commit: 1d568bfbf7494a2168ef8d652b64675afbbd76e5 Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> AuthorDate: Wed Jan 14 21:08:33 2026 +0000 Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org> CommitDate: Wed Jan 14 22:52:05 2026 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1d568bfb
sci-biology/mothur: drop 1.27.0-r1 Closes: https://bugs.gentoo.org/681640 Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org> sci-biology/mothur/Manifest | 1 - .../mothur/files/mothur-1.27.0-makefile.patch | 52 ------------ .../mothur/files/mothur-1.27.0-overflows.patch | 93 ---------------------- sci-biology/mothur/mothur-1.27.0-r1.ebuild | 42 ---------- 4 files changed, 188 deletions(-) diff --git a/sci-biology/mothur/Manifest b/sci-biology/mothur/Manifest index 012b9574a8c3..e5cb8a9ee5a7 100644 --- a/sci-biology/mothur/Manifest +++ b/sci-biology/mothur/Manifest @@ -1,3 +1,2 @@ -DIST mothur-1.27.0.zip 7095054 BLAKE2B 96a6410d36f64ff50591955aa22bfddf6217c7568022c8c7f70ab70c65d57af2217477de56b6f9ceaf11237cdc5380bd354cf6564002357546539585d0f58221 SHA512 81821ca95d4ce3f0d1e6aa920c4fe3fddd70f716157312ed0590c1c4ad728e6786bfe79f6badddcfb060ed5d1996cc1b5062c320a59209fef35f68e687ba3dd5 DIST mothur-1.48.0.tar.gz 1652711 BLAKE2B 39e1d2a32a63d441267b4e0e739505bdcb3ab392c169c96d60e816dbd9fab6b92745e8a9eaae31062711f2de0130dae540bba34c6bd97e76a921711f58c11f65 SHA512 a43ef6a223238d40e51c15043360ba9cae86347affea2f1a4e365635fb0949981ad32001b88d4061a033b2a002e944df16923a0622a40bf061791f06143467e1 DIST mothur-1.48.2.tar.gz 24702253 BLAKE2B 4342640e70f08763c4bc1605441a9526ef967bd5832d103db3095c470ea82c2c554dd03775e8ffdf02a983ee4dfdb43ba008dcf7ff19b99321a0204843f98710 SHA512 0c3496d08131d15db3933165eba832a135ca3bce8010e7a2b4a84802c91d6f5efa54711498148d7cc190420b75a94babf20d6c435a5e07c730924f1f3f966586 diff --git a/sci-biology/mothur/files/mothur-1.27.0-makefile.patch b/sci-biology/mothur/files/mothur-1.27.0-makefile.patch deleted file mode 100644 index 52a02585df14..000000000000 --- a/sci-biology/mothur/files/mothur-1.27.0-makefile.patch +++ /dev/null @@ -1,52 +0,0 @@ - makefile | 14 ++++++-------- - 1 files changed, 6 insertions(+), 8 deletions(-) - -diff --git a/makefile b/makefile -index db7c904..109488f 100644 ---- a/makefile -+++ b/makefile -@@ -10,18 +10,18 @@ - # - - USEMPI ?= no --64BIT_VERSION ?= yes -+64BIT_VERSION ?= no - USEREADLINE ?= yes - CYGWIN_BUILD ?= no - USECOMPRESSION ?= no - MOTHUR_FILES="\"Enter_your_default_path_here\"" - RELEASE_DATE = "\"8/8/2012\"" - VERSION = "\"1.27.0\"" --FORTAN_COMPILER = gfortran --FORTRAN_FLAGS = -+FORTAN_COMPILER = ${FC} -+FORTRAN_FLAGS = ${FCFLAGS} - - # Optimize to level 3: --CXXFLAGS += -O3 -+#CXXFLAGS += -O3 - - ifeq ($(strip $(64BIT_VERSION)),yes) - #if you are using centos uncomment the following lines -@@ -69,7 +69,7 @@ endif - - - ifeq ($(strip $(USEMPI)),yes) -- CXX = mpic++ -+# CXX = mpic++ - CXXFLAGS += -DUSE_MPI - endif - -@@ -95,11 +95,9 @@ OBJECTS=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) - OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) - OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f)) - --mothur : fortranSource $(OBJECTS) uchime -+mothur : fortranSource $(OBJECTS) - $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) - -- strip mothur -- - uchime: - cd uchime_src && ./mk && mv uchime .. && cd .. - diff --git a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch b/sci-biology/mothur/files/mothur-1.27.0-overflows.patch deleted file mode 100644 index 0b612cf7b529..000000000000 --- a/sci-biology/mothur/files/mothur-1.27.0-overflows.patch +++ /dev/null @@ -1,93 +0,0 @@ - chimerauchimecommand.cpp | 2 +- - clearcutcommand.cpp | 32 ++++++++++++++++---------------- - 2 files changed, 17 insertions(+), 17 deletions(-) - -diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp -index bd31c19..2070840 100644 ---- a/chimerauchimecommand.cpp -+++ b/chimerauchimecommand.cpp -@@ -1264,7 +1264,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc - } - - if (ucl) { -- char* tempucl = new char[5]; -+ char* tempucl = new char[6]; - strcpy(tempucl, "--ucl"); - cPara.push_back(tempucl); - } -diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp -index 6a0eb25..2e8164e 100644 ---- a/clearcutcommand.cpp -+++ b/clearcutcommand.cpp -@@ -269,35 +269,35 @@ int ClearcutCommand::execute() { - - vector<char*> cPara; - -- char* tempClearcut = new char[8]; -+ char* tempClearcut = new char[16]; - strcpy(tempClearcut, "clearcut"); - cPara.push_back(tempClearcut); - - //you gave us a distance matrix -- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); } -+ if (phylipfile != "") { char* temp = new char[16]; strcpy(temp, "--distance"); cPara.push_back(temp); } - - //you gave us a fastafile -- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); } -+ if (fastafile != "") { char* temp = new char[16]; strcpy(temp, "--alignment"); cPara.push_back(temp); } - -- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); } -- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); } -- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); } -+ if (version) { char* temp = new char[16]; strcpy(temp, "--version"); cPara.push_back(temp); } -+ if (verbose) { char* temp = new char[16]; strcpy(temp, "--verbose"); cPara.push_back(temp); } -+ if (quiet) { char* temp = new char[16]; strcpy(temp, "--quiet"); cPara.push_back(temp); } - if (seed != "*") { - string tempSeed = "--seed=" + seed; - char* temp = new char[tempSeed.length()]; - strcpy(temp, tempSeed.c_str()); - cPara.push_back(temp); - } -- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); } -- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } -- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } -+ if (norandom) { char* temp = new char[16]; strcpy(temp, "--norandom"); cPara.push_back(temp); } -+ if (shuffle) { char* temp = new char[16]; strcpy(temp, "--shuffle"); cPara.push_back(temp); } -+ if (neighbor) { char* temp = new char[16]; strcpy(temp, "--neighbor"); cPara.push_back(temp); } - - string tempIn = "--in=" + inputFile; - char* tempI = new char[tempIn.length()]; - strcpy(tempI, tempIn.c_str()); - cPara.push_back(tempI); - -- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); } -+ if (stdoutWanted) { char* temp = new char[16]; strcpy(temp, "--stdout"); cPara.push_back(temp); } - else{ - string tempOut = "--out=" + outputName; - -@@ -306,10 +306,10 @@ int ClearcutCommand::execute() { - cPara.push_back(temp); - } - -- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); } -- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); } -- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); } -- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); } -+ if (DNA) { char* temp = new char[16]; strcpy(temp, "--DNA"); cPara.push_back(temp); } -+ if (protein) { char* temp = new char[16]; strcpy(temp, "--protein"); cPara.push_back(temp); } -+ if (jukes) { char* temp = new char[16]; strcpy(temp, "--jukes"); cPara.push_back(temp); } -+ if (kimura) { char* temp = new char[16]; strcpy(temp, "--kimura"); cPara.push_back(temp); } - if (matrixout != "") { - string tempMatrix = "--matrixout=" + outputDir + matrixout; - char* temp = new char[tempMatrix.length()]; -@@ -326,8 +326,8 @@ int ClearcutCommand::execute() { - cPara.push_back(temp); - } - -- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); } -- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); } -+ if (expblen) { char* temp = new char[16]; strcpy(temp, "--expblen"); cPara.push_back(temp); } -+ if (expdist) { char* temp = new char[16]; strcpy(temp, "--expdist"); cPara.push_back(temp); } - - char** clearcutParameters; - clearcutParameters = new char*[cPara.size()]; diff --git a/sci-biology/mothur/mothur-1.27.0-r1.ebuild b/sci-biology/mothur/mothur-1.27.0-r1.ebuild deleted file mode 100644 index 3f5603e9ecb5..000000000000 --- a/sci-biology/mothur/mothur-1.27.0-r1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic fortran-2 toolchain-funcs - -DESCRIPTION="A suite of algorithms for ecological bioinformatics" -HOMEPAGE="https://www.mothur.org/"; -SRC_URI="https://www.mothur.org/w/images/c/cb/Mothur.${PV}.zip -> ${P}.zip" -S="${WORKDIR}/${PN^}.source" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="amd64 ~x86" -IUSE="mpi +readline" - -RDEPEND=" - sci-biology/uchime - mpi? ( virtual/mpi )" -DEPEND="${RDEPEND}" -BDEPEND="app-arch/unzip" - -PATCHES=( - "${FILESDIR}"/${P}-makefile.patch - "${FILESDIR}"/${P}-overflows.patch -) - -src_configure() { - use mpi && export CXX=mpicxx || tc-export CXX - use amd64 && append-cppflags -DBIT_VERSION -} - -src_compile() { - emake \ - USEMPI=$(usex mpi) \ - USEREADLINE=$(usex readline) -} - -src_install() { - dobin mothur -}
