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Fri, 26 Aug 2022 04:23:44 GMT (envelope-from git) Date: Fri, 26 Aug 2022 04:23:44 GMT Message-Id: <202208260423.27Q4NiVb062612@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: 5aec6e4a190d - main - biology/paml: Update to 4.10.5 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1661487824; 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mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 commit 5aec6e4a190d0d6a6f78ce9c5674fd5bf6b4b5d0 Author: Joseph Mingrone AuthorDate: 2022-08-26 04:19:52 +0000 Commit: Joseph Mingrone CommitDate: 2022-08-26 04:22:46 +0000 biology/paml: Update to 4.10.5 https://github.com/abacus-gene/paml/releases/tag/v4.10.0 https://github.com/abacus-gene/paml/releases/tag/untagged-a5659203e8ec0ddb58b8 https://github.com/abacus-gene/paml/releases/tag/v4.10.5 Sponsored by: The FreeBSD Foundation --- biology/paml/Makefile | 20 +++++++++---------- biology/paml/distinfo | 6 +++--- biology/paml/files/patch-src_paml.h | 14 ------------- biology/paml/pkg-plist | 40 +++++++++++++++++++++++++------------ 4 files changed, 39 insertions(+), 41 deletions(-) diff --git a/biology/paml/Makefile b/biology/paml/Makefile index a8c84d9fb60c..d0f49022b3f7 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -1,21 +1,22 @@ PORTNAME= paml -PORTVERSION= 4.9j +DISTVERSIONPREFIX= v +DISTVERSION= 4.10.5 CATEGORIES= biology -MASTER_SITES= http://abacus.gene.ucl.ac.uk/software/ -DISTNAME= ${PORTNAME}${DISTVERSION} MAINTAINER= jrm@FreeBSD.org COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML) LICENSE= GPLv3 -USES= dos2unix gmake tar:tgz - -DOS2UNIX_GLOB= *.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \ +USES= dos2unix gmake +DOS2UNIX_GLOB= *.aa *.c *.ctl *.dat *.HKYG5 *.nexus *.nuc *.phy *.result *.tre \ *.trees *.txt *.xml paupblock paupend +USE_GITHUB= yes +GH_ACCOUNT= abacus-gene BINARIES= baseml basemlg chi2 codeml evolver evolverNSbranches \ - evolverNSbranchsites evolverNSsites pamp yn00 + evolverNSbranchsites evolverNSsites infinitesites mcmctree pamp \ + yn00 OPTIONS_DEFINE= DOCS EXAMPLES @@ -37,15 +38,12 @@ do-install: do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR} + ${INSTALL_DATA} ${WRKSRC}/README.md ${STAGEDIR}${DOCSDIR} do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \ ${STAGEDIR}${EXAMPLESDIR}) (cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) -.for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup* - ${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR} -.endfor .include diff --git a/biology/paml/distinfo b/biology/paml/distinfo index c6e205ca7ab2..f52a021a50de 100644 --- a/biology/paml/distinfo +++ b/biology/paml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1574435935 -SHA256 (paml4.9j.tgz) = 97aac6cb8f23844202545e9ba4e42020231c2a30051b36f4e4d2f423e270d461 -SIZE (paml4.9j.tgz) = 6562281 +TIMESTAMP = 1661485713 +SHA256 (abacus-gene-paml-v4.10.5_GH0.tar.gz) = 1bb40ea7c976d961a4f46b76e950423f6f252d7060bc621cbf29c9743b88a063 +SIZE (abacus-gene-paml-v4.10.5_GH0.tar.gz) = 3393889 diff --git a/biology/paml/files/patch-src_paml.h b/biology/paml/files/patch-src_paml.h deleted file mode 100644 index c7e35c89038f..000000000000 --- a/biology/paml/files/patch-src_paml.h +++ /dev/null @@ -1,14 +0,0 @@ ---- src/paml.h.orig 2020-08-20 16:14:50 UTC -+++ src/paml.h -@@ -372,9 +372,9 @@ void copySptree(void); - void printSptree(void); - - --enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes; -+enum SeqTypes {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq}; - --enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions; -+enum OutTreeOptions {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32}; - - - /* use mean (0; default) for discrete gamma instead of median (1) */ diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist index 9c0041d7c15f..8ba55f7dfe03 100644 --- a/biology/paml/pkg-plist +++ b/biology/paml/pkg-plist @@ -1,5 +1,17 @@ +bin/baseml +bin/basemlg +bin/chi2 +bin/codeml +bin/evolver +bin/evolverNSbranches +bin/evolverNSbranchsites +bin/evolverNSsites +bin/infinitesites +bin/mcmctree +bin/pamp +bin/yn00 %%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf -%%PORTDOCS%%%%DOCSDIR%%/README.txt +%%PORTDOCS%%%%DOCSDIR%%/README.md %%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf %%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf %%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt @@ -77,7 +89,6 @@ %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/FigTree.tre %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt @@ -85,7 +96,7 @@ %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc @@ -154,6 +165,19 @@ %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/codeml-M0.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.aln +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.tree +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata-maintree.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree-ml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree-ml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend @@ -161,13 +185,3 @@ %%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees %%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl -bin/baseml -bin/basemlg -bin/chi2 -bin/codeml -bin/evolver -bin/evolverNSbranches -bin/evolverNSbranchsites -bin/evolverNSsites -bin/pamp -bin/yn00