From nobody Fri Aug 11 20:44:46 2023 X-Original-To: dev-commits-ports-main@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4RMwlL4qtlz4mRY9; Fri, 11 Aug 2023 20:44:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4RMwlL4PMSz3Vlk; Fri, 11 Aug 2023 20:44:46 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691786686; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=NUkt4Nq4Gfo38veVGzcgQb79O4yS9dF4p9peV4Ldzbw=; b=SRoECBpcVtWMInfVLoUaL7MbVzfF3hRNuPaLq59r7AQur3FV8EOzSPvucpB3rJVEggYMsQ LC/M73GaftxpfEx3U71AL/ZK0jkHNJcTHYM/cz5Jp4U9WMh6i7RnPi34SoNbJIIkY30U0X 4nNIUFoS8eumszxCNZKquLNOn/+gev4+eO5D5Y5rk9l29uH3K9GD6X8Y+myW1FV5fsvYW8 Kyz5K7JkEMoknGGQ2hqbiwNdmCdm7PrMVlLqNfNX98+kd/8rPipFXZAiaV9HyyrQArX0OY l3x3jOiyy/HSweMxMmC9aR8Pvs8yE1DpO4OiZG4JiIc/MY1Qo8CKU3u2CsOFKA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1691786686; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=NUkt4Nq4Gfo38veVGzcgQb79O4yS9dF4p9peV4Ldzbw=; b=buRRUVMoy1Qo9wv75FHWSYzsHVVW9VBvXc1mhB+6OxtLNXfWT/352L/f+BJPxAsLw48sse vxp8eEmb9oLvDxEDwSqmxqVMHvbY3Lhme3nnnmyLBx+2xKgA+Ei3bsNFDkLA9WNK1gtrTO l3keENqbSqX9DUSfiVmp3EF9cHOcTsSXOF2Bsh4tCbPXHatosO54GZCKcedyUnfWiX4Lew hS+LDN1+BzAdBZqd3cSU0jaOoGjxemEf7X4+hjZFdUOMO0BH8VyhtyzmfFqXT624O/y5ZA YySoQKNLu8/YPNiulHXBgL+/1uRRlGCNhFS132xFx8qlRwwtjNzE2pb4j9GwiA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1691786686; a=rsa-sha256; cv=none; b=t1/koTNI/vY/ltvSM282dCE5b4aG0HT+N/Hpqy0vHS3c5/ndSI78Xh8CVus0MBYHbCogc9 +sKVoLG2XqBOZglZYMj8fcQBg1LNVes7fXRaA1EshpwOseOwGRoUYePycunR2Bu6RUKV1R 2Vyl7J571sXYTgXBkghcG01UmyPNfMQybOSsJuKeLFTQaU2E6geS69Zip2AB71EMY284VH kEoPoXsbcbP29qDRe3jPIRN2+gxYe0SVsGaS52VfLU5Y3hUuTNMlueRwrejNYdPVc5xvrW GQo0Ly8TXYMhdLb88nZN+/YDnUx29zb5oklUg7XAWMoDNDVNOa8Gn/NVt77Z7w== ARC-Authentication-Results: i=1; mx1.freebsd.org; none Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4RMwlL3RvMztD7; Fri, 11 Aug 2023 20:44:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 37BKikDf055131; Fri, 11 Aug 2023 20:44:46 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 37BKikup055128; Fri, 11 Aug 2023 20:44:46 GMT (envelope-from git) Date: Fri, 11 Aug 2023 20:44:46 GMT Message-Id: <202308112044.37BKikup055128@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: c978aad1b084 - main - biology/biolibc: Update to 0.2.5 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: c978aad1b08481c3d43e9e3a274472b3874c4970 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=c978aad1b08481c3d43e9e3a274472b3874c4970 commit c978aad1b08481c3d43e9e3a274472b3874c4970 Author: Jason W. Bacon AuthorDate: 2023-08-11 20:35:11 +0000 Commit: Jason W. Bacon CommitDate: 2023-08-11 20:35:11 +0000 biology/biolibc: Update to 0.2.5 Make header files C++ compatible (extern C) bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p bl_gff_extract_attribute(): Improve performance gff -> gff3 to distinguish from past and future GFF specs Silence some compiler warnings Changes: https://github.com/auerlab/biolibc/releases --- biology/biolibc/Makefile | 3 +- biology/biolibc/distinfo | 6 +-- biology/biolibc/pkg-plist | 126 +++++++++++++++++++++++----------------------- 3 files changed, 67 insertions(+), 68 deletions(-) diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile index faa55208aa26..e107ad437a58 100644 --- a/biology/biolibc/Makefile +++ b/biology/biolibc/Makefile @@ -1,6 +1,5 @@ PORTNAME= biolibc -DISTVERSION= 0.2.4-3 -DISTVERSIONSUFFIX= -g3dc616d +DISTVERSION= 0.2.5 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/biolibc/distinfo b/biology/biolibc/distinfo index 983b7255c1b5..11c338872a43 100644 --- a/biology/biolibc/distinfo +++ b/biology/biolibc/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1686231530 -SHA256 (auerlab-biolibc-0.2.4-3-g3dc616d_GH0.tar.gz) = a1fd8a7afce75de928ae06711e479f1c653ffd75344b52ee3dfa6ded8cbb6df6 -SIZE (auerlab-biolibc-0.2.4-3-g3dc616d_GH0.tar.gz) = 141067 +TIMESTAMP = 1691785366 +SHA256 (auerlab-biolibc-0.2.5_GH0.tar.gz) = 5273dbf4e5135ac8f11e503c3ef516ec1c73906b1ec196a0a28606d88d3d394a +SIZE (auerlab-biolibc-0.2.5_GH0.tar.gz) = 141426 diff --git a/biology/biolibc/pkg-plist b/biology/biolibc/pkg-plist index dfbe6a49d997..a5a415d739ef 100644 --- a/biology/biolibc/pkg-plist +++ b/biology/biolibc/pkg-plist @@ -20,14 +20,14 @@ include/biolibc/fastx-accessors.h include/biolibc/fastx-mutators.h include/biolibc/fastx-rvs.h include/biolibc/fastx.h -include/biolibc/gff-accessors.h -include/biolibc/gff-index-accessors.h -include/biolibc/gff-index-mutators.h -include/biolibc/gff-index-rvs.h -include/biolibc/gff-index.h -include/biolibc/gff-mutators.h -include/biolibc/gff-rvs.h -include/biolibc/gff.h +include/biolibc/gff3-accessors.h +include/biolibc/gff3-index-accessors.h +include/biolibc/gff3-index-mutators.h +include/biolibc/gff3-index-rvs.h +include/biolibc/gff3-index.h +include/biolibc/gff3-mutators.h +include/biolibc/gff3-rvs.h +include/biolibc/gff3.h include/biolibc/overlap-accessors.h include/biolibc/overlap-mutators.h include/biolibc/overlap-rvs.h @@ -321,61 +321,61 @@ man/man3/bl_fastx_set_fasta.3.gz man/man3/bl_fastx_set_fastq.3.gz man/man3/bl_fastx_set_format.3.gz man/man3/bl_fastx_write.3.gz -man/man3/bl_gff_copy.3.gz -man/man3/bl_gff_copy_header.3.gz -man/man3/bl_gff_dup.3.gz -man/man3/bl_gff_extract_attribute.3.gz -man/man3/bl_gff_free.3.gz -man/man3/bl_gff_index_add.3.gz -man/man3/bl_gff_index_seek_reverse.3.gz -man/man3/bl_gff_index_set_array_size.3.gz -man/man3/bl_gff_index_set_count.3.gz -man/man3/bl_gff_index_set_end.3.gz -man/man3/bl_gff_index_set_end_ae.3.gz -man/man3/bl_gff_index_set_end_cpy.3.gz -man/man3/bl_gff_index_set_file_pos.3.gz -man/man3/bl_gff_index_set_file_pos_ae.3.gz -man/man3/bl_gff_index_set_file_pos_cpy.3.gz -man/man3/bl_gff_index_set_seqid.3.gz -man/man3/bl_gff_index_set_seqid_ae.3.gz -man/man3/bl_gff_index_set_seqid_cpy.3.gz -man/man3/bl_gff_index_set_start.3.gz -man/man3/bl_gff_index_set_start_ae.3.gz -man/man3/bl_gff_index_set_start_cpy.3.gz -man/man3/bl_gff_init.3.gz -man/man3/bl_gff_read.3.gz -man/man3/bl_gff_sam_cmp.3.gz -man/man3/bl_gff_sam_overlap.3.gz -man/man3/bl_gff_set_attributes.3.gz -man/man3/bl_gff_set_attributes_ae.3.gz -man/man3/bl_gff_set_attributes_array_size.3.gz -man/man3/bl_gff_set_attributes_cpy.3.gz -man/man3/bl_gff_set_attributes_len.3.gz -man/man3/bl_gff_set_end.3.gz -man/man3/bl_gff_set_feature_id.3.gz -man/man3/bl_gff_set_feature_id_ae.3.gz -man/man3/bl_gff_set_feature_id_cpy.3.gz -man/man3/bl_gff_set_feature_name.3.gz -man/man3/bl_gff_set_feature_name_ae.3.gz -man/man3/bl_gff_set_feature_name_cpy.3.gz -man/man3/bl_gff_set_feature_parent.3.gz -man/man3/bl_gff_set_feature_parent_ae.3.gz -man/man3/bl_gff_set_feature_parent_cpy.3.gz -man/man3/bl_gff_set_file_pos.3.gz -man/man3/bl_gff_set_gene_name_cpy.3.gz -man/man3/bl_gff_set_phase.3.gz -man/man3/bl_gff_set_score.3.gz -man/man3/bl_gff_set_seqid_ae.3.gz -man/man3/bl_gff_set_seqid_cpy.3.gz -man/man3/bl_gff_set_source_ae.3.gz -man/man3/bl_gff_set_source_cpy.3.gz -man/man3/bl_gff_set_start.3.gz -man/man3/bl_gff_set_strand.3.gz -man/man3/bl_gff_set_type_ae.3.gz -man/man3/bl_gff_set_type_cpy.3.gz -man/man3/bl_gff_skip_header.3.gz -man/man3/bl_gff_to_bed.3.gz -man/man3/bl_gff_write.3.gz +man/man3/bl_gff3_copy.3.gz +man/man3/bl_gff3_copy_header.3.gz +man/man3/bl_gff3_dup.3.gz +man/man3/bl_gff3_extract_attribute.3.gz +man/man3/bl_gff3_free.3.gz +man/man3/bl_gff3_index_add.3.gz +man/man3/bl_gff3_index_seek_reverse.3.gz +man/man3/bl_gff3_index_set_array_size.3.gz +man/man3/bl_gff3_index_set_count.3.gz +man/man3/bl_gff3_index_set_end.3.gz +man/man3/bl_gff3_index_set_end_ae.3.gz +man/man3/bl_gff3_index_set_end_cpy.3.gz +man/man3/bl_gff3_index_set_file_pos.3.gz +man/man3/bl_gff3_index_set_file_pos_ae.3.gz +man/man3/bl_gff3_index_set_file_pos_cpy.3.gz +man/man3/bl_gff3_index_set_seqid.3.gz +man/man3/bl_gff3_index_set_seqid_ae.3.gz +man/man3/bl_gff3_index_set_seqid_cpy.3.gz +man/man3/bl_gff3_index_set_start.3.gz +man/man3/bl_gff3_index_set_start_ae.3.gz +man/man3/bl_gff3_index_set_start_cpy.3.gz +man/man3/bl_gff3_init.3.gz +man/man3/bl_gff3_read.3.gz +man/man3/bl_gff3_sam_cmp.3.gz +man/man3/bl_gff3_sam_overlap.3.gz +man/man3/bl_gff3_set_attributes.3.gz +man/man3/bl_gff3_set_attributes_ae.3.gz +man/man3/bl_gff3_set_attributes_array_size.3.gz +man/man3/bl_gff3_set_attributes_cpy.3.gz +man/man3/bl_gff3_set_attributes_len.3.gz +man/man3/bl_gff3_set_end.3.gz +man/man3/bl_gff3_set_feature_id.3.gz +man/man3/bl_gff3_set_feature_id_ae.3.gz +man/man3/bl_gff3_set_feature_id_cpy.3.gz +man/man3/bl_gff3_set_feature_name.3.gz +man/man3/bl_gff3_set_feature_name_ae.3.gz +man/man3/bl_gff3_set_feature_name_cpy.3.gz +man/man3/bl_gff3_set_feature_parent.3.gz +man/man3/bl_gff3_set_feature_parent_ae.3.gz +man/man3/bl_gff3_set_feature_parent_cpy.3.gz +man/man3/bl_gff3_set_file_pos.3.gz +man/man3/bl_gff3_set_gene_name_cpy.3.gz +man/man3/bl_gff3_set_phase.3.gz +man/man3/bl_gff3_set_score.3.gz +man/man3/bl_gff3_set_seqid_ae.3.gz +man/man3/bl_gff3_set_seqid_cpy.3.gz +man/man3/bl_gff3_set_source_ae.3.gz +man/man3/bl_gff3_set_source_cpy.3.gz +man/man3/bl_gff3_set_start.3.gz +man/man3/bl_gff3_set_strand.3.gz +man/man3/bl_gff3_set_type_ae.3.gz +man/man3/bl_gff3_set_type_cpy.3.gz +man/man3/bl_gff3_skip_header.3.gz +man/man3/bl_gff3_to_bed.3.gz +man/man3/bl_gff3_write.3.gz man/man3/bl_next_start_codon.3.gz man/man3/bl_next_stop_codon.3.gz man/man3/bl_overlap_print.3.gz