/usr/bin/perl |g' t_coffee_source/*.[ch]
sudo -u fink-bld [ENV] sh -c /tmp/fink.AmsRd
./install tcoffee -exec=/sw/bin -plugins=/sw/bin
------- Installing T-Coffee Modes

------- The installer will now install the tcoffee components 
rm: *.o: No such file or directory
make: *** [clean] Error 1
    --- rm *.o

------- Compiling T-Coffee
make -i CC=/sw/lib/gcc4.9/bin/gcc-fsf-4.9  t_coffee 
util.c: In function 'get_os':
util.c:4785:7: warning: 'tmpnam' is deprecated (declared at /usr/include/stdio.h:274): This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations]
       file=tmpnam (NULL);
       ^
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_constraints_list.o util_constraints_list.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_job_handling.o util_job_handling.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dps.o util_dps.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_domain_constraints_list.o util_domain_constraints_list.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_analyse_constraints_list.o util_analyse_constraints_list.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_aln_analyze.o util_aln_analyze.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o aln_convertion_util.o aln_convertion_util.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_declare.o util_declare.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o hsearch.o hsearch.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o random.o random.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_make_tree.o util_make_tree.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util.o util.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o reformat_struc.o reformat_struc.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o reformat.o reformat.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o aln_compare.o aln_compare.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o io_func.o io_func.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o pb_util_read_sequence.o pb_util_read_sequence.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o pb_util_read_seq_util.o pb_util_read_seq_util.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o tree_util.o tree_util.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_graph_maln.o util_graph_maln.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_clean_maln.o util_dp_clean_maln.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_ssec_pwaln.o util_dp_ssec_pwaln.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_sim.o util_dp_sim.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_mm_nw.o util_dp_mm_nw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_gotoh_nw.o util_dp_gotoh_nw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_suboptimal_nw.o util_dp_suboptimal_nw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_cdna_fasta_nw.o util_dp_cdna_fasta_nw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_generic_fasta_nw.o util_dp_generic_fasta_nw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_fasta_nw.o util_dp_fasta_nw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_fasta_sw.o util_dp_fasta_sw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_gotoh_sw.o util_dp_gotoh_sw.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_est.o util_dp_est.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_domain_dp_drivers.o util_domain_dp_drivers.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_dp_drivers.o util_dp_drivers.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o util_domain_dp.o util_domain_dp.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o CUSTOM_evaluate_for_struc.o CUSTOM_evaluate_for_struc.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o evaluate_for_struc.o evaluate_for_struc.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o evaluate_for_domain.o evaluate_for_domain.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o evaluate_dirichlet.o evaluate_dirichlet.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o evaluate.o evaluate.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o showpair.o showpair.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o fsa_dp.o fsa_dp.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o pavie_dp.o pavie_dp.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o dev1.o dev1.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o dev2.o dev2.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o dev3.o dev3.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o dev4.o dev4.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o fastal.o fastal.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o parttree.o parttree.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o tree.o tree.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o diagonal.o diagonal.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o fastal_opt_parsing.o fastal_opt_parsing.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o scoring.o scoring.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o iteration.o iteration.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o Stack.o Stack.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o Vector.o Vector.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o classes.o classes.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o km_util.o km_util.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o kmeans.o kmeans.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o km_coffee.o km_coffee.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9    -c -o t_coffee.o t_coffee.c
    --- /sw/lib/gcc4.9/bin/gcc-fsf-4.9  -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o  -lm
/bin/rm -rf /sw/build.build/root-tcoffee-9.03.r1318-202
/bin/mkdir -p /sw/build.build/root-tcoffee-9.03.r1318-202/sw
/bin/mkdir -p /sw/build.build/root-tcoffee-9.03.r1318-202/DEBIAN
/usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-tcoffee-9.03.r1318-202
sudo -u fink-bld [ENV] sh -c /tmp/fink.BszY6
mkdir -p /sw/build.build/root-tcoffee-9.03.r1318-202/sw/bin
cp t_coffee_source/t_coffee /sw/build.build/root-tcoffee-9.03.r1318-202/sw/bin
mkdir -p /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/tcoffee
cp -R example /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/tcoffee
sudo -u fink-bld [ENV] sh -c /tmp/fink.STpQ7
/usr/bin/install -d -m 700 /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/doc/tcoffee
/bin/cp -r license.txt /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/doc/tcoffee/
/bin/chmod -R go=u-w /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/doc/tcoffee
/bin/rm -f /sw/build.build/root-tcoffee-9.03.r1318-202/sw/info/dir /sw/build.build/root-tcoffee-9.03.r1318-202/sw/info/dir.old /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/info/dir /sw/build.build/root-tcoffee-9.03.r1318-202/sw/share/info/dir.old
Reverting ownership of install dir to root
Writing control file...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-tcoffee-9.03.r1318-202 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci
dpkg-deb: building package `tcoffee' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/tcoffee_9.03.r1318-202_darwin-x86_64.deb'.
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-tcoffee-9.03.r1318-202
(Reading database ... 11303 files and directories currently installed.)
Removing fink-buildlock-tcoffee-9.03.r1318-202 ...