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Thu, 28 Jul 2022 03:43:52 GMT (envelope-from git) Date: Thu, 28 Jul 2022 03:43:52 GMT Message-Id: <202207280343.26S3hqFh049790@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-branches@FreeBSD.org From: Yuri Victorovich Subject: git: d60e95e52e7d - 2022Q3 - biology/cufflinks: Unbreak List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/2022Q3 X-Git-Reftype: branch X-Git-Commit: d60e95e52e7df0240c9fd0e3267e9752c6ab8bd0 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1658979832; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch 2022Q3 has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=d60e95e52e7df0240c9fd0e3267e9752c6ab8bd0 commit d60e95e52e7df0240c9fd0e3267e9752c6ab8bd0 Author: Yuri Victorovich AuthorDate: 2022-07-28 03:43:06 +0000 Commit: Yuri Victorovich CommitDate: 2022-07-28 03:43:46 +0000 biology/cufflinks: Unbreak (cherry picked from commit 8fd55d46d939263df2c327093c6bb21d74a29c0d) --- biology/cufflinks/Makefile | 5 ++-- biology/cufflinks/files/patch-configure.ac | 9 ++++++++ biology/cufflinks/files/patch-src_GBase.h | 11 ++++++++- biology/cufflinks/files/patch-src_codons.cpp | 24 ++++++++++++++++++++ biology/cufflinks/files/patch-src_gdna.cpp | 34 ++++++++++++++++++++++++++++ biology/cufflinks/files/patch-src_gdna.h | 12 ++++++++++ biology/cufflinks/files/patch-src_gff.cpp | 11 +++++++++ biology/cufflinks/files/patch-src_gff.h | 34 ++++++++++++++++++++++++++++ 8 files changed, 137 insertions(+), 3 deletions(-) diff --git a/biology/cufflinks/Makefile b/biology/cufflinks/Makefile index 99de4da20665..caaf6e63305a 100644 --- a/biology/cufflinks/Makefile +++ b/biology/cufflinks/Makefile @@ -17,11 +17,12 @@ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libhts.so:biology/htslib -BROKEN= error: expected ';' at end of declaration - USES= autoreconf compiler:c++11-lang eigen:3 gmake python shebangfix + SHEBANG_FILES= src/cuffmerge + GNU_CONFIGURE= yes + USE_GITHUB= yes GH_ACCOUNT= cole-trapnell-lab diff --git a/biology/cufflinks/files/patch-configure.ac b/biology/cufflinks/files/patch-configure.ac index 5d8f553f27ad..4347dcbe7503 100644 --- a/biology/cufflinks/files/patch-configure.ac +++ b/biology/cufflinks/files/patch-configure.ac @@ -23,6 +23,15 @@ esac AC_ARG_ENABLE(vectorize, [ --enable-vectorize Enable GCC auto-vectorization], +@@ -111,7 +112,7 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling + [ext_LDFLAGS="-lprofiler -ltcmalloc"], []) + + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" +-CXXFLAGS="$CFLAGS -std=c++03" ++CXXFLAGS="$CFLAGS -std=c++14" + CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" + user_LDFLAGS="$LDFLAGS" + LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" @@ -120,7 +121,6 @@ LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" AC_CHECK_MEMBERS([struct sysinfo.totalram], [], [], [#include ]) AC_CHECK_DECLS([sysctl, CTL_HW, HW_PHYSMEM], [], [], [#include ]) diff --git a/biology/cufflinks/files/patch-src_GBase.h b/biology/cufflinks/files/patch-src_GBase.h index d7475a73dcb4..757bd8831c36 100644 --- a/biology/cufflinks/files/patch-src_GBase.h +++ b/biology/cufflinks/files/patch-src_GBase.h @@ -1,4 +1,4 @@ ---- src/GBase.h.orig 2019-05-25 22:08:19 UTC +--- src/GBase.h.orig 2019-07-06 16:28:01 UTC +++ src/GBase.h @@ -1,6 +1,6 @@ #ifndef G_BASE_DEFINED @@ -8,3 +8,12 @@ //mostly for MinGW #define _POSIX_SOURCE #endif +@@ -71,7 +71,7 @@ typedef int16_t int16; + typedef uint16_t uint16; + + typedef unsigned char uchar; +-typedef unsigned char byte; ++typedef unsigned char bytex; + + #ifndef MAXUINT + #define MAXUINT ((unsigned int)-1) diff --git a/biology/cufflinks/files/patch-src_codons.cpp b/biology/cufflinks/files/patch-src_codons.cpp new file mode 100644 index 000000000000..0867df1e5bdf --- /dev/null +++ b/biology/cufflinks/files/patch-src_codons.cpp @@ -0,0 +1,24 @@ +--- src/codons.cpp.orig 2022-07-28 03:23:12 UTC ++++ src/codons.cpp +@@ -48,9 +48,9 @@ static bool isCodonTableReady=codonTableInit(); + + unsigned short packCodon(char n1, char n2, char n3) { + //assumes they are uppercase already! +- byte b1=n1-'A'; +- byte b2=n2-'A'; +- byte b3=n3-'A'; ++ bytex b1=n1-'A'; ++ bytex b2=n2-'A'; ++ bytex b3=n3-'A'; + b1 |= (b2 << 5); + b2 = (b2 >> 3) | (b3 << 2); + return ( ((unsigned short)b2) << 8) + b1; +@@ -68,7 +68,7 @@ bool codonTableInit() { + + + char Codon::translate() { +- for (byte i=0;i<3;i++) nuc[i]=toupper(nuc[i]); ++ for (bytex i=0;i<3;i++) nuc[i]=toupper(nuc[i]); + unsigned short aacode=packCodon(nuc[0], nuc[1], nuc[2]); + return codonTable[aacode]; + } diff --git a/biology/cufflinks/files/patch-src_gdna.cpp b/biology/cufflinks/files/patch-src_gdna.cpp new file mode 100644 index 000000000000..c305e2a0b8b1 --- /dev/null +++ b/biology/cufflinks/files/patch-src_gdna.cpp @@ -0,0 +1,34 @@ +--- src/gdna.cpp.orig 2022-07-28 03:26:30 UTC ++++ src/gdna.cpp +@@ -11,8 +11,8 @@ const char* IUPAC_COMP ="TtGgAaCcAaKkYyWwSsRrMmBbDdHh + #define G_2BIT 2 // 10 + #define T_2BIT 3 // 11 + +-static byte ntCompTable[256]; +-static byte nt2bit[256]; //maps any character to a 2bit base value (with N = A) ++static bytex ntCompTable[256]; ++static bytex nt2bit[256]; //maps any character to a 2bit base value (with N = A) + static char v_2bit2nt[4] = {'A','C','G','T'}; + + //---------------------- +@@ -21,9 +21,9 @@ static bool gdna_Ready=gDnaInit(); + + //---------------------- + +-byte gdna2bit(char* &nt, int n) { ++bytex gdna2bit(char* &nt, int n) { + // Pack n bases into a byte (n can be 1..4) +-byte out = 0; ++bytex out = 0; + while (n && *nt) { + n--; + out <<= 2; +@@ -43,7 +43,7 @@ char ntComplement(char c) { + return ntCompTable[(int)c]; + } + +-char g2bit2base(byte v2bit) { ++char g2bit2base(bytex v2bit) { + return v_2bit2nt[v2bit & 0x03 ]; + } + diff --git a/biology/cufflinks/files/patch-src_gdna.h b/biology/cufflinks/files/patch-src_gdna.h new file mode 100644 index 000000000000..73ec345a705e --- /dev/null +++ b/biology/cufflinks/files/patch-src_gdna.h @@ -0,0 +1,12 @@ +--- src/gdna.h.orig 2022-07-28 03:14:39 UTC ++++ src/gdna.h +@@ -9,7 +9,7 @@ char* reverseComplement(char* seq, int slen=0); + + bool gDnaInit(); + +-byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4) +-char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T' ++bytex gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4) ++char g2bit2base(bytex v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T' + + #endif diff --git a/biology/cufflinks/files/patch-src_gff.cpp b/biology/cufflinks/files/patch-src_gff.cpp new file mode 100644 index 000000000000..3bca48213b0a --- /dev/null +++ b/biology/cufflinks/files/patch-src_gff.cpp @@ -0,0 +1,11 @@ +--- src/gff.cpp.orig 2022-07-28 03:24:45 UTC ++++ src/gff.cpp +@@ -21,7 +21,7 @@ const uint gfo_flag_BY_EXON = 0x00000020; //c + const uint gfo_flag_DISCARDED = 0x00000100; + const uint gfo_flag_LST_KEEP = 0x00000200; + const uint gfo_flag_LEVEL_MSK = 0x00FF0000; +-const byte gfo_flagShift_LEVEL = 16; ++const bytex gfo_flagShift_LEVEL = 16; + + void gffnames_ref(GffNames* &n) { + if (n==NULL) n=new GffNames(); diff --git a/biology/cufflinks/files/patch-src_gff.h b/biology/cufflinks/files/patch-src_gff.h new file mode 100644 index 000000000000..53cb996ef782 --- /dev/null +++ b/biology/cufflinks/files/patch-src_gff.h @@ -0,0 +1,34 @@ +--- src/gff.h.orig 2022-07-28 03:20:26 UTC ++++ src/gff.h +@@ -42,7 +42,7 @@ extern const uint gfo_flag_DISCARDED; //should not be + extern const uint gfo_flag_LST_KEEP; //GffObj from GffReader::gflst is to be kept (not deallocated) + //when GffReader is destroyed + extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent +-extern const byte gfo_flagShift_LEVEL; ++extern const bytex gfo_flagShift_LEVEL; + + extern bool gff_show_warnings; + +@@ -508,18 +508,18 @@ class GffObj:public GSeg { (public) + if (v) flags |= gfo_flag_CHILDREN_PROMOTED; + else flags &= ~gfo_flag_CHILDREN_PROMOTED; + } +- void setLevel(byte v) { ++ void setLevel(bytex v) { + if (v==0) flags &= ~gfo_flag_LEVEL_MSK; + else flags &= ~(((uint)v) << gfo_flagShift_LEVEL); + } +- byte incLevel() { ++ bytex incLevel() { + uint v=((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL); + v++; + flags &= ~(v << gfo_flagShift_LEVEL); + return v; + } +- byte getLevel() { +- return ((byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL)); ++ bytex getLevel() { ++ return ((bytex)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL)); + } + + bool isValidTranscript() {