From owner-freebsd-ports-bugs@FreeBSD.ORG Wed Apr 2 17:20:02 2008 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id D3694106564A for ; Wed, 2 Apr 2008 17:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id BD2BE8FC19 for ; Wed, 2 Apr 2008 17:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.2/8.14.2) with ESMTP id m32HK2TG078716 for ; Wed, 2 Apr 2008 17:20:02 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.2/8.14.1/Submit) id m32HK2F7078715; Wed, 2 Apr 2008 17:20:02 GMT (envelope-from gnats) Date: Wed, 2 Apr 2008 17:20:02 GMT Message-Id: <200804021720.m32HK2F7078715@freefall.freebsd.org> To: freebsd-ports-bugs@FreeBSD.org From: Fernan Aguero Cc: Subject: Re: ports/122374: [Update] biology/primer3 : update to 1.1.3 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Fernan Aguero List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 02 Apr 2008 17:20:03 -0000 The following reply was made to PR ports/122374; it has been noted by GNATS. From: Fernan Aguero To: bug-followup@FreeBSD.ORG Cc: edwin@FreeBSD.ORG, wenheping@gmail.com Subject: Re: ports/122374: [Update] biology/primer3 : update to 1.1.3 Date: Wed, 2 Apr 2008 14:06:34 -0300 --9amGYk9869ThD9tj Content-Type: text/plain; charset=us-ascii Content-Disposition: inline > Maintainer of biology/primer3, > > Please note that PR ports/122374 has just been submitted. > > If it contains a patch for an upgrade, an enhancement or a bug fix > you agree on, reply to this email stating that you approve the patch > and a committer will take care of it. > > The full text of the PR can be found at: > http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/122374 > > -- > Edwin Groothuis via the GNATS Auto Assign Tool > edwin@FreeBSD.org Please find a revised patch using PLIST macros. Thanks! --9amGYk9869ThD9tj Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="primer3.diff" diff -ruN --exclude CVS /usr/ports/biology/primer3/Makefile primer3/Makefile --- /usr/ports/biology/primer3/Makefile Fri Dec 29 20:40:53 2006 +++ primer3/Makefile Wed Apr 2 14:01:15 2008 @@ -6,17 +6,17 @@ # PORTNAME= primer3 -PORTVERSION= 1.0.1 +PORTVERSION= 1.1.3 CATEGORIES= biology -MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} -MASTER_SITE_SUBDIR= ${PORTNAME} -DISTNAME= ${PORTNAME}_${PORTVERSION} +MASTER_SITES= SF +DISTNAME= ${PORTNAME}-${PORTVERSION} MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= Primer3 helps to choose primers for PCR reactions +USE_GMAKE= yes WRKSRC= ${WRKDIR}/${DISTNAME}/src -DOCUMENTS= README.${PORTNAME}_${PORTVERSION}.txt example +DOCUMENTS= README.txt example post-patch: @${REINPLACE_CMD} \ @@ -29,7 +29,7 @@ do-install: @${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3 @${MKDIR} ${DATADIR} - @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright.txt ${DATADIR} + @${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/COPYING.txt ${DATADIR} .if !defined(NOPORTDOCS) @${MKDIR} ${DOCSDIR} .for file in ${DOCUMENTS} @@ -42,6 +42,6 @@ .endif post-install: - @${CAT} ${DATADIR}/Copyright.txt + @${CAT} ${DATADIR}/COPYING.txt .include diff -ruN --exclude CVS /usr/ports/biology/primer3/distinfo primer3/distinfo --- /usr/ports/biology/primer3/distinfo Fri Dec 29 20:40:53 2006 +++ primer3/distinfo Wed Apr 2 14:01:15 2008 @@ -1,3 +1,3 @@ -MD5 (primer3_1.0.1.tar.gz) = 4fa33b8667cec1b88f1516d175eb1bed -SHA256 (primer3_1.0.1.tar.gz) = 2f7641d66d75b4830a01d31dbc96c61ffad2b1f047287009906902558a9e165e -SIZE (primer3_1.0.1.tar.gz) = 902576 +MD5 (primer3-1.1.3.tar.gz) = 3d027d5dcbdb88c0f9622938f9d38534 +SHA256 (primer3-1.1.3.tar.gz) = ad3071fd1a8da8caae6f30b799cae4b7e53f00476ca0441b37bddf8995d1fa38 +SIZE (primer3-1.1.3.tar.gz) = 943678 diff -ruN --exclude CVS /usr/ports/biology/primer3/pkg-plist primer3/pkg-plist --- /usr/ports/biology/primer3/pkg-plist Fri Dec 29 20:40:53 2006 +++ primer3/pkg-plist Wed Apr 2 14:02:01 2008 @@ -1,7 +1,7 @@ bin/primer3 -%%PORTDOCS%%%%DOCSDIR%%/README.primer3_1.0.1.txt +%%PORTDOCS%%%%DOCSDIR%%/README.txt %%PORTDOCS%%%%DOCSDIR%%/example -%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_gen.pl +%%PORTDOCS%%%%EXAMPLESDIR%%/Makefile %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_input %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_input %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_score_output @@ -14,20 +14,14 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production.lib %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Ns.lib %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Xs.lib +%%PORTDOCS%%%%EXAMPLESDIR%%/oligotm.txt +%%PORTDOCS%%%%EXAMPLESDIR%%/oligotm_test.pl %%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_input %%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_output %%PORTDOCS%%%%EXAMPLESDIR%%/p3test.pl %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_input -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.int -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-03.txt.for @@ -40,8 +34,16 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-21.txt.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP04-07.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP04-07.txt.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.int +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/targets_test.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/targets_test.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_formatted_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_output @@ -52,224 +54,236 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_check_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_end_pathology_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_end_pathology_output +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.in 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-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out2 -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out2 +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.in +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out2 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_input -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_input @@ -278,22 +292,10 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.int -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.for -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.rev -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.int %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.rev @@ -303,18 +305,29 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.int %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.int +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.rev +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.for +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.for %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.rev %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_formatted_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_formatted_output -%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_formatted_output @@ -327,8 +340,8 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_output +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_output -%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_formatted_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_input @@ -347,15 +360,20 @@ %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_formatted_output %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_input %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_output +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_formatted_output +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_input +%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_output +%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib2 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib3 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib4 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib5 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib6 -%%DATADIR%%/Copyright.txt -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%EXAMPLESDIR%%/primer1_list_last -@dirrm %%EXAMPLESDIR%%/primer_global_err -@dirrm %%EXAMPLESDIR%%/primer_list_last -@dirrm %%EXAMPLESDIR%% +%%PORTDOCS%%%%EXAMPLESDIR%%/vgrep.pl +%%DATADIR%%/COPYING.txt @dirrm %%DATADIR%% +@dirrm %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last +@dirrm %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err +@dirrm %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last +@dirrm %%PORTDOCS%%%%EXAMPLESDIR%% +@dirrm %%PORTDOCS%%%%DOCSDIR%% --9amGYk9869ThD9tj--