commit: 76b3d8cb77d339f9156450915a764889f97786ee Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Fri Jan 27 11:03:02 2023 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Fri Jan 27 11:07:30 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=76b3d8cb
sci-biology/consed: treeclean Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 6 - sci-biology/consed/Manifest | 2 - sci-biology/consed/consed-29.ebuild | 110 ---- .../consed/files/consed-29-fix-build-system.patch | 197 ------ sci-biology/consed/files/consed-29-fix-c++14.patch | 376 ----------- .../consed/files/consed-29-fix-perl-shebang.patch | 701 --------------------- sci-biology/consed/files/consed-29-fix-qa.patch | 294 --------- sci-biology/consed/metadata.xml | 8 - 8 files changed, 1694 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index d442ec3896a7..e0d52cd0dce6 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -703,12 +703,6 @@ app-eselect/eselect-sh # https://github.com/kdave/btrfs-progs/issues/562 =sys-fs/btrfs-progs-6.1 -# David Seifert <[email protected]> (2022-12-26) -# Lots of K&R C, hidden behind an annoying authwall, fails with modern -# GCC and Clang (-fcommon), license prohibits distributing, EAPI 6, -# last release 8 years ago. Removal on 2023-01-25. -sci-biology/consed - # Ionen Wolkens <[email protected]> (2022-12-24) # Upstream dropped wxGTK support in >=games-emulation/pcsx2-1.7.3773, # and it now always requires Qt6. Masked given Qt6 is also masked in diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest deleted file mode 100644 index eb7d7f06c3ee..000000000000 --- a/sci-biology/consed/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd -DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93 diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild deleted file mode 100644 index 32eba4cb16d0..000000000000 --- a/sci-biology/consed/consed-29.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit flag-o-matic toolchain-funcs - -DESCRIPTION="A genome sequence finishing program" -HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"; -SRC_URI=" - ${P}-sources.tar.gz - ${P}-linux.tar.gz" - -LICENSE="phrap" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="examples" - -COMMON_DEPEND=" - x11-libs/libX11 - x11-libs/motif:0 - sci-biology/samtools:0.1-legacy -" -DEPEND=" - ${COMMON_DEPEND} - virtual/pkgconfig -" -RDEPEND=" - ${COMMON_DEPEND} - dev-lang/perl - >=sci-biology/phred-071220-r1 - >=sci-biology/phrap-1.080812-r2 -" - -S="${WORKDIR}" - -RESTRICT="fetch" -PATCHES=( - "${FILESDIR}/${PN}-29-fix-build-system.patch" - "${FILESDIR}/${PN}-29-fix-c++14.patch" - "${FILESDIR}/${PN}-29-fix-qa.patch" - "${FILESDIR}/${PN}-29-fix-perl-shebang.patch" -) - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\"" - einfo "and place it into your DISTDIR directory," - einfo "obtain the file" - einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\"" - einfo "and place it into your DISTDIR directory." -} - -src_prepare() { - default - - sed \ - -e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \ - -e "s:/usr/local/genome:${EPREFIX}/usr:" \ - -e "s:niceExe = \"/bin/nice\":niceExe = \"${EPREFIX}/usr/bin/nice\":" \ - -e "s:/wt1/gordon/genome:${EPREFIX}/usr/bin:" \ - -i scripts/* contributions/* || die -} - -src_configure() { - append-cflags -std=gnu99 - append-lfs-flags -} - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - CXX="$(tc-getCXX)" \ - CFLAGS="${CFLAGS}" \ - CXXFLAGS="${CXXFLAGS}" \ - CPPFLAGS="${CPPFLAGS}" \ - LDFLAGS="${LDFLAGS}" \ - SAMTOOLS_CPPFLAGS="-I${EPREFIX}/usr/include/bam-0.1-legacy" \ - LIBS="-L${EPREFIX}/usr/$(get_libdir)" \ - X11_LIBS="$($(tc-getPKG_CONFIG) --libs x11)" \ - SAMTOOLS_LIBS="-lbam-0.1-legacy" -} - -src_install() { - dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} scripts/* contributions/* - - insinto /usr/lib/screenLibs - doins misc/*.{fa*,seq} - - if use examples; then - insinto /usr/share/${PN}/examples - doins -r \ - standard polyphred autofinish assembly_view 454_newbler \ - align454reads align454reads_answer solexa_example \ - solexa_example_answer selectRegions selectRegionsAnswer - fi - - cat > 99consed <<-_EOF_ || die - CONSED_HOME=${EPREFIX}/usr - CONSED_PARAMETERS=${EPREFIX}/etc/consedrc - _EOF_ - doenvd 99consed - - dodoc README.txt *_announcement.txt -} - -pkg_postinst() { - einfo "Package documentation is available at" - einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"; -} diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch deleted file mode 100644 index 30819f93ac80..000000000000 --- a/sci-biology/consed/files/consed-29-fix-build-system.patch +++ /dev/null @@ -1,197 +0,0 @@ -Make build system semi-sane: -* Respect CC, CXX, CFLAGS, CXXFLAGS, CPPFLAGS, LDFLAGS and LIBS -* Remove default optimisation flags -* Remove -fpermissive from DEFS (as source builds fine now) -* Add large file support (LFS) via CPPFLAGS and not in Makefile - ---- a/makefile -+++ b/makefile -@@ -47,23 +47,20 @@ - # - # compilation - # --CXX= g++ --KRCC= gcc --CC=gcc -+CXX ?= g++ -+CC ?= gcc - - # - # --CFLGS= -w -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -fpermissive -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -D_FILE_OFFSET_BITS=64 -DSAMTOOLS_AVAILABLE -+DEFS = -DINLINE_RWTPTRORDEREDVECTOR -DINLINE_RWTVALORDEREDVECTOR -DINLINE_MBTVALVECTOR -DLINUX_COMPILE -DSOCKLEN_T_DEFINED -D__BOOL_DEFINED -DANSI_C -DOFSTREAM_OPEN_WITHOUT_PERMISSIONS -DNO_POUND_POUND_MACROS -DUSE_USING_IN_PUBLIC_TEMPLATE_CLASSES -DINT_CHAR_OPERATOR -DSAMTOOLS_AVAILABLE - --OPT= -O - # - # Include directory for template classes must be included - # in both compilation & link lines, even if .h file is - # found in default path. C front, gotta love it. - # --INC= -I/usr/X11R6/include -I/me1/gordon/samtools/samtools-0.1.18 -+INCLUDES = $(SAMTOOLS_CPPFLAGS) - --DEPENDENCIES= - # - # - # Linking -@@ -80,12 +77,9 @@ - # /lib/ld-linux.so.2 (0x003ee000) - # - # To fix cut/paste bug, I've made X11 always dynamic. --CLIBS= -lX11 --LPATH= -L/usr/X11R6/lib --ARCHIVES= /usr/X11R6/lib/libXm.a \ --/usr/X11R6/lib/libXt.a /usr/X11R6/lib/libSM.a \ --/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \ --/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a -+ -+MOTIF_LIBS ?= -lXm -lXt -+ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS) - - - -@@ -94,7 +88,6 @@ - # - #LDFLGS= -g - # static linking --LDFLGS= -g -rdynamic - - # - # the subdirectory used by cfront compilers gets cleaned -@@ -112,10 +105,10 @@ - # general compilation rules for .cpp, .cxx, .c files - # - .cpp.o: -- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< - - .c.o: -- $(CXX) $(CFLGS) $(OPT) $(INC) -c $< -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c $< - - # - # targets file included in generated makefile -@@ -593,17 +586,23 @@ - writeToRewriteReferenceFile.o \ - xsynchronize.o - -+SUBDIRS := misc/454 misc/mktrace misc/phd2fasta -+ -+all: consed $(SUBDIRS) -+ -+$(SUBDIRS): -+ $(MAKE) -C $@ -+ -+.PHONY: all $(SUBDIRS) -+ - consed: $(CONSED_OBJS) makefile checkLicenseKeyStub.o -- $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ -- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) -+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) - - trial_consed: $(CONSED_OBJS) makefile checkLicenseKey.o -- $(CXX) $(INC) $(LDFLGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o \ -- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) -+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o trial_consed $(CONSED_OBJS) checkLicenseKey.o $(ALL_LIBS) - - pure: $(CONSED_OBJS) makefile checkLicenseKeyStub.o -- $(PURIFY) $(CXX) $(INC) $(LDFLGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o \ -- $(ARCHIVES) $(LPATH) $(WARNINGS) $(CLIBS) $(XLIBS) -+ $(CXX) $(LDFLAGS) $(CXXFLAGS) -o consed $(CONSED_OBJS) checkLicenseKeyStub.o $(ALL_LIBS) - - clean: - rm -rf *.o core $(TEMPLATE_DIR) -@@ -613,15 +612,15 @@ - # the Solaris 5.x compiler cannot optimize the following - - consedResources.o: -- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources.cpp -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources.cpp - - consedResources2.o: -- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c consedResources2.cpp -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c consedResources2.cpp - - # tlingit cannot optimize the following: - - guiEditResources.o: -- $(CXX) $(WARNINGS) $(CFLGS) $(INC) $(DEPENDENCIES) -c guiEditResources.cpp -+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $(DEFS) -c guiEditResources.cpp - - guiEditResources.o : \ - assemblyViewTagTypeAndLine.h assert.h bIsNumericDouble.h \ ---- a/misc/454/Makefile -+++ b/misc/454/Makefile -@@ -0,0 +1,16 @@ -+CC ?= cc -+LIBM = -lm -+ -+DEFS = -DANSI_C -+ -+OBJS= sff2scf.c -+ -+sff2scf: $(OBJS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) -+ -+.c.o: -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< -+ -+clean: -+ rm -f $(OBJS) sff2scf -+ ---- a/misc/mktrace/Makefile -+++ b/misc/mktrace/Makefile -@@ -1,13 +1,17 @@ --CC= cc --CFLAGS= -g --CLIB= -lm -+CC ?= cc -+LIBM = -lm -+ -+DEFS = -DANSI_C - - OBJS= mktrace.o readFASTA.o writeSCF.o synTrace.o \ - freeTrace.o rwUtil.o writePhd.o getTime.o \ - readQUAL.o - - mktrace: $(OBJS) -- $(CC) $(CFLAGS) -o mktrace $(OBJS) $(CLIB) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) -+ -+.c.o: -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< - - clean: - rm -f $(OBJS) mktrace ---- a/misc/phd2fasta/Makefile -+++ b/misc/phd2fasta/Makefile -@@ -1,8 +1,9 @@ --CC=cc --CFLAGS=-O -w --CLIB=-lm -+CC ?= cc -+LIBM = -lm - --OBJ= phd2fasta.o \ -+DEFS = -DANSI_C -+ -+OBJS= phd2fasta.o \ - readParam.o initParam.o checkParam.o \ - freeParam.o helpParam.o \ - readFOF.o readDIR.o readFOX.o \ -@@ -15,10 +16,11 @@ - - INC= phd2fasta.h - --SRC = $(OBJ:.o=.c) -- --phd2fasta: $(OBJ) -- $(CC) $(CFLAGS) -o phd2fasta $(OBJ) $(CLIB) -+phd2fasta: $(OBJS) -+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $^ $(LIBM) -+ -+.c.o: -+ $(CC) $(CFLAGS) $(CPPFLAGS) $(DEFS) -c $< - - clean: - rm -f $(OBJ) phd2fasta diff --git a/sci-biology/consed/files/consed-29-fix-c++14.patch b/sci-biology/consed/files/consed-29-fix-c++14.patch deleted file mode 100644 index 212b8d63d1e3..000000000000 --- a/sci-biology/consed/files/consed-29-fix-c++14.patch +++ /dev/null @@ -1,376 +0,0 @@ -Fix building with C++14: -* Add 'noexcept(false)' to throwing destructors in C++11 mode -* Properly guard C declarations with extern "C" scopes -* Avoid erroneous overloaded suffix operator errors, due to missing spaces -* Add explicit casts to avoid -Wnarrowing errors -* Add 'this->' for dependent identifiers in derived class templates, - previously required -fpermissive - ---- a/bvAlignedReads.cpp -+++ b/bvAlignedReads.cpp -@@ -126,7 +126,11 @@ - } - - --bvAlignedReads :: ~bvAlignedReads() { -+bvAlignedReads :: ~bvAlignedReads() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+{ - - - assert( pBamView_->aBVAlignedReads_.remove( this ) ); ---- a/bvAlignedReads.h -+++ b/bvAlignedReads.h -@@ -81,7 +81,11 @@ - const FileName& filReferenceSequenceFile, - bamView* pBamView ); - -- ~bvAlignedReads(); -+ ~bvAlignedReads() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+ ; - - bool operator==( const bvAlignedReads& myBVAlignedReads ) const { - return( this == &myBVAlignedReads ); ---- a/chromatData.h -+++ b/chromatData.h -@@ -58,6 +58,9 @@ - #ifndef CHROMATDATA_DEFINED - #define CHROMATDATA_DEFINED - -+#ifdef __cplusplus -+extern "C" { -+#endif - - #ifndef FLOAT - #define FLOAT double -@@ -131,4 +134,8 @@ - int freeChromatData(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/compareContigs.cpp -+++ b/compareContigs.cpp -@@ -126,6 +126,9 @@ - - - compareContigs :: ~compareContigs() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif - { - - if ( !bCalledFromMakeJoins_ ) { ---- a/compareContigs.h -+++ b/compareContigs.h -@@ -137,7 +137,11 @@ - compareContigs( ContigWin* pContigWin, const int nConsPos1); - compareContigs(); // for assemblyView - -- ~compareContigs(); -+ ~compareContigs() -+#if __cplusplus >= 201103L -+ noexcept(false) -+#endif -+ ; - - // this makes RWTPtrOrderedVector in ConsEd happy - bool operator==( const compareContigs& compC ) const { - ---- a/filePopupAndGetAceFilename.cpp -+++ b/filePopupAndGetAceFilename.cpp -@@ -317,7 +317,7 @@ - struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); - - strftime( szDateTime, nDateTimeSize, -- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", -+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", - pTM ); - - RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); -@@ -620,7 +620,7 @@ - struct tm* pTM = localtime( &( pAceFile->stat_.st_mtime ) ); - - strftime( szDateTime, nDateTimeSize, -- quote(%H)":"quote(%M)":"quote(%S)" %e-%h-%Y", -+ quote(%H) ":" quote(%M) ":" quote(%S) " %e-%h-%Y", - pTM ); - - RWCString soDescription = RWCString( szDateTime ) + " " + (*pAceFile); ---- a/findTraceExtrema.h -+++ b/findTraceExtrema.h -@@ -44,8 +44,15 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - int findTraceExtrema( ChromatData *chromatData ); - -+#ifdef __cplusplus -+} -+#endif - - #endif - ---- a/makeUpper.h -+++ b/makeUpper.h -@@ -42,6 +42,14 @@ - #ifndef MAKEUPPER_INCLUDED - #define MAKEUPPER_INCLUDED - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - void makeUpper( char* szStringOfMixedCase ); - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/nextPhredPipeline.cpp -+++ b/nextPhredPipeline.cpp -@@ -476,7 +476,7 @@ - void nextPhredPipeline :: openAndLockControlFile() { - - -- nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR ); -+ nFDControlFile_ = open( filControlFile_.data(), O_CREAT |O_RDWR, 0600); - if ( nFDControlFile_ == -1 ) { - THROW_FILE_ERROR( filControlFile_ ); - } ---- a/readABI.h -+++ b/readABI.h -@@ -56,10 +56,18 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - #ifdef ANSI_C - ChromatData *readABI( char *fn, int *status ); - #else - ChromatData *readABI(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/readData.h -+++ b/readData.h -@@ -44,6 +44,14 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - ChromatData *readData( char *filename, int* status ); - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/readESD.h -+++ b/readESD.h -@@ -53,6 +53,10 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - typedef unsigned int4 DWORD; - typedef unsigned char TCHAR; - typedef char BYTE; -@@ -187,5 +191,7 @@ - ChromatData *readESD(); - #endif - -- -+#ifdef __cplusplus -+} -+#endif - ---- a/readSCF.h -+++ b/readSCF.h -@@ -56,6 +56,10 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - /* ---- Constants ---- */ - #define SCF_MAGIC (((((int4)'.'<<8)+(int4)'s'<<8)+(int4)'c'<<8)+(int4)'f') - #define scale(V,OLDMAX,NEWMAX) (int2)( (FLOAT) V * (FLOAT) NEWMAX / (FLOAT) OLDMAX ) -@@ -144,4 +148,8 @@ - int readSCF3(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif ---- a/readsense_bitmaps.h -+++ b/readsense_bitmaps.h -@@ -56,10 +56,10 @@ - static const int forward_bitmap_height = 19; - static char forward_bitmap_bits[] = { - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, -- 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, -- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0xff, 0x3f, 0x00, 0xf8, 0xff, 0xff, 0x07, -- 0xf8, 0xff, 0xff, 0x0f, 0xf8, 0xff, 0xff, 0x07, 0xf8, 0xff, 0x1f, 0x00, -- 0xf8, 0xff, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, -+ 0x00, 0x00, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, -+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, (char)0xff, 0x3f, 0x00, (char)0xf8, (char)0xff, (char)0xff, 0x07, -+ (char)0xf8, (char)0xff, (char)0xff, 0x0f, (char)0xf8, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, 0x1f, 0x00, -+ (char)0xf8, (char)0xff, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x38, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00}; - -@@ -67,10 +67,10 @@ - static const int reverse_bitmap_height = 19; - static char reverse_bitmap_bits[] = { - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, -- 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, 0xf8, 0x07, -- 0x00, 0xc0, 0xff, 0x07, 0x00, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, -- 0xfc, 0xff, 0xff, 0x07, 0xf8, 0xff, 0xff, 0x07, 0x00, 0xfe, 0xff, 0x07, -- 0x00, 0xc0, 0xff, 0x07, 0x00, 0x00, 0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, -+ 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x07, 0x00, 0x00, (char)0xf8, 0x07, -+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, -+ (char)0xfc, (char)0xff, (char)0xff, 0x07, (char)0xf8, (char)0xff, (char)0xff, 0x07, 0x00, (char)0xfe, (char)0xff, 0x07, -+ 0x00, (char)0xc0, (char)0xff, 0x07, 0x00, 0x00, (char)0xf8, 0x07, 0x00, 0x00, 0x00, 0x07, - 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, - 0x00, 0x00, 0x00, 0x00}; - ---- a/readType.h -+++ b/readType.h -@@ -56,11 +56,19 @@ - - #include "chromatData.h" - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - #ifdef ANSI_C - int readType( char *filename ); - #else - int readType(); - #endif - -+#ifdef __cplusplus -+} -+#endif -+ - #endif - ---- a/rwtptrsortedvector.h -+++ b/rwtptrsortedvector.h -@@ -57,7 +57,6 @@ - #ifdef USE_USING_IN_PUBLIC_TEMPLATE_CLASSES - using RWTPtrOrderedVector<TP>::nCurrentLength_; - using RWTPtrOrderedVector<TP>::isEmpty; -- using RWTPtrOrderedVector<TP>::nCurrentLength_; - using RWTPtrOrderedVector<TP>::length; - using RWTPtrOrderedVector<TP>::ppArray_; - using RWTPtrOrderedVector<TP>::data; -@@ -84,7 +83,7 @@ - if ( nInsertBeforeIndex == RW_NPOS ) - nInsertBeforeIndex = nCurrentLength_; - -- insertAt( nInsertBeforeIndex, pVal ); -+ this->insertAt( nInsertBeforeIndex, pVal ); - } - - // don't copy this. copy mbtValOrderedVectorOfRWCString's method instead ---- a/rwtvalsortedvector.h -+++ b/rwtvalsortedvector.h -@@ -74,7 +74,7 @@ - if ( nPos == RW_NPOS ) - nPos = nCurrentLength_; - -- insertAt( nPos, val ); -+ this->insertAt( nPos, val ); - } - - ---- a/rwUtil.h -+++ b/rwUtil.h -@@ -51,6 +51,10 @@ - *|***************************************************************************|* - */ - -+#ifdef __cplusplus -+extern "C" { -+#endif -+ - #ifdef ANSI_C - int2 inSwpSint2( char *ptr ); - int4 inSwpSint4( char *ptr ); -@@ -97,3 +101,6 @@ - int writeUint4(); - #endif - -+#ifdef __cplusplus -+} -+#endif ---- a/soGetDateTime.cpp -+++ b/soGetDateTime.cpp -@@ -62,13 +62,13 @@ - else if ( nFormat == nDotInMiddle ) { - strftime( szDateTime, - nDateTimeSize, -- "%y%m%d."quote(%H)quote(%M)quote(%S), -+ "%y%m%d." quote(%H)quote(%M)quote(%S), - localtime( &timee ) ); - } - else { - strftime( szDateTime, - nDateTimeSize, -- "%y%m%d:"quote(%H)quote(%M)quote(%S), -+ "%y%m%d:" quote(%H)quote(%M)quote(%S), - localtime( &timee ) ); - } - ---- a/szGetTime.h -+++ b/szGetTime.h -@@ -42,9 +42,15 @@ - #ifndef szGetTime_included - #define szGetTime_included - --char *szGetTime(); -+#ifdef __cplusplus -+extern "C" { -+#endif - -+char *szGetTime(); - -+#ifdef __cplusplus -+} -+#endif - - #endif - diff --git a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch b/sci-biology/consed/files/consed-29-fix-perl-shebang.patch deleted file mode 100644 index a27a3537a8d1..000000000000 --- a/sci-biology/consed/files/consed-29-fix-perl-shebang.patch +++ /dev/null @@ -1,701 +0,0 @@ -Make perl shebangs portable, such that the scripts can also be used on Gentoo Prefix. -Rationale: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/ - ---- a/contributions/ace2fof -+++ b/contributions/ace2fof -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # .-----------------------------------------------------------------------------------. - # | | -@@ -107,6 +107,7 @@ - # | | - # `-----------------------------------------------------------------------------------' - #Fixed this file for taking Aracne's Ace file by syang 05152002 -+use warnings; - use strict; - use POSIX qw(fmod); - ---- a/contributions/ace2OligosWithComments.perl -+++ b/contributions/ace2OligosWithComments.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # ace2Oligos.perl - # -@@ -18,6 +18,8 @@ - # Rev: 020528 to print comments in oligo tags upon request (Peter Kos) - # - -+use warnings; -+ - $szUsage = "\nUsage: $0 (name of ace file) (name of oligo file) [Print|Comment|PrintComment]\n"; - - die "$szUsage" if (( $#ARGV != 1 ) && ( $#ARGV != 2 )); ---- a/contributions/aceContigs2Phds.perl -+++ b/contributions/aceContigs2Phds.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # aceContigs2Phd.perl - # -@@ -13,6 +13,8 @@ - # Acknowledgements: Borrowed as much as I could from determineReadTypes.Perl - # and fasta2Phd.perl - -+use warnings; -+ - $szUsage = "Usage: aceContigs2Phds.perl [-s minimum-contig-size] <name of ace file>"; - $nContigLimit = 2000; - ---- a/contributions/acestatus.pl -+++ b/contributions/acestatus.pl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # acestatus.pl - # author: Cliff Wollam -@@ -14,6 +14,7 @@ - # USAGE FROM THE COMMAND LINE: - # acestatus.pl ace_filename - -+use warnings; - use strict; - - if($#ARGV >= 0) { ---- a/contributions/cons.perl -+++ b/contributions/cons.perl -@@ -1,5 +1,6 @@ --#!/usr/bin/perl -+#!/usr/bin/env perl - -+use warnings; - use strict; - use Cwd; - ---- a/contributions/mergeAces.perl -+++ b/contributions/mergeAces.perl -@@ -1,4 +1,4 @@ --#! /usr/local/bin/perl -w -+#!/usr/bin/env perl - - # Bugs and complaints to Bill Gilliland, [email protected]. - # mergeAces.perl v. 0.2 5/22/01 -@@ -9,6 +9,7 @@ - # project directory (if it doesn't already exist) with all the cgrams - # and phd files of the original projects. - -+use warnings; - use Getopt::Long; - use File::Copy; - $pathRoot = $ENV{"PWD"}; ---- a/contributions/phredPhrapWithPhdBalls -+++ b/contributions/phredPhrapWithPhdBalls -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # phredPhrapWithPhdBalls - # modified from phredPhrap by Ben Allen at LANL -@@ -73,6 +73,7 @@ - # Rev: 120312 to not duplicate consensus tags during miniassembly - # Rev: 120717 Ben Allen (LANL) to use reads from phdballs as well as phd_dir - -+use warnings; - - $szVersion = "120312"; - ---- a/contributions/recover_consensus_tags -+++ b/contributions/recover_consensus_tags -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # Purpose: Transfers all consensus tags from a set of old assemblies to - # a new assembly. -@@ -14,6 +14,7 @@ - # rct ace_filename <only ace file to be transfer (optional)> - # You must be in the edit_dir where the ace file is located - -+use warnings; - use strict; - - ---- a/contributions/revert_fof -+++ b/contributions/revert_fof -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: If the user really screws up a read, to back out all changes. - # You must reassemble after using this. -@@ -19,6 +19,8 @@ - # phd extensions. - # revert_fof use file of files to give reads to revert 3/14/01 SL - -+use warnings; -+ - $szUsage = "Enter a file of files name, please!"; - - die $szUsage if ( $#ARGV != 0 ); ---- a/contributions/sff2phd.perl -+++ b/contributions/sff2phd.perl -@@ -1,4 +1,5 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+use warnings; - use strict; - # SFF to PHD files converter, with 454 paired reads and MID support - # Version 0.15 - 111229 ---- a/contributions/sff2phd_Samborskyy -+++ b/contributions/sff2phd_Samborskyy -@@ -1,4 +1,5 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+use warnings; - use strict; - # SFF to PHD files converter, with 454 paired reads and MID support - # Version 0.10 - 101110 ---- a/scripts/ace2Fasta.perl -+++ b/scripts/ace2Fasta.perl -@@ -1,7 +1,9 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Purpose: makes a contigs file out of an ace file - -+use warnings; -+ - $szUsage = "Usage: ace2Contigs.perl (ace file)"; - - ---- a/scripts/ace2Oligos.perl -+++ b/scripts/ace2Oligos.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # ace2Oligos.perl - # -@@ -16,6 +16,8 @@ - # Rev: 000330 to handle comments in oligo tags - # - -+use warnings; -+ - $szUsage = "Usage: ace2Oligos.perl (name of ace file) (name of oligo file)"; - - if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { ---- a/scripts/add454Reads.perl -+++ b/scripts/add454Reads.perl -@@ -1,11 +1,11 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # add454Reads.perl - # part of Consed package - # - # DG with help from Hao Wang to screen vector - -- -+use warnings; - use File::Basename; - - ---- a/scripts/addReads2Consed.perl -+++ b/scripts/addReads2Consed.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Purpose: called by consed in order to add new reads to an - # existing assembly without reassemblying -@@ -29,6 +29,7 @@ - # Rev: 080320 (David Gordon) to use discrep_lists instead of alignments - # Rev: 130828 (David Gordon) to handle slashes (/) in read names - -+use warnings; - - $szVersion = "130828"; - if ( $#ARGV >= 0 ) { ---- a/scripts/addSangerReads.perl -+++ b/scripts/addSangerReads.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # addSangerReads.perl - -@@ -32,7 +32,7 @@ - # added is printed in a report ending with ".log". The name of this - # file is listed in auto.fof - -- -+use warnings; - - - $szVersion = "120717"; ---- a/scripts/addSolexaReads.perl -+++ b/scripts/addSolexaReads.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # addSolexaReads.perl - -@@ -54,7 +54,7 @@ - - $szUsage = "addSolexaReads.perl -ace (ace file) -fastqfof (solexa files) -fasta (fasta file) -readsList (file of list of desired reads) where -readsList is optional"; - -- -+use warnings; - use Getopt::Long; - - GetOptions( "ace=s" => \$szAceFile, ---- a/scripts/alignRNA2Genomic.perl -+++ b/scripts/alignRNA2Genomic.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # alignRNA2Genomic.perl - -@@ -6,6 +6,8 @@ - # consed-ready ace and phd ball with the RNA aligned against the - # genomic with introns being represented by large gaps - -+use warnings; -+ - $szVersion = "120717"; - - if ( $#ARGV == 0 ) { ---- a/scripts/alignSolexaReads2Refs.perl -+++ b/scripts/alignSolexaReads2Refs.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # Input: a file where each line looks like this: - # (solexa seq file) (read prefix) -@@ -10,6 +10,7 @@ - - # Output: a list of alignment files - -+use warnings; - - defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || - ( $szConsedHome = "/usr/local/genome" ); ---- a/scripts/amplifyTranscripts.perl -+++ b/scripts/amplifyTranscripts.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: runs consed -autoPCRAmplify in order to pick pcr primers - # for a large group of regions -@@ -40,7 +40,7 @@ - # That is, the left primers are given in top strand orientation, and - # the right primers are given in bottom strand orientation. - -- -+use warnings; - - defined( $szConsedHome = $ENV{'CONSED_HOME'} ) || - ( $szConsedHome = "/usr/local/genome" ); ---- a/scripts/autoPrimers.perl -+++ b/scripts/autoPrimers.perl -@@ -1,5 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - -+use warnings; - - $szUsage = "autoPrimers.perl (fasta file of targets)"; - $szVersion = "141226"; ---- a/scripts/bam2Ace.perl -+++ b/scripts/bam2Ace.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - - # Purpose: runs: -@@ -6,6 +6,7 @@ - # 2) consed -renameDuplicates - # 3) consed -removeColumnsOfPads - -+use warnings; - - $szUsage = "usage: bam2Ace.perl -bamFile (bam file) -regionsFile (regions file) (see README.txt for format of the regions file) -exec (consed executable name) -newAceFile (new ace file name) where the -exec (exec) is optional"; - ---- a/scripts/convertBedToBamScape.perl -+++ b/scripts/convertBedToBamScape.perl -@@ -1,4 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+ -+use warnings; - - $szUsage = "usage: convertBedToBamScape.perl (Bed file) (BamScape file) (fasta file of all sequences) (conversion of reference names--optional)"; - ---- a/scripts/countEditedBases.perl -+++ b/scripts/countEditedBases.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # countEditedBases.perl - # -@@ -11,6 +11,8 @@ - # - # - -+use warnings; -+ - while(<>) { - if ( /^CO / ) { - @aWords = split; ---- a/scripts/determineReadTypes.perl -+++ b/scripts/determineReadTypes.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # determineReadTypes.perl - # - # Purpose: to write into the phd file information about the template -@@ -173,6 +173,7 @@ - # - ############################################################### - -+use warnings; - - # you can remove or comment out this line when you are satisfied with - # your customized version of this file. ---- a/scripts/fasta2Ace.perl -+++ b/scripts/fasta2Ace.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # manyFasta2Ace.perl - # -@@ -13,6 +13,7 @@ - # - # NOTE: you must run this in edit_dir - -+use warnings; - use Getopt::Long; - - $szRevision = "141212"; ---- a/scripts/fasta2PhdBall.perl -+++ b/scripts/fasta2PhdBall.perl -@@ -1,4 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+ -+use warnings; - - $nQuality = 20; - ---- a/scripts/fasta2Phd.perl -+++ b/scripts/fasta2Phd.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # fasta2Phd.perl - # -@@ -20,6 +20,7 @@ - # June 2002, Bill Gilliland to allow the user to specify - # the quality value - -+use warnings; - use Getopt::Long; - GetOptions( "quality=i" => \$qualityValue); - ---- a/scripts/fastq2Phrap.perl -+++ b/scripts/fastq2Phrap.perl -@@ -1,4 +1,6 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl -+ -+use warnings; - - $szUsage = "fastq2Phrap.perl (fastq) or for paired reads fastq2Phrap.perl (fastq1) (fastq2) where fastq1 and fastq2 have corresponding mate pairs--e.g., the 5th read in fastq1 is the mate of the 5th read in fastq2--these fastq files are assumed to be in ../solexa_dir--not the current directory\n"; - ---- a/scripts/filter454Reads.perl -+++ b/scripts/filter454Reads.perl -@@ -1,6 +1,6 @@ --#!/usr/bin/perl -w -- -+#!/usr/bin/env perl - -+use warnings; - use File::Basename; - - ---- a/scripts/findSequenceMatchesForConsed.perl -+++ b/scripts/findSequenceMatchesForConsed.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # findSequenceMatchesForConsed.perl - -@@ -16,6 +16,8 @@ - # REVISIONS: 021127 (DG) to write (project).(date).(time).fasta instead of - # (project).fasta.screen.ace.1.(date).(time).fasta - -+use warnings; -+ - $szVersion = "021127"; - - $szUsage = "Usage: findSequenceMatchesForConsed.perl (ace file) (crossmatch parameters, if any)"; ---- a/scripts/fixContigEnd.perl -+++ b/scripts/fixContigEnd.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # fixContigEnd.perl - -@@ -7,6 +7,7 @@ - # consed -ace (acefile) -fixContigEnds - # - -+use warnings; - - $szUsage = "fixContigEnd.perl (fasta file of reads for input) (fof for ace file, output)"; - ---- a/scripts/lib2Phd.perl -+++ b/scripts/lib2Phd.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # lib2Phd.perl - # -@@ -23,6 +23,8 @@ - # accept fasta library files as input. The output file is named - # according to the first, non-space block of text on each fasta defline. - -+use warnings; -+ - $nQuality = 20; - - $szUsage = "Usage: lib2Phd.perl <name of file with fasta library>"; ---- a/scripts/makePhdBall.perl -+++ b/scripts/makePhdBall.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: concatenate all phd file into a single phd.ball - # for the purpose of fast startup of consed -@@ -9,6 +9,7 @@ - # - # February 2008, David Gordon - -+use warnings; - - if ( $#ARGV >= 0 ) { - if ( $ARGV[0] eq "-v" || $ARGV[0] eq "-V" ) { ---- a/scripts/makeRegionsFile.perl -+++ b/scripts/makeRegionsFile.perl -@@ -1,10 +1,12 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # makeRegionsFile.perl - # To be used with consed -bam2Ace - # Takes a fasta file of sequences and makes a regions file that - # specifies the entire length of each sequence. - -+use warnings; -+ - $szUsage = "makeRegionsFile.perl (name of fasta file)"; - - $szVersion = "110914"; ---- a/scripts/orderPrimerPairs.perl -+++ b/scripts/orderPrimerPairs.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: puts the primers in 96 well format for ordering. - # creates a file that can be emailed to -@@ -13,6 +13,8 @@ - # 2) a file of primer pairs, sorted by product size - # 3) a fasta file of the primers, for your convenience for analysis - -+use warnings; -+ - $| = 1; - - $szUsage = "orderPrimerPairs.perl"; ---- a/scripts/phd2Ace.perl -+++ b/scripts/phd2Ace.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # phd2Ace.perl - # -@@ -13,6 +13,8 @@ - # REV: 981002 (David Gordon) for new ace format - # 981210 (DG) to eliminate warning message - -+use warnings; -+ - $szPhdDirPath = "../phd_dir"; - - $szUsage = "Usage: phd2Ace.perl <filename (without directory) of phd file>\nThe phd file is assumed to reside in $szPhdDirPath"; ---- a/scripts/phredPhrap -+++ b/scripts/phredPhrap -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # phredPhrap - # -@@ -70,6 +70,8 @@ - # Rev: 110609 to allow masking of vector sequence when doing miniassemblies - # Rev: 120312 to not duplicate consensus tags during miniassembly - -+use warnings; -+ - $szVersion = "120312"; - - ---- a/scripts/picard2Regions.perl -+++ b/scripts/picard2Regions.perl -@@ -1,10 +1,12 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # PURPOSE: takes a file of locations in the format for bamScape custom - # navigation (Picard IntervalList format), adds 2000 bases of context - # to each side of each location, and prints a region file in format to - # be used by bam2Ace - -+use warnings; -+ - $szRevision = "140903"; # David Gordon - - if ( defined( $ARGV[0] ) && ---- a/scripts/removeReads -+++ b/scripts/removeReads -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # PURPOSE: removes a list of chromats from an assembly. After running this, - # you must reassemble to create an ace file without the given phd files. -@@ -16,6 +16,8 @@ - # removeReads (name of fof's) - # - -+use warnings; -+ - $szUsage = "Usage: removeReads listOfReads.fof"; - - die "$szUsage" if ( $#ARGV != 0 ); ---- a/scripts/revertToUneditedRead -+++ b/scripts/revertToUneditedRead -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # PURPOSE: If the user really screws up a read, to back out all changes. - # You must reassemble after using this. -@@ -16,6 +16,7 @@ - # REV: 7/24/98 (DG) - # REV: 8/28/2013 (DG) to handle readnames with slashes (/) - -+use warnings; - - $szUsage = "Usage: revertToUneditedRead (read name without any .phd.# extension)"; - ---- a/scripts/selectOneRegion.perl -+++ b/scripts/selectOneRegion.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # selectOneRegion.perl - # -@@ -11,6 +11,7 @@ - # and you will create an ace file chr15_51000000.ace or chr15_51000000.ace.1 - # (or higher extension) - -+use warnings; - use Getopt::Long; - - ---- a/scripts/selectRegions.perl -+++ b/scripts/selectRegions.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - - # selectRegions.perl - # -@@ -43,7 +43,7 @@ - # my_new_ace.ace says what the ace file should be called (the - # extension may not start at 1 if there is already a .1 - -- -+use warnings; - - $SIG{__WARN__} = dieWhenGetWarning; - sub dieWhenGetWarning { ---- a/scripts/tagRepeats.perl -+++ b/scripts/tagRepeats.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # PROGRAM: tagRepeats.perl - # PURPOSE: to put consensus tags on any found ALU or any other -@@ -10,6 +10,7 @@ - # INPUTS: The ace file. You must also provide a fasta file of the - # ALU or any other sequence you want to tag - -+use warnings; - - $szVersion = "090209"; - if ( $#ARGV >= 0 ) { ---- a/scripts/testSocket.perl -+++ b/scripts/testSocket.perl -@@ -1,7 +1,8 @@ --#! /usr/local/bin/perl -w -+#!/usr/bin/env perl - - # open a socket to consed -- -+ -+use warnings; - use IO::Socket; - - # Consed makes a file which has nothing but the port number. ---- a/scripts/transferConsensusTags.perl -+++ b/scripts/transferConsensusTags.perl -@@ -1,4 +1,4 @@ --#!/usr/bin/perl -w -+#!/usr/bin/env perl - # - # Purpose: Transfers consensus tags from an old assembly to - # a new assembly. -@@ -44,6 +44,8 @@ - # Nov 2001, DG to handle cloneEnd tags which have orientation - # Mar 2012, DG to prevent duplicating tags after miniassembly - -+use warnings; -+ - $szUsage = "Usage: transferConsensusTags.perl (old ace file) (new ace file) (file of list of old contigs with consensus tags to be transferred)"; - - if ( $ARGV[0] eq "-V" || $ARGV[0] eq "-v" ) { diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch deleted file mode 100644 index 90e180da0174..000000000000 --- a/sci-biology/consed/files/consed-29-fix-qa.patch +++ /dev/null @@ -1,294 +0,0 @@ -Fix various QA violations, due to -* implicit declarations -* incorrect printf() format specifiers -* incorrect function prototypes -* remove unsafe gets() fucntion - ---- a/misc/454/sff2scf.c -+++ b/misc/454/sff2scf.c -@@ -39,6 +39,7 @@ - void writeScfFile(char *filearg, char *outfile); - void writeScfCommand(char *filearg, char *outfile); - -+int sffinfo(int argc, char *argv[], FILE* pTempFile ); - - int main(int argc, char *argv[]) - { ---- a/misc/mktrace/mktrace.c -+++ b/misc/mktrace/mktrace.c -@@ -70,9 +70,9 @@ - else - { - printf( "enter FASTA filename: " ); -- gets( ifnm ); -+ fgets( ifnm, sizeof(ifnm), stdin ); - printf( "enter output filename: " ); -- gets( ofnm ); -+ fgets( ofnm, sizeof(ofnm), stdin ); - } - - /* -@@ -192,7 +192,7 @@ - /* - ** Write phd file. - */ -- if( writePhd( ofnm, numBase, seq, qual, pos, numPoint, trace ) == ERROR ) -+ if( writePhd( ofnm, numBase, seq, qual, pos, numPoint ) == ERROR ) - { - fprintf( stderr, "mktrace: error: bad status: writePhd\n" ); - free( seq ); ---- a/misc/mktrace/mktrace.h -+++ b/misc/mktrace/mktrace.h -@@ -37,8 +37,8 @@ - int writeSCF( char *filename, int numBase, char *seq, int numPoint, float **trace ); - int freeTrace( float **trace ); - char *readFASTA( char *filename, char *entryName, char *comments, int *len ); --int writePhd( char *ofnm, int numBase, char *seq, int *pos, int numPoint ); - int *readQUAL( char *filename, char *entryName, char *comments, int *len ); -+char *getTime( void ); - #else - int writePhd(); - float **synTrace(); ---- a/misc/phd2fasta/phd2fasta.h -+++ b/misc/phd2fasta/phd2fasta.h -@@ -276,6 +276,10 @@ - Comments *comments, Seq *seq, TagList *tagList, char *emsg ); - int checkIntString( char *string ); - int delimiterTest( char *string, unsigned int mask ); -+int checkParam( Option *option ); -+char* getVersion( void ); -+int showDoc( void ); -+char* getTime( void ); - #else - Option *getOption(); - struct Tag *allocTag(); ---- a/misc/phd2fasta/readStdTag.c -+++ b/misc/phd2fasta/readStdTag.c -@@ -699,11 +699,11 @@ - if( fstat ) - { - fprintf( stderr, -- "readStdTag: %s: line: %d: unexpected delimiter %s\n", -+ "readStdTag: %s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); -- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", -+ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); ---- a/misc/phd2fasta/readWholeReadTag.c -+++ b/misc/phd2fasta/readWholeReadTag.c -@@ -393,11 +393,11 @@ - if( fstat ) - { - fprintf( stderr, -- "readWholeReadTag: %s: line: %d: unexpected delimiter %s\n", -+ "readWholeReadTag: %s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); -- sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n", -+ sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n", - filename, - nline, - line ); ---- a/misc/phd2fasta/writeFasta.c -+++ b/misc/phd2fasta/writeFasta.c -@@ -39,7 +39,7 @@ - #include "phd2fasta.h" - - #ifdef ANSI_C --writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, -+int writeFasta( FILE *sfp, FILE *qfp, FILE *bfp, - int outBasePosOption, - Comments *comments, Seq *seq, TagList *tagList, char *emsg ) - #else ---- a/motifutils.cpp -+++ b/motifutils.cpp -@@ -202,13 +202,13 @@ - void printButtonEvent( XButtonEvent* pEvent ) { - - printf( "type = %d\n", pEvent->type ); -- printf( "serial = %d\n", pEvent->serial ); -+ printf( "serial = %lu\n", pEvent->serial ); - printf( "send_event = %s\n", szPrintBool( pEvent->send_event ) ); -- printf( "*display = %x\n", pEvent->display ); -- printf( "window = %x\n", pEvent->window ); -- printf( "root = %x\n", pEvent->root ); -- printf( "subwindow = %x\n", pEvent->subwindow ); -- printf( "time = %d\n", pEvent->time ); -+ printf( "*display = %p\n", pEvent->display ); -+ printf( "window = %lu\n", pEvent->window ); -+ printf( "root = %lu\n", pEvent->root ); -+ printf( "subwindow = %lu\n", pEvent->subwindow ); -+ printf( "time = %lu\n", pEvent->time ); - printf( "x = %d\n", pEvent->x ); - printf( "y = %d\n", pEvent->y ); - printf( "x_root = %d\n", pEvent->x_root ); ---- a/parseAceFile.cpp -+++ b/parseAceFile.cpp -@@ -45,6 +45,7 @@ - using namespace std; - #include "basesegment.h" - #include <stdio.h> -+#include <stddef.h> - #include <string.h> - #include <sstream> - #include "mbt_errors.h" -@@ -292,7 +293,7 @@ - char* szPossibleComp = szReadName + nLength - nCOMP; - - if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) { -- szPossibleComp = '\0'; -+ szPossibleComp = NULL; - return( true ); - } - else ---- a/phaster2PhdBall.cpp -+++ b/phaster2PhdBall.cpp -@@ -547,7 +547,7 @@ - - int nTokens = - sscanf( soLine_.data(), -- "%s %*s %d %d %lld %s %s %*s %d %d %lld %s %s\n", -+ "%s %*s %d %d %ld %s %s %*s %d %d %ld %s %s\n", - soReadName_.data(), - &nRead1Left_, - &nRead1Right_, ---- a/printAutoFinishMiscInfo.cpp -+++ b/printAutoFinishMiscInfo.cpp -@@ -80,7 +80,7 @@ - int nError = stat( (char*) soAceFileFullPathname.data(), &statBuffer ); - - if (nError == 0 ) { -- fprintf( pAO,"size: %d date: %s\n", -+ fprintf( pAO,"size: %ld date: %s\n", - (long) statBuffer.st_size, - ctime( &( statBuffer.st_mtime )) ); - ---- a/printAutoFinishParameters.cpp -+++ b/printAutoFinishParameters.cpp -@@ -206,7 +206,7 @@ - pCP->nInexactSearchForStringMaxPerCentMismatch_ ); - - fprintf( pAO, "! when using the inexact search for string, allow up to this\n"); -- fprintf( pAO, "! % mismatch: the sum of the insertion, deletion, and substitution\n"); -+ fprintf( pAO, "! %% mismatch: the sum of the insertion, deletion, and substitution\n"); - fprintf( pAO, "! differences divided by the length of the query string\n"); - fprintf( pAO, "! (YES)\n"); - fprintf( pAO, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n", -@@ -825,7 +825,7 @@ - fprintf( pAO, "! template will be 1500 bases from the forward read. But if this template\n"); - fprintf( pAO, "! has an insert that is shorter than average, the walk may walk into vector.\n"); - fprintf( pAO, "! To be conservative, we may want to assume that the insert is somewhat \n"); -- fprintf( pAO, "! shorter than average. By default, we assume that it is 90% as large as \n"); -+ fprintf( pAO, "! shorter than average. By default, we assume that it is 90%% as large as \n"); - fprintf( pAO, "! the average. This parameter gives that percentage. This parameter\n"); - fprintf( pAO, "! is used both by Consed and Autofinish.\n"); - fprintf( pAO, "! (OK)\n"); -@@ -1249,9 +1249,9 @@ - pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ ); - - fprintf( pAO, "! Autofinish computes the per cent of existing reads are aligned at\n"); -- fprintf( pAO, "! each base position. Typically, this number starts at around 0% at\n"); -- fprintf( pAO, "! base position 1, rises to close to 100% at around base position 300,\n"); -- fprintf( pAO, "! and then drops again to 0% at base position 800 or so. This number\n"); -+ fprintf( pAO, "! each base position. Typically, this number starts at around 0%% at\n"); -+ fprintf( pAO, "! base position 1, rises to close to 100%% at around base position 300,\n"); -+ fprintf( pAO, "! and then drops again to 0%% at base position 800 or so. This number\n"); - fprintf( pAO, "! specifies how high the number must be for Autofinish to consider an\n"); - fprintf( pAO, "! Autofinish read to cover a single subclone region.\n"); - fprintf( pAO, "! (OK)\n"); -@@ -1295,7 +1295,7 @@ - ( ( pCP->bCheckIfTooManyWalks_ ) ? "true" : "false" ) ); - - fprintf( pAO, "! this just checks if the number of walks, pcr ends, and unknown reads\n"); -- fprintf( pAO, "! exceeds 20% of the total number of reads. If this is exceeded, then \n"); -+ fprintf( pAO, "! exceeds 20%% of the total number of reads. If this is exceeded, then \n"); - fprintf( pAO, "! a warning message is given. Typically, such a warning indicates\n"); - fprintf( pAO, "! that you have incorrectly customized determineReadTypes.perl\n"); - fprintf( pAO, "! (OK)\n"); -@@ -1446,7 +1446,7 @@ - ( ( pCP->bProcessMatePairsAtStartup_ ) ? "true" : "false" ) ); - - fprintf( pAO, "! This is necessary to show the mate pair flags, but it does add\n"); -- fprintf( pAO, "! around 15% to startup time.\n"); -+ fprintf( pAO, "! around 15%% to startup time.\n"); - fprintf( pAO, "! (OK)\n"); - fprintf( pAO, "consed.maximumNumberOfTracesShown: %d\n", - pCP->nMaximumNumberOfTracesShown_ ); -@@ -1796,7 +1796,7 @@ - (char*)pCP->soStoreTracePeakPositions_.data() ); - - fprintf( pAO, "! never, always or whenChromatAvailable\n"); -- fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%,\n"); -+ fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%%,\n"); - fprintf( pAO, "! especially if the assembler is Newbler. always means it will store\n"); - fprintf( pAO, "! the positions if they are present in the phd file/ball.\n"); - fprintf( pAO, "! \"whenChromatAvailable\" means it will store trace peak positions for\n"); ---- a/readPrimerScreenSequences.cpp -+++ b/readPrimerScreenSequences.cpp -@@ -167,7 +167,7 @@ - ++nSequenceNumber ) { - if ( pnLengthOfSequence[ nSequenceNumber ] != - strlen( pszSequence[ nSequenceNumber ] ) ) { -- sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %d for sequence number %d", -+ sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %zu for sequence number %d", - pnLengthOfSequence[ nSequenceNumber ], - strlen( pszSequence[ nSequenceNumber ] ), - nSequenceNumber ); ---- a/rwcstring.cpp -+++ b/rwcstring.cpp -@@ -235,7 +235,7 @@ - - nMaxLength_ = nDefaultLengthForConversions; - -- nCurrentLength_ = sprintf( sz_, "%d", lNumberToConvert ); -+ nCurrentLength_ = sprintf( sz_, "%ld", lNumberToConvert ); - - if ( nCurrentLength_ > nMaxLength_ ) { - // big trouble--might not even make it here--might segmentation fault ---- a/someOtherProgramSentACommandToConsed.cpp -+++ b/someOtherProgramSentACommandToConsed.cpp -@@ -89,7 +89,7 @@ - - char szLine2[ nMaxLine ]; - -- sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine ); -+ sprintf( szLine2, "# of chars = %zu %s", strlen( szLine ), szLine ); - - cout << szLine2 << endl; - ---- a/tag.cpp -+++ b/tag.cpp -@@ -466,7 +466,7 @@ - fprintf( pPhdFile, "DATE: %s\n", soDate_.data() ); - - if ( lID_ != nUndefinedTagID ) { -- fprintf( pPhdFile, "ID: %d\n", lID_ ); -+ fprintf( pPhdFile, "ID: %ld\n", lID_ ); - } - - ---- a/userDefinedTagField.cpp -+++ b/userDefinedTagField.cpp -@@ -64,7 +64,7 @@ - - void userDefinedIntegerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { - -- fprintf( pFile, "%s %d\n", -+ fprintf( pFile, "%s %ld\n", - pUserDefinedTagFieldType_->soFieldName_.data(), - l_ ); - } -@@ -119,7 +119,7 @@ - - void userDefinedPointerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) { - -- fprintf( pFile, "%s %d\n", -+ fprintf( pFile, "%s %ld\n", - pUserDefinedTagFieldType_->soFieldName_.data(), - lID_ ); - diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml deleted file mode 100644 index ccdff086e20b..000000000000 --- a/sci-biology/consed/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata>
