Sat Aug 12 14:49:18 2023 UTC ()
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


(bacon)
diff -r1.12 -r1.13 pkgsrc/biology/biolibc/Makefile
diff -r1.11 -r1.12 pkgsrc/biology/biolibc/PLIST
diff -r1.11 -r1.12 pkgsrc/biology/biolibc/buildlink3.mk
diff -r1.13 -r1.14 pkgsrc/biology/biolibc/distinfo
cvs diff -r1.12 -r1.13 pkgsrc/biology/biolibc/Makefile (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/Makefile 2023/06/14 18:41:24 1.12
+++ pkgsrc/biology/biolibc/Makefile 2023/08/12 14:49:18 1.13
@@ -1,19 +1,18 @@ @@ -1,19 +1,18 @@
1# $NetBSD: Makefile,v 1.12 2023/06/14 18:41:24 bacon Exp $ 1# $NetBSD: Makefile,v 1.13 2023/08/12 14:49:18 bacon Exp $
2 2
3DISTNAME= biolibc-0.2.4.3 3DISTNAME= biolibc-0.2.5
4CATEGORIES= biology 4CATEGORIES= biology
5MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/} 5MASTER_SITES= ${MASTER_SITE_GITHUB:=auerlab/}
6GITHUB_TAG= 3dc616d0903a024cb48f5f646680edf62c9eeeb1 
7 6
8OWNER= bacon@NetBSD.org 7OWNER= bacon@NetBSD.org
9HOMEPAGE= https://github.com/auerlab/biolibc 8HOMEPAGE= https://github.com/auerlab/biolibc
10COMMENT= Low-level high-performance bioinformatics library 9COMMENT= Low-level high-performance bioinformatics library
11LICENSE= 2-clause-bsd 10LICENSE= 2-clause-bsd
12 11
13.include "../../mk/bsd.prefs.mk" 12.include "../../mk/bsd.prefs.mk"
14 13
15.if ${OPSYS} == Darwin 14.if ${OPSYS} == Darwin
16BUILD_TARGET= apple 15BUILD_TARGET= apple
17INSTALL_TARGET= apple-install 16INSTALL_TARGET= apple-install
18.else 17.else
19INSTALL_TARGET= install-strip 18INSTALL_TARGET= install-strip
cvs diff -r1.11 -r1.12 pkgsrc/biology/biolibc/PLIST (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/PLIST 2023/06/14 18:41:24 1.11
+++ pkgsrc/biology/biolibc/PLIST 2023/08/12 14:49:18 1.12
@@ -1,44 +1,44 @@ @@ -1,44 +1,44 @@
1@comment $NetBSD: PLIST,v 1.11 2023/06/14 18:41:24 bacon Exp $ 1@comment $NetBSD: PLIST,v 1.12 2023/08/12 14:49:18 bacon Exp $
2include/biolibc/align-accessors.h 2include/biolibc/align-accessors.h
3include/biolibc/align-mutators.h 3include/biolibc/align-mutators.h
4include/biolibc/align-rvs.h 4include/biolibc/align-rvs.h
5include/biolibc/align.h 5include/biolibc/align.h
6include/biolibc/bed-accessors.h 6include/biolibc/bed-accessors.h
7include/biolibc/bed-mutators.h 7include/biolibc/bed-mutators.h
8include/biolibc/bed-rvs.h 8include/biolibc/bed-rvs.h
9include/biolibc/bed.h 9include/biolibc/bed.h
10include/biolibc/biolibc.h 10include/biolibc/biolibc.h
11include/biolibc/biostring.h 11include/biolibc/biostring.h
12include/biolibc/fasta-accessors.h 12include/biolibc/fasta-accessors.h
13include/biolibc/fasta-mutators.h 13include/biolibc/fasta-mutators.h
14include/biolibc/fasta-rvs.h 14include/biolibc/fasta-rvs.h
15include/biolibc/fasta.h 15include/biolibc/fasta.h
16include/biolibc/fastq-accessors.h 16include/biolibc/fastq-accessors.h
17include/biolibc/fastq-mutators.h 17include/biolibc/fastq-mutators.h
18include/biolibc/fastq-rvs.h 18include/biolibc/fastq-rvs.h
19include/biolibc/fastq.h 19include/biolibc/fastq.h
20include/biolibc/fastx-accessors.h 20include/biolibc/fastx-accessors.h
21include/biolibc/fastx-mutators.h 21include/biolibc/fastx-mutators.h
22include/biolibc/fastx-rvs.h 22include/biolibc/fastx-rvs.h
23include/biolibc/fastx.h 23include/biolibc/fastx.h
24include/biolibc/gff-accessors.h 24include/biolibc/gff3-accessors.h
25include/biolibc/gff-index-accessors.h 25include/biolibc/gff3-index-accessors.h
26include/biolibc/gff-index-mutators.h 26include/biolibc/gff3-index-mutators.h
27include/biolibc/gff-index-rvs.h 27include/biolibc/gff3-index-rvs.h
28include/biolibc/gff-index.h 28include/biolibc/gff3-index.h
29include/biolibc/gff-mutators.h 29include/biolibc/gff3-mutators.h
30include/biolibc/gff-rvs.h 30include/biolibc/gff3-rvs.h
31include/biolibc/gff.h 31include/biolibc/gff3.h
32include/biolibc/overlap-accessors.h 32include/biolibc/overlap-accessors.h
33include/biolibc/overlap-mutators.h 33include/biolibc/overlap-mutators.h
34include/biolibc/overlap-rvs.h 34include/biolibc/overlap-rvs.h
35include/biolibc/overlap.h 35include/biolibc/overlap.h
36include/biolibc/pos-list-accessors.h 36include/biolibc/pos-list-accessors.h
37include/biolibc/pos-list-mutators.h 37include/biolibc/pos-list-mutators.h
38include/biolibc/pos-list-rvs.h 38include/biolibc/pos-list-rvs.h
39include/biolibc/pos-list.h 39include/biolibc/pos-list.h
40include/biolibc/sam-accessors.h 40include/biolibc/sam-accessors.h
41include/biolibc/sam-buff-accessors.h 41include/biolibc/sam-buff-accessors.h
42include/biolibc/sam-buff-mutators.h 42include/biolibc/sam-buff-mutators.h
43include/biolibc/sam-buff-rvs.h 43include/biolibc/sam-buff-rvs.h
44include/biolibc/sam-buff.h 44include/biolibc/sam-buff.h
@@ -312,81 +312,81 @@ man/man3/bl_fastx_desc_len.3 @@ -312,81 +312,81 @@ man/man3/bl_fastx_desc_len.3
312man/man3/bl_fastx_free.3 312man/man3/bl_fastx_free.3
313man/man3/bl_fastx_init.3 313man/man3/bl_fastx_init.3
314man/man3/bl_fastx_plus.3 314man/man3/bl_fastx_plus.3
315man/man3/bl_fastx_plus_len.3 315man/man3/bl_fastx_plus_len.3
316man/man3/bl_fastx_qual.3 316man/man3/bl_fastx_qual.3
317man/man3/bl_fastx_qual_len.3 317man/man3/bl_fastx_qual_len.3
318man/man3/bl_fastx_read.3 318man/man3/bl_fastx_read.3
319man/man3/bl_fastx_seq.3 319man/man3/bl_fastx_seq.3
320man/man3/bl_fastx_seq_len.3 320man/man3/bl_fastx_seq_len.3
321man/man3/bl_fastx_set_fasta.3 321man/man3/bl_fastx_set_fasta.3
322man/man3/bl_fastx_set_fastq.3 322man/man3/bl_fastx_set_fastq.3
323man/man3/bl_fastx_set_format.3 323man/man3/bl_fastx_set_format.3
324man/man3/bl_fastx_write.3 324man/man3/bl_fastx_write.3
325man/man3/bl_gff_copy.3 325man/man3/bl_gff3_copy.3
326man/man3/bl_gff_copy_header.3 326man/man3/bl_gff3_copy_header.3
327man/man3/bl_gff_dup.3 327man/man3/bl_gff3_dup.3
328man/man3/bl_gff_extract_attribute.3 328man/man3/bl_gff3_extract_attribute.3
329man/man3/bl_gff_free.3 329man/man3/bl_gff3_free.3
330man/man3/bl_gff_index_add.3 330man/man3/bl_gff3_index_add.3
331man/man3/bl_gff_index_seek_reverse.3 331man/man3/bl_gff3_index_seek_reverse.3
332man/man3/bl_gff_index_set_array_size.3 332man/man3/bl_gff3_index_set_array_size.3
333man/man3/bl_gff_index_set_count.3 333man/man3/bl_gff3_index_set_count.3
334man/man3/bl_gff_index_set_end.3 334man/man3/bl_gff3_index_set_end.3
335man/man3/bl_gff_index_set_end_ae.3 335man/man3/bl_gff3_index_set_end_ae.3
336man/man3/bl_gff_index_set_end_cpy.3 336man/man3/bl_gff3_index_set_end_cpy.3
337man/man3/bl_gff_index_set_file_pos.3 337man/man3/bl_gff3_index_set_file_pos.3
338man/man3/bl_gff_index_set_file_pos_ae.3 338man/man3/bl_gff3_index_set_file_pos_ae.3
339man/man3/bl_gff_index_set_file_pos_cpy.3 339man/man3/bl_gff3_index_set_file_pos_cpy.3
340man/man3/bl_gff_index_set_seqid.3 340man/man3/bl_gff3_index_set_seqid.3
341man/man3/bl_gff_index_set_seqid_ae.3 341man/man3/bl_gff3_index_set_seqid_ae.3
342man/man3/bl_gff_index_set_seqid_cpy.3 342man/man3/bl_gff3_index_set_seqid_cpy.3
343man/man3/bl_gff_index_set_start.3 343man/man3/bl_gff3_index_set_start.3
344man/man3/bl_gff_index_set_start_ae.3 344man/man3/bl_gff3_index_set_start_ae.3
345man/man3/bl_gff_index_set_start_cpy.3 345man/man3/bl_gff3_index_set_start_cpy.3
346man/man3/bl_gff_init.3 346man/man3/bl_gff3_init.3
347man/man3/bl_gff_read.3 347man/man3/bl_gff3_read.3
348man/man3/bl_gff_sam_cmp.3 348man/man3/bl_gff3_sam_cmp.3
349man/man3/bl_gff_sam_overlap.3 349man/man3/bl_gff3_sam_overlap.3
350man/man3/bl_gff_set_attributes.3 350man/man3/bl_gff3_set_attributes.3
351man/man3/bl_gff_set_attributes_ae.3 351man/man3/bl_gff3_set_attributes_ae.3
352man/man3/bl_gff_set_attributes_array_size.3 352man/man3/bl_gff3_set_attributes_array_size.3
353man/man3/bl_gff_set_attributes_cpy.3 353man/man3/bl_gff3_set_attributes_cpy.3
354man/man3/bl_gff_set_attributes_len.3 354man/man3/bl_gff3_set_attributes_len.3
355man/man3/bl_gff_set_end.3 355man/man3/bl_gff3_set_end.3
356man/man3/bl_gff_set_feature_id.3 356man/man3/bl_gff3_set_feature_id.3
357man/man3/bl_gff_set_feature_id_ae.3 357man/man3/bl_gff3_set_feature_id_ae.3
358man/man3/bl_gff_set_feature_id_cpy.3 358man/man3/bl_gff3_set_feature_id_cpy.3
359man/man3/bl_gff_set_feature_name.3 359man/man3/bl_gff3_set_feature_name.3
360man/man3/bl_gff_set_feature_name_ae.3 360man/man3/bl_gff3_set_feature_name_ae.3
361man/man3/bl_gff_set_feature_name_cpy.3 361man/man3/bl_gff3_set_feature_name_cpy.3
362man/man3/bl_gff_set_feature_parent.3 362man/man3/bl_gff3_set_feature_parent.3
363man/man3/bl_gff_set_feature_parent_ae.3 363man/man3/bl_gff3_set_feature_parent_ae.3
364man/man3/bl_gff_set_feature_parent_cpy.3 364man/man3/bl_gff3_set_feature_parent_cpy.3
365man/man3/bl_gff_set_file_pos.3 365man/man3/bl_gff3_set_file_pos.3
366man/man3/bl_gff_set_gene_name_cpy.3 366man/man3/bl_gff3_set_gene_name_cpy.3
367man/man3/bl_gff_set_phase.3 367man/man3/bl_gff3_set_phase.3
368man/man3/bl_gff_set_score.3 368man/man3/bl_gff3_set_score.3
369man/man3/bl_gff_set_seqid_ae.3 369man/man3/bl_gff3_set_seqid_ae.3
370man/man3/bl_gff_set_seqid_cpy.3 370man/man3/bl_gff3_set_seqid_cpy.3
371man/man3/bl_gff_set_source_ae.3 371man/man3/bl_gff3_set_source_ae.3
372man/man3/bl_gff_set_source_cpy.3 372man/man3/bl_gff3_set_source_cpy.3
373man/man3/bl_gff_set_start.3 373man/man3/bl_gff3_set_start.3
374man/man3/bl_gff_set_strand.3 374man/man3/bl_gff3_set_strand.3
375man/man3/bl_gff_set_type_ae.3 375man/man3/bl_gff3_set_type_ae.3
376man/man3/bl_gff_set_type_cpy.3 376man/man3/bl_gff3_set_type_cpy.3
377man/man3/bl_gff_skip_header.3 377man/man3/bl_gff3_skip_header.3
378man/man3/bl_gff_to_bed.3 378man/man3/bl_gff3_to_bed.3
379man/man3/bl_gff_write.3 379man/man3/bl_gff3_write.3
380man/man3/bl_next_start_codon.3 380man/man3/bl_next_start_codon.3
381man/man3/bl_next_stop_codon.3 381man/man3/bl_next_stop_codon.3
382man/man3/bl_overlap_print.3 382man/man3/bl_overlap_print.3
383man/man3/bl_overlap_set_all.3 383man/man3/bl_overlap_set_all.3
384man/man3/bl_overlap_set_feature1_len.3 384man/man3/bl_overlap_set_feature1_len.3
385man/man3/bl_overlap_set_feature2_len.3 385man/man3/bl_overlap_set_feature2_len.3
386man/man3/bl_overlap_set_overlap_end.3 386man/man3/bl_overlap_set_overlap_end.3
387man/man3/bl_overlap_set_overlap_len.3 387man/man3/bl_overlap_set_overlap_len.3
388man/man3/bl_overlap_set_overlap_start.3 388man/man3/bl_overlap_set_overlap_start.3
389man/man3/bl_pos_list_add_position.3 389man/man3/bl_pos_list_add_position.3
390man/man3/bl_pos_list_allocate.3 390man/man3/bl_pos_list_allocate.3
391man/man3/bl_pos_list_free.3 391man/man3/bl_pos_list_free.3
392man/man3/bl_pos_list_from_csv.3 392man/man3/bl_pos_list_from_csv.3
cvs diff -r1.11 -r1.12 pkgsrc/biology/biolibc/buildlink3.mk (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/buildlink3.mk 2023/06/14 18:41:24 1.11
+++ pkgsrc/biology/biolibc/buildlink3.mk 2023/08/12 14:49:18 1.12
@@ -1,14 +1,14 @@ @@ -1,14 +1,14 @@
1# $NetBSD: buildlink3.mk,v 1.11 2023/06/14 18:41:24 bacon Exp $ 1# $NetBSD: buildlink3.mk,v 1.12 2023/08/12 14:49:18 bacon Exp $
2 2
3BUILDLINK_TREE+= biolibc 3BUILDLINK_TREE+= biolibc
4 4
5.if !defined(BIOLIBC_BUILDLINK3_MK) 5.if !defined(BIOLIBC_BUILDLINK3_MK)
6BIOLIBC_BUILDLINK3_MK:= 6BIOLIBC_BUILDLINK3_MK:=
7 7
8BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.4.3 8BUILDLINK_API_DEPENDS.biolibc+= biolibc>=0.2.5
9BUILDLINK_PKGSRCDIR.biolibc?= ../../biology/biolibc 9BUILDLINK_PKGSRCDIR.biolibc?= ../../biology/biolibc
10 10
11.include "../../devel/libxtend/buildlink3.mk" 11.include "../../devel/libxtend/buildlink3.mk"
12.endif # BIOLIBC_BUILDLINK3_MK 12.endif # BIOLIBC_BUILDLINK3_MK
13 13
14BUILDLINK_TREE+= -biolibc 14BUILDLINK_TREE+= -biolibc
cvs diff -r1.13 -r1.14 pkgsrc/biology/biolibc/distinfo (expand / switch to unified diff)

--- pkgsrc/biology/biolibc/distinfo 2023/06/14 18:41:24 1.13
+++ pkgsrc/biology/biolibc/distinfo 2023/08/12 14:49:18 1.14
@@ -1,5 +1,5 @@ @@ -1,5 +1,5 @@
1$NetBSD: distinfo,v 1.13 2023/06/14 18:41:24 bacon Exp $ 1$NetBSD: distinfo,v 1.14 2023/08/12 14:49:18 bacon Exp $
2 2
3BLAKE2s (biolibc-0.2.4.3-3dc616d0903a024cb48f5f646680edf62c9eeeb1.tar.gz) = 61670347aa31e917a033129b1b227b6dd60c7e50d5f9e1979e4aee9c23cb3af3 3BLAKE2s (biolibc-0.2.5.tar.gz) = ea2f46e8c6b26da34c2d10603ae1974e680e5df3a1ce8110235dc1afe1d24ec5
4SHA512 (biolibc-0.2.4.3-3dc616d0903a024cb48f5f646680edf62c9eeeb1.tar.gz) = af53733a126b224e3b195a20dc8bfcbb250d5bd2e2526db10e941cbda3ec730f9f431522bb4b5d1564481d11dcdf16848e46ad544f151e2a78d89a4dc76ab6a8 4SHA512 (biolibc-0.2.5.tar.gz) = 647d8b19d007775f140b4b2d23bc8048ee6896e34b2d046109c71b1be13955a79991bb7dfbda8887db852265825d18b58e16195173624efb9bd19e6d1f5d13ba
5Size (biolibc-0.2.4.3-3dc616d0903a024cb48f5f646680edf62c9eeeb1.tar.gz) = 141047 bytes 5Size (biolibc-0.2.5.tar.gz) = 141426 bytes