From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 05F7B1381F3 for ; Tue, 27 Aug 2013 16:08:55 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 8BC8CE0F10; Tue, 27 Aug 2013 16:08:54 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 17BAFE0F10 for ; Tue, 27 Aug 2013 16:08:53 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id F1A8A33EC6E for ; Tue, 27 Aug 2013 16:08:52 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 9BE7EE545F for ; Tue, 27 Aug 2013 16:08:51 +0000 (UTC) From: "André Erdmann" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "André Erdmann" Message-ID: <1377619643.92dde02e08880b42d92e542ca8f448bfdb89e98f.dywi@gentoo> Subject: [gentoo-commits] proj/R_overlay:master commit in: config/simple-deprules.d/ X-VCS-Repository: proj/R_overlay X-VCS-Files: config/simple-deprules.d/missing X-VCS-Directories: config/simple-deprules.d/ X-VCS-Committer: dywi X-VCS-Committer-Name: André Erdmann X-VCS-Revision: 92dde02e08880b42d92e542ca8f448bfdb89e98f X-VCS-Branch: master Date: Tue, 27 Aug 2013 16:08:51 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: fb30a352-ac93-4c9e-af62-d8399144bcaf X-Archives-Hash: e0acd190bd2ff70919fbea69e976c5b0 commit: 92dde02e08880b42d92e542ca8f448bfdb89e98f Author: André Erdmann mailerd de> AuthorDate: Tue Aug 27 16:07:23 2013 +0000 Commit: André Erdmann mailerd de> CommitDate: Tue Aug 27 16:07:23 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/R_overlay.git;a=commit;h=92dde02e add new "missing" dep rule file --- config/simple-deprules.d/missing | 555 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 555 insertions(+) diff --git a/config/simple-deprules.d/missing b/config/simple-deprules.d/missing new file mode 100644 index 0000000..f7ecf3e --- /dev/null +++ b/config/simple-deprules.d/missing @@ -0,0 +1,555 @@ +#! NOPARSE +# ------------------------------------ +# FORMAT +# +# +# {} +# {} +# {[} +# {package: from [-- optional|mandatory]} +# {[} +# +# ------------------------------------ + +<= 1.0.3(http://hadoop.apache.org/core/) or CDH3(http://www.cloudera.com) + package: hive 0.1.15 from CRAN + +ABCtoolbox + http://www.cmpg.iee.unibe.ch/content/softwares__services/computer_programs/abctoolbox/index_eng.html + package: abctools 0.2 from CRAN + +ADMB version 11 (http://admb-project.org/) foruse.admb=TRUE + http://admb-project.org/ + package: marked 1.0.9 from CRAN + package: marked 1.1.2 from CRAN + +An ODBC3 driver manager + package: RODBC 1.3.6 from CRAN + package: RODBC 1.3.7 from CRAN + dev-db/unixODBC, dev-db/sqliteodbc, dev-db/myodbc, dev-db/psqlodbc, ...? + +asreml +asreml-R +asreml-R 3.x + http://www.vsni.co.uk/software/asreml + package: dlmap 1.12 from CRAN + package: dlmap 1.13 from CRAN + package: mpMap 1.14 from CRAN + package: nadiv 2.8 from R-Forge + package: nadiv 2.9 from CRAN + package: nadiv 2.11 from CRAN + package: nadiv 2.12 from CRAN + package: wgaim 1.2 from CRAN + package: wgaim 1.3.0 from CRAN + package: wgaim 1.4.0 from CRAN + +Bayescan 2.1. See README. + http://cmpg.unibe.ch/software/bayescan/ + package: AFLPsim 0.1.3 from CRAN + package: AFLPsim 0.1.4 from CRAN + +bio3d + http://thegrantlab.org/bio3d/index.html + package: Rknots 1.2.1 from CRAN -- optional + +boxshade + http://sourceforge.net/projects/boxshade/ + http://gpo.zugaina.org/sci-biology/boxshade-bin + package: BioTools 0.0.1 from R-Forge + +calibayesR + package: basisR 0.1.5 from R-Forge -- optional + +CnaStruct + package: jointSeg 0.3.11 from R-Forge -- optional + +cudaMatrixOps + package: LargeRegression 1.0 from CRAN -- optional + +Cytoscape (>= 2.8.0) (if used for visualization ofresults +CytoscapeRPC plugin (>= 1.8) + http://www.cytoscape.org/download.html + * clicking "Proceed to Download" works even if nothing filled out + package: categoryCompare 1.0.0 + package: categoryCompare 1.0.2 + +Debian or Ubuntu system with access to Goto Blas + needs to be checked whether virtual/blas would suffice + package: gcbd 0.2.4 from CRAN + +DESeq2 (>= 1.0.17) + http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html + "in BIOC since 2.12" + package: metaRNASeq 0.3 from R-Forge + +DSA + package: tmle 1.2.0.1 from CRAN -- optional + Theres a newer version available, tmle 1.2.0.3, which does no longer suggest + DSA. + +fCalendar + package: FinTS 0.4.4 from R-Forge -- optional + fCalendar is available in CRAN-Archive + +FEAR + http://www.clemson.edu/economics/faculty/wilson/software/fear/fear.html + seems to have its own license! + + 6. You are prohibited from the following activities, unless specifically permitted by OWNER: + [...] + ii. distributing, selling, sub-licensing, or otherwise making the software available for use by a third party; and + + package: Benchmarking 0.20 from CRAN -- optional + package: Benchmarking 0.21 from CRAN -- optional + package: Benchmarking 0.22 from CRAN -- optional + package: Benchmarking 0.23 from CRAN -- optional + +Fedora: poppler-glib-devel] + app-text/poppler? + package: Rpoppler 0.0.0 from CRAN -- mandatory + package: Rpoppler 0.0.1 from CRAN -- mandatory + +fUtilities + CRAN-Archive + package: FinTS 0.4.4 from R-Forge -- optional + +GAPS-JAGS (==1.0.2) + *** TODO, cannot access upstream site currently *** + package: CoGAPS 1.6.0 + +glcoxph + http://datamining.dongguk.ac.kr/Rlib/index.html + http://datamining.dongguk.ac.kr/Rlib/glcoxph/ + package: plsRcox 0.7.0 from CRAN -- optional + package: plsRcox 0.9 from CRAN -- optional + +Hadoop core >= 0.19.1 +Hadoop core >= 0.20.3(http://hadoop.apache.org/core/) + http://hadoop.apache.org/ + package: hive 0.1.15 from R-Forge -- mandatory + package: RHive 0.0.6 from CRAN -- mandatory + package: RHive 0.0.7 from CRAN -- mandatory + +happy.hbrem + http://www.well.ox.ac.uk/happy/happyR.shtml + package: mpMap 1.14 from CRAN -- optional + +Hive >= 0.8(http://hive.apache.org/) + http://hive.apache.org/ + package: RHive 0.0.6 from CRAN -- mandatory + package: RHive 0.0.7 from CRAN -- mandatory + +IBGEPesq + *** TODO *** + package: dicionariosIBGE 1.1.1 from CRAN -- optional + +IBM ILOG CPLEX (>= 12.1) + http://www-03.ibm.com/software/products/us/en/ibmilogcpleoptistud/ + $$ + package: cplexAPI 1.2.3 from CRAN -- mandatory + package: cplexAPI 1.2.2 from CRAN -- mandatory + package: cplexAPI 1.2.9 from CRAN -- mandatory + +INLA + http://www.r-inla.org/download + package: abn 0.83 from CRAN + package: diseasemapping 0.6 from CRAN + package: diseasemapping 0.7 from R-Forge + package: inlaDevel 0.001 from R-Forge + package: lgcp 0.9.7 from CRAN + package: lgcp 1.3.2 from CRAN + +Internal files Xba.CQV + nothing useful found. + package: RLMM 1.18.0 from BIOC -- mandatory + +KEGGREST + http://bioconductor.org/packages/2.12/bioc/html/KEGGREST.html + "in BIOC since 2.12" + package: opm 0.10.22 from R-Forge + package: opm 0.10.32 from R-Forge + +kinship +kinship (>= 1.1.0-9) + CRAN-Archive + package: multic 0.3.2 -- optional + package: pbatR 2.2.9 from CRAN -- optional + +Komodo Edit (http://www.openkomodo.com) + http://www.openkomodo.com/ + http://www.activestate.com/komodo-edit + package: svKomodo 0.9.58 from R-Forge -- mandatory + package: svKomodo 0.9.59 from CRAN -- mandatory + package: svKomodo 0.9.60 from R-Forge -- mandatory + +kopls + http://kopls.sourceforge.net/ + package: Metabonomic 3.5 from CRAN + +libapparmor-dev + sys-libs/libapparmor is available in hardened-dev + http://git.overlays.gentoo.org/gitweb/?p=proj/hardened-dev.git;a=summary + package: RAppArmor 0.8.3 from CRAN + !!! Older versions (0.5.0, 0.6.0) do not declare any apparmor dependency. + +libraries() [Debian/Ubuntu:libpoppler-glib-dev + see "Fedora: poppler-glib-devel]" // app-text/poppler? + +libsbml (>=3.0.3) + http://sbml.org/Software/libSBML + http://sourceforge.net/projects/sbml/files/libsbml/ + package: rsbml 2.14.4 -- mandatory + +LINDO API 8.0 + http://www.lindo.com/index.php?option=com_content&view=article&id=1.. + package: rLindo 8.0.1 from CRAN -- mandatory + +lodplot + CRAN-Archive + package: quantsmooth 1.22.0 -- mandatory + +MAGMA library +MAGMA shared libraries (== release 0.2) +MAGMA shared libraries (== release 1.3.0) + http://icl.cs.utk.edu/magma/ + http://icl.cs.utk.edu/magma/software/index.html + package: HiPLARM 0.1 from CRAN + package: magma 0.2.2.1 from CRAN + package: magma 1.3.0.2 from CRAN + +mark.exe (>= 6.2) (or mark32.exe andmark64.exe) + name implies windows-only + upstream site http://www.phidot.org/software/mark/download/ is dead. + package: RMark 2.1.3 from CRAN -- mandatory + package: RMark 2.1.5 from CRAN -- mandatory + package: RMark 2.1.6.1 from CRAN -- mandatory + +MERLIN fromurl{www.sph.umich.edu/csg/abecasis/merlin} must be installedand pointed to in the PATH environment variable. + www.sph.umich.edu/csg/abecasis/merlin + http://www.sph.umich.edu/csg/abecasis/merlin/download/ + packages: paramlink * from CRAN + +MonetDB installation + http://www.monetdb.org/ + http://dev.monetdb.org/downloads/sources/Latest/ + package: MonetDB_R 0.7.9 from R-Forge + package: MonetDB_R 0.7.5 from R-Forge + package: MonetDB_R 0.7.10 from R-Forge + package: MonetDB_R 0.7.3 from R-Forge + package: MonetDB_R 0.7.4 from R-Forge + package: MonetDB_R 0.7.8 from R-Forge + package: MonetDB_R 0.7 from R-Forge + +MOSEK +MOSEK (http://www.mosek.com) +MOSEK License +MOSEK License foruse of Rmosek. +MOSEK Optimization Software + package: REBayes 0.40 from CRAN + package: Rmosek 1.2.3 from CRAN + package: Rmosek 1.2.5 from R-Forge + package: REBayes 0.32 from CRAN + package: Rmosek 1.2.4 from CRAN + +notepad.exe + explicit windows dependency (->mark.exe, ...) + package: RMark 2.1.3 from CRAN + package: RMark 2.1.5 from CRAN + package: RMark 2.1.6.1 from CRAN + +NW RFC SDK downloaded + SAP software? + package: RSAP 0.9 from CRAN + +OpenBugs +OpenBUGS (>= 3.2.2) +OpenBUGS (>=3.2.2) +OpenBUGS (http://www.openbugs.info/w/Downloads) + http://www.openbugs.info/w/ + http://www.openbugs.info/w/Downloads + package: BTSPAS 2012.0217 from CRAN + package: rbugs 0.5.9 from CRAN + package: rbugs 0.5.6 from CRAN + package: BTSPAS 2012.0219 from CRAN + package: R2OpenBUGS 3.2.2.2 from CRAN + package: BRugs 0.8.3 from CRAN + package: R2OpenBUGS 3.2.2.1 from CRAN + package: BRugs 0.8.1 from CRAN + package: BRugs 0.8.0 from CRAN + package: rriskBayes 2.3 from CRAN + package: rriskBayes 2.2 from CRAN + +OpenMx + http://openmx.psyc.virginia.edu/ + http://gitorious.org/openmx/openmx.git + package: MBESS 3.3.2 from CRAN + package: simsem 0.5.3 from CRAN + package: MBESS 3.3.3 from CRAN + package: semTools 0.4.0 from CRAN + +OPIOctopus900 + http://people.eng.unimelb.edu.au/aturpin/opi/octo900.html + package: OPI 1.2 from R-Forge -- optional + package: OPI 1.2.2 from R-Forge -- optional + package: OPI 1.6 from R-Forge -- optional + package: OPI 1.2.1 from R-Forge -- optional + package: OPI 1.5 from R-Forge -- optional + package: OPI 1.4 from CRAN -- optional + package: OPI 1.1 from CRAN -- optional + +optionally qacct) + http://en.wikipedia.org/wiki/Sun_Grid_Engine + http://www.oracle.com/technetwork/oem/grid-engine-166852.html + package: Rsge 0.6.3 from CRAN + +Oracle client + dev-db/oracle-instantclient-basic? + package: ora 2.0.0 from CRAN + +Oracle Instant Client or Oracle Database Client + dev-db/oracle-instantclient-basic? + package: ROracle 1.1.10 from CRAN + package: ROracle 1.1.3 from CRAN + package: ROracle 1.1.5 from CRAN + +pdf2 + http://r-forge.r-project.org/projects/pdf2/ + https://r-forge.r-project.org/R/?group_id=193 + R-Forge: "failed to build" + package: SGP 0.9.9.0 from CRAN + +PLASMA library + kde-base/plasma-runtime? + kde-base/libplasmagenericshell? + package: HiPLARM 0.1 from CRAN + +ply2ascii(http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/) + ? + +polynomial + built-in "poly"? + package list not correct due to false positives + package: sqlsurvey 0.6.7 from R-Forge + package: glmBfp 0.0.26 from R-Forge + package: lava_nlin 0.2.4 from R-Forge + package: glmBfp 0.0.35 from R-Forge + package: smoothtest 2.0.3 from R-Forge + package: sqlsurvey 0.4.2 from R-Forge + package: nFDR 0.0.1 from CRAN + package: epr 1.0 from CRAN + package: polspline 1.1.5 from CRAN + package: CompetingRiskFrailty 2.0 + package: ptw 1.0.5 from CRAN + package: simPH 0.7.2 from CRAN + package: multipol 1.0.6 from CRAN + package: polspline 1.1.8 from CRAN + package: polydect 0.1.2 from CRAN + package: lpint 1.0 from CRAN + package: gaussquad 1.0.1 from CRAN + package: quantchem 0.13 from CRAN + package: PoMoS 1.1.1 from CRAN + package: orthopolynom 1.0.5 from CRAN + package: locpol 0.4.0 from CRAN + package: mfp 1.4.9 from CRAN + package: NonpModelCheck 1.0 from CRAN + package: polynom 1.3.6 from CRAN + package: locpol 0.5.0 from CRAN + package: nsga2R 1.0 from CRAN + package: mirt 0.8.0 from CRAN + package: locpol 0.6.0 from CRAN + package: gptk 1.05 from CRAN + package: ptw 1.0.4 from CRAN + package: mirt 0.2.6 from CRAN + package: orthopolynom 1.0.3 from CRAN + package: gaussquad 1.0.2 from CRAN + package: PolynomF 0.94 from CRAN + package: mpoly 0.0.3 from CRAN + package: multipol 1.0.5 from CRAN + package: MonoPoly 0.2.7 from CRAN + package: EQL 1.0.0 from CRAN + package: BayesNI 0.1 from CRAN + package: bfp 0.0.25 from R-Forge + package: TwoWaySurvival 2.2 + package: Lmoments 1.1.5 from CRAN + package: DPpackage 1.1.5 from CRAN + package: epr 2.0 from CRAN + package: DPpackage 1.1.6 from CRAN + package: RSA 0.7.1 from CRAN + package: mirt 0.4.0 from CRAN + package: marelac 2.1.2 from R-Forge + package: bdynsys 1.0 from CRAN + package: quantchem 0.12.1 from CRAN + package: boolfun 0.2.7 from CRAN + package: gptk 1.06 from CRAN + package: genlasso 1.0 from CRAN + package: boolfun 0.2.8 from CRAN + package: tmg 0.1 from CRAN + package: wombsoft 2.0 from CRAN + package: mpoly 0.0.1 from CRAN + package: ptw 1.0.3 from CRAN + package: widenet 0.1.2 from CRAN + +Poppler Glib interface headers + app-text/poppler? + package: Rpoppler 0.0.1 from CRAN + package: Rpoppler 0.0.0 from CRAN + +PostgreSQL JDBCdriver + dev-java/jdbc-postgresql? + +Protocol Buffer compiler (to create C++ header andsource files from .proto descriptions) + ? + +qsarr + https://r-forge.r-project.org/projects/qsarr/ + R-Forge: "failed to build" + package: qsarm 1.1 from R-Forge + +qstat + http://en.wikipedia.org/wiki/Sun_Grid_Engine + http://www.oracle.com/technetwork/oem/grid-engine-166852.html + or CAN BE RESOLVED: games-util/qstat? + package: IsoGeneGUI 1.11.0 from R-Forge + package: IsoGeneGUI 1.12.0 + package: Rsge 0.6.3 from CRAN + +R-Forge build/check environment(http://R-Forge.R-project.org) + ? + package: RForgeTools 0.4.13 + package: rfTools 0.5.8.0 + package: rfTools 0.5.8.2 + package: rfTools 0.5.8.5 + package: rfTools 0.5.8.6 + +rayproject + http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/sources/ + package: Morpho 0.24.1 from CRAN + package: Morpho 0.25 from CRAN + package: Morpho 0.25.1 from CRAN + +RdbiPgSQL + in BIOC 1.6, 1.7 + package: RForgeTools 0.4.13 from R-Forge -- optional + +rdp-classifier + http://sourceforge.net/projects/rdp-classifier/? + package: BioTools 0.0.1 from R-Forge -- mandatory + +rel_32.exe (see README.txt) + windows only + package: RMark 2.1.3 from CRAN + package: RMark 2.1.5 from CRAN + package: RMark 2.1.6.1 from CRAN + +Requires SGE (qsub + http://en.wikipedia.org/wiki/Sun_Grid_Engine + http://www.oracle.com/technetwork/oem/grid-engine-166852.html + package: Rsge 0.6.3 from CRAN + +retistruct (>= 0.4.10) +retistruct (>= 0.5.7) + https://r-forge.r-project.org/R/?group_id=1436 + "failed to build" + package: retistructgui 0.5.8 from R-Forge + package: retistructdemos 0.5.8 from R-Forge + +revoIPC(>= 1.0-1) + CRAN Archive + package: doSMP 1.0.3 from R-Forge + +Rlsf + CRAN Archive + package: MSToolkit 3.0.3 from R-Forge + package: MSToolkit 2.0 from CRAN + +RNMImport + ? + package: MSToolkit 3.2.1 from R-Forge -- optional + package: MSToolkit 3.0.3 from R-Forge -- optional + package: MSToolkit 3.2.0 from R-Forge -- optional + +rpvm + CRAN Archive + package: snow 0.3.10 from CRAN + package: snow 0.3.12 from CRAN + package: snowFT 1.2.0 from CRAN + package: varSelRF 0.7.3 from CRAN + package: race 0.1.59 from CRAN + +rtreebase + treebase from CRAN? + package: PhyloOrchard 0.1 from R-Forge + +SAGA GIS (2.0.4 - 2.0.8) +SAGA GIS (2.0.4 - 2.1.0) + http://www.saga-gis.org/en/index.html + http://sourceforge.net/projects/saga-gis/ + package: RSAGA 0.93.2.1 from CRAN + package: RSAGA 0.93.1 from CRAN + package: RSAGA 0.93.6 from CRAN + +SciViews-K(http://www.sciviews.org/SciViews-K) + http://www.sciviews.org/SciViews-K/ + package: svKomodo 0.9.58 + package: svKomodo 0.9.59 + package: svKomodo 0.9.60 + +The standalone program xgobi must be installedadditionally +xgobi must be installed additionally + http://www2.research.att.com/areas/stat/xgobi/ + package: xgobi 1.2.14 + package: xgobi 1.2.15 + +TODO!!! + cannot be resolved. + package: svDialogs 0.9.53 from R-Forge + package: svDialogs 0.9.52 from CRAN + package: svDialogs 0.9.54 from R-Forge + +traceR + ? + nlmeU 0.70.3 does no longer suggest this package + package: nlmeU 0.60.14 from R-Forge -- optional + +trimesh_project + http://sourceforge.net/projects/morpho-rpackage/files/Auxiliaries/sources/ ? + package: Morpho 0.24.1 from CRAN + package: Morpho 0.25 from CRAN + package: Morpho 0.25.1 from CRAN + +twMisc + R-Forge, failed to build + package: twMiscRgl 0.5.1 from R-Forge + package: twSnowfall 0.8.81 from R-Forge + +Ubigraph (http://ubietylab.net/ubigraph/index.html) + http://ubietylab.net/ubigraph/index.html + package: RUbigraph 0.1.1 -- mandatory + +WinBUGS (>= 1.4) +WinBUGS 1.4 + http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml + seems to be windows-only + TOOD: check if the listed packages "really" need WinBUGS + package: dclone 2.0.0 from R-Forge + package: JMbayes 0.4.1 from CRAN + package: dclone 1.8.1 from R-Forge + package: dclone 1.8.0 from R-Forge + package: JMbayes 0.2.0 from CRAN + package: R2WinBUGS 2.1.19 from CRAN + package: R2WinBUGS 2.1.18 from CRAN + +WNdb-3.0.tar.gz fromwordnet.princeton.edu + http://wordnet.princeton.edu/wordnet/download/current-version/ + http://wordnetcode.princeton.edu/3.0/WNdb-3.0.tar.gz + package: wordnet 0.1.9 + package: wordnet 0.1.8 + +Xba.regions (or otherregions file) + *** see "Internal files Xba.CQV" above // nothing found *** + +ypaddon + https://bitbucket.org/remkoduursma/ypaddon + https://bitbucket.org/remkoduursma/ypaddon/downloads + package: YplantQMC 0.5 from CRAN + package: YplantQMC 0.5.2 from R-Forge