Index: head/biology/iolib/Makefile =================================================================== --- head/biology/iolib/Makefile (revision 480877) +++ head/biology/iolib/Makefile (revision 480878) @@ -1,28 +1,29 @@ # Created by: Wen Heping # $FreeBSD$ PORTNAME= io_lib DISTVERSIONPREFIX= ${PORTNAME}- -DISTVERSION= 1-14-9 +DISTVERSION= 1-14-10 CATEGORIES= biology MAINTAINER= danilo@FreeBSD.org COMMENT= General purpose trace file (and Experiment File) reading interface LICENSE= BSD3CLAUSE BROKEN_mips= fails to compile: bgzip.c: error: invalid operands to binary & BROKEN_mips64= fails to compile: bgzip.c: error: invalid operands to binary & BROKEN_powerpc64= fails to compile: bgzip.c: error: invalid operands to binary & LIB_DEPENDS= libcurl.so:ftp/curl +USES= autoreconf gmake libtool + USE_GITHUB= yes GH_ACCOUNT= jkbonfield -USES= autoreconf gmake libtool GNU_CONFIGURE= yes USE_LDCONFIG= yes INSTALL_TARGET= install-strip .include Index: head/biology/iolib/distinfo =================================================================== --- head/biology/iolib/distinfo (revision 480877) +++ head/biology/iolib/distinfo (revision 480878) @@ -1,3 +1,3 @@ -TIMESTAMP = 1488270338 -SHA256 (jkbonfield-io_lib-io_lib-1-14-9_GH0.tar.gz) = 077044d525e9dd76f94ee83b0ab19cd655b08348cc81bbdaa84e39c622280a4a -SIZE (jkbonfield-io_lib-io_lib-1-14-9_GH0.tar.gz) = 1396092 +TIMESTAMP = 1538157628 +SHA256 (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 4bd576e52bb7e6be6c2efe42db2764b713c8b61b44a025ad0567dba052b6db1c +SIZE (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 3391479 Index: head/biology/iolib/pkg-plist =================================================================== --- head/biology/iolib/pkg-plist (revision 480877) +++ head/biology/iolib/pkg-plist (revision 480878) @@ -1,115 +1,115 @@ bin/append_sff bin/convert_trace bin/cram_dump bin/cram_filter bin/cram_index bin/cram_size bin/extract_fastq bin/extract_qual bin/extract_seq bin/get_comment bin/hash_exp bin/hash_extract bin/hash_list bin/hash_sff bin/hash_tar bin/index_tar bin/io_lib-config bin/makeSCF bin/scf_dump bin/scf_info bin/scf_update bin/scram_flagstat bin/scram_merge bin/scram_pileup bin/scram_test bin/scramble bin/srf2fasta bin/srf2fastq bin/srf_dump_all bin/srf_extract_hash bin/srf_extract_linear bin/srf_filter bin/srf_index_hash bin/srf_info bin/srf_list bin/trace_dump bin/ztr_dump include/io_lib/Read.h include/io_lib/abi.h include/io_lib/alf.h include/io_lib/array.h include/io_lib/bam.h include/io_lib/bgzip.h include/io_lib/binning.h include/io_lib/compress.h include/io_lib/compression.h include/io_lib/cram.h include/io_lib/cram_codecs.h include/io_lib/cram_decode.h include/io_lib/cram_encode.h include/io_lib/cram_index.h include/io_lib/cram_io.h include/io_lib/cram_stats.h include/io_lib/cram_structs.h include/io_lib/deflate_interlaced.h include/io_lib/dstring.h include/io_lib/error.h include/io_lib/expFileIO.h include/io_lib/fpoint.h include/io_lib/hash_table.h include/io_lib/io_lib_config.h include/io_lib/jenkins_lookup3.h include/io_lib/mFILE.h include/io_lib/mach-io.h include/io_lib/md5.h include/io_lib/misc.h include/io_lib/open_trace_file.h include/io_lib/os.h include/io_lib/plain.h include/io_lib/pooled_alloc.h include/io_lib/sam_header.h include/io_lib/scf.h include/io_lib/scf_extras.h include/io_lib/scram.h include/io_lib/seqIOABI.h include/io_lib/sff.h include/io_lib/srf.h include/io_lib/stdio_hack.h include/io_lib/string_alloc.h include/io_lib/tar_format.h include/io_lib/thread_pool.h include/io_lib/traceType.h include/io_lib/translate.h include/io_lib/vlen.h include/io_lib/xalloc.h include/io_lib/zfio.h include/io_lib/ztr.h lib/libstaden-read.a lib/libstaden-read.so -lib/libstaden-read.so.11 -lib/libstaden-read.so.11.1.0 +lib/libstaden-read.so.13 +lib/libstaden-read.so.13.0.0 man/man1/scramble.1.gz man/man1/srf2fasta.1.gz man/man1/srf2fastq.1.gz man/man1/srf_index_hash.1.gz man/man1/srf_info.1.gz man/man1/srf_list.1.gz man/man3/ExperimentFile.3.gz man/man3/exp2read.3.gz man/man3/fread_reading.3.gz man/man3/fread_scf.3.gz man/man3/fwrite_reading.3.gz man/man3/fwrite_scf.3.gz man/man3/read2exp.3.gz man/man3/read2scf.3.gz man/man3/read_allocate.3.gz man/man3/read_deallocate.3.gz man/man3/read_reading.3.gz man/man3/read_scf.3.gz man/man3/read_scf_header.3.gz man/man3/scf2read.3.gz man/man3/write_reading.3.gz man/man3/write_scf.3.gz man/man3/write_scf_header.3.gz man/man4/Read.4.gz Index: head/biology/p5-Bio-SCF/Makefile =================================================================== --- head/biology/p5-Bio-SCF/Makefile (revision 480877) +++ head/biology/p5-Bio-SCF/Makefile (revision 480878) @@ -1,23 +1,23 @@ # Created by: Wen Heping # $FreeBSD$ PORTNAME= Bio-SCF PORTVERSION= 1.03 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= wen@FreeBSD.org COMMENT= Read and Update SCF Chromatographic Sequence Files BUILD_DEPENDS= ${LOCALBASE}/include/io_lib/scf.h:biology/iolib RUN_DEPENDS:= ${BUILD_DEPENDS} CFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib USES= perl5 USE_PERL5= configure .include