ports/82154: Update port biology/primer3 to current release (1.0.0)

George Hartzell hartzell at alerce.com
Sun Jun 12 00:40:28 UTC 2005 

>Number:         82154
>Category:       ports
>Synopsis:       Update port biology/primer3 to current release (1.0.0)
>Confidential:   no
>Severity:       non-critical
>Priority:       medium
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Sun Jun 12 00:40:26 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator:     George Hartzell
>Release:        FreeBSD 5.4-STABLE i386
>Organization:
>Environment:
System: FreeBSD ash.alerce.com 5.4-STABLE FreeBSD 5.4-STABLE #8: Thu Jun 9 14:35:17 PDT 2005 root at ash.alerce.com:/usr/obj/usr/src/sys/ASH i386


>Description:
  	The attached patch updates the primer3 port (biology/primer3)
	to the current release (1.0.0)
>How-To-Repeat:
	
>Fix:

	

--- primer3-diff begins here ---
Index: Makefile
===================================================================
RCS file: /home/ncvs/ports/biology/primer3/Makefile,v
retrieving revision 1.5
diff -c -2 -r1.5 Makefile
*** Makefile	27 Feb 2004 22:20:43 -0000	1.5
--- Makefile	12 Jun 2005 00:30:07 -0000
***************
*** 7,14 ****
  
  PORTNAME=	primer3
! PORTVERSION=	0.9
  CATEGORIES=	biology
  MASTER_SITES=	http://frodo.wi.mit.edu/primer3/
! DISTNAME=	${PORTNAME}_${PORTVERSION:S/./_/}_test
  
  MAINTAINER=	tonym at biolateral.com.au
--- 7,14 ----
  
  PORTNAME=	primer3
! PORTVERSION=	1.0.0
  CATEGORIES=	biology
  MASTER_SITES=	http://frodo.wi.mit.edu/primer3/
! DISTNAME=	${PORTNAME}_${PORTVERSION}
  
  MAINTAINER=	tonym at biolateral.com.au
***************
*** 19,24 ****
  CPIO=		cpio --quiet -pdum -R
  DOCUMENTS=	README example
- CGI_EXAMPLES=	primer3_www.cgi		primer3_www_help.html \
- 		primer3_www_results.cgi	primer3_www_results_help.html
  
  post-patch:
--- 19,22 ----
***************
*** 34,40 ****
  	@${MKDIR} ${DATADIR}
  	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright ${DATADIR}
- .for file in ${CGI_EXAMPLES}
- 	@${INSTALL_DATA} ${WRKSRC}/${file} ${DATADIR}
- .endfor
  .if !defined(NOPORTDOCS)
  	@${MKDIR} ${DOCSDIR}
--- 32,35 ----
***************
*** 42,46 ****
  	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR}
  .endfor
! 	@${RMDIR} ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp
  	@${MKDIR} ${EXAMPLESDIR}
  	@cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | \
--- 37,41 ----
  	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/${file} ${DOCSDIR}
  .endfor
! 	@${RM} -rf ${WRKDIR}/${DISTNAME}/test/primer*_list_tmp
  	@${MKDIR} ${EXAMPLESDIR}
  	@cd ${WRKDIR}/${DISTNAME}/test && ${FIND} * | \
Index: distinfo
===================================================================
RCS file: /home/ncvs/ports/biology/primer3/distinfo,v
retrieving revision 1.2
diff -c -2 -r1.2 distinfo
*** distinfo	31 Mar 2004 03:06:20 -0000	1.2
--- distinfo	12 Jun 2005 00:12:35 -0000
***************
*** 1,2 ****
! MD5 (primer3_0_9_test.tar.gz) = 1ae09013c982eb67953cc4dd5b837088
! SIZE (primer3_0_9_test.tar.gz) = 948375
--- 1,2 ----
! MD5 (primer3_1.0.0.tar.gz) = 58605ee607f6218a2a775345b10d15fa
! SIZE (primer3_1.0.0.tar.gz) = 936696
Index: pkg-plist
===================================================================
RCS file: /home/ncvs/ports/biology/primer3/pkg-plist,v
retrieving revision 1.3
diff -c -2 -r1.3 pkg-plist
*** pkg-plist	22 Oct 2003 09:29:51 -0000	1.3
--- pkg-plist	12 Jun 2005 00:28:20 -0000
***************
*** 36,45 ****
  %%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.rev
  %%PORTDOCS%%share/examples/primer3/primer1_output
- %%PORTDOCS%%share/examples/primer3/primer_boundary1_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_boundary1_input
  %%PORTDOCS%%share/examples/primer3/primer_boundary1_output
- %%PORTDOCS%%share/examples/primer3/primer_boundary_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_boundary_input
- %%PORTDOCS%%share/examples/primer3/primer_boundary_output
  %%PORTDOCS%%share/examples/primer3/primer_check_input
  %%PORTDOCS%%share/examples/primer3/primer_check_output
--- 36,42 ----
***************
*** 262,269 ****
  %%PORTDOCS%%share/examples/primer3/primer_human_output
  %%PORTDOCS%%share/examples/primer3/primer_input
- %%PORTDOCS%%share/examples/primer3/primer_internal1_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_internal1_input
- %%PORTDOCS%%share/examples/primer3/primer_internal1_output
- %%PORTDOCS%%share/examples/primer3/primer_internal_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_internal_input
  %%PORTDOCS%%share/examples/primer3/primer_internal_output
--- 259,263 ----
***************
*** 302,317 ****
  %%PORTDOCS%%share/examples/primer3/primer_list_last/targets_test.for
  %%PORTDOCS%%share/examples/primer3/primer_list_last/targets_test.rev
- %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_input
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_output
- %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_input
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_output
- %%PORTDOCS%%share/examples/primer3/primer_mispriming_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_input
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_long_lib_input
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_long_lib_output
  %%PORTDOCS%%share/examples/primer3/primer_mispriming_output
- %%PORTDOCS%%share/examples/primer3/primer_must_use_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_must_use_input
  %%PORTDOCS%%share/examples/primer3/primer_must_use_output
--- 296,307 ----
***************
*** 321,325 ****
  %%PORTDOCS%%share/examples/primer3/primer_obj_fn_output
  %%PORTDOCS%%share/examples/primer3/primer_output
- %%PORTDOCS%%share/examples/primer3/primer_position_penalty_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_position_penalty_input
  %%PORTDOCS%%share/examples/primer3/primer_position_penalty_output
--- 311,314 ----
***************
*** 335,339 ****
  %%PORTDOCS%%share/examples/primer3/primer_syntax_input
  %%PORTDOCS%%share/examples/primer3/primer_syntax_output
- %%PORTDOCS%%share/examples/primer3/primer_task_formated_output
  %%PORTDOCS%%share/examples/primer3/primer_task_input
  %%PORTDOCS%%share/examples/primer3/primer_task_output
--- 324,327 ----
***************
*** 345,354 ****
  %%PORTDOCS%%share/examples/primer3/repeat_lib5
  %%PORTDOCS%%share/examples/primer3/repeat_lib6
  bin/primer3
  share/primer3/Copyright
- share/primer3/primer3_www.cgi
- share/primer3/primer3_www_help.html
- share/primer3/primer3_www_results.cgi
- share/primer3/primer3_www_results_help.html
  @dirrm share/primer3
  %%PORTDOCS%%@dirrm %%DOCSDIR%%/
--- 333,357 ----
  %%PORTDOCS%%share/examples/primer3/repeat_lib5
  %%PORTDOCS%%share/examples/primer3/repeat_lib6
+ %%PORTDOCS%%share/examples/primer3/long_seq_tm_test.pl
+ %%PORTDOCS%%share/examples/primer3/not_for_production_Ns.lib
+ %%PORTDOCS%%share/examples/primer3/not_for_production_Xs.lib
+ %%PORTDOCS%%share/examples/primer3/primer_boundary1_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_boundary_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_boundary_output
+ %%PORTDOCS%%share/examples/primer3/primer_internal1_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_internal1_output
+ %%PORTDOCS%%share/examples/primer3/primer_internal_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_lib_amb_codes_input
+ %%PORTDOCS%%share/examples/primer3/primer_lib_amb_codes_output
+ %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary1_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_mispriming_boundary2_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_mispriming_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_must_use_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_position_penalty_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_task_formatted_output
+ %%PORTDOCS%%share/examples/primer3/primer_template_mispriming_input
+ %%PORTDOCS%%share/examples/primer3/primer_template_mispriming_output
  bin/primer3
  share/primer3/Copyright
  @dirrm share/primer3
  %%PORTDOCS%%@dirrm %%DOCSDIR%%/
--- primer3-diff ends here ---


>Release-Note:
>Audit-Trail:
>Unformatted:

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