diff --git a/specs/R-CRAN-ActivePathways.spec b/specs/R-CRAN-ActivePathways.spec index b2cc9db5f..2996db4b1 100644 --- a/specs/R-CRAN-ActivePathways.spec +++ b/specs/R-CRAN-ActivePathways.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ActivePathways -%global packver 2.0.4 +%global packver 2.0.5 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.0.4 +Version: 2.0.5 Release: 1%{?dist}%{?buildtag} Summary: Integrative Pathway Enrichment Analysis of Multivariate Omics Data @@ -27,15 +27,15 @@ Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and -processes. This approach allows researchers to interpret a series of omics -datasets in the context of known biology and gene function, and discover +processes. Genes can be integrated using directional constraints that +reflect how the input datasets are expected interact with one another. +This approach allows researchers to interpret a series of omics datasets +in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. -The first version of the package is part of the following publication: -Integrative Pathway Enrichment Analysis of Multivariate Omics Data. -Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee -MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; -Reimand J, PCAWG Consortium. Nature Communications (2020) -. +The recent version of the package is part of the following publication: +Directional integration and pathway enrichment analysis for multi-omics +data. Slobodyanyuk M^, Bahcheli AT^, Klein ZP, Bayati M, Strug LJ, Reimand +J. Nature Communications (2024) . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-BFF.spec b/specs/R-CRAN-BFF.spec index 9fdf4ade8..f43d78df5 100644 --- a/specs/R-CRAN-BFF.spec +++ b/specs/R-CRAN-BFF.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname BFF -%global packver 3.0.1 +%global packver 4.2.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.0.1 +Version: 4.2.1 Release: 1%{?dist}%{?buildtag} Summary: Bayes Factor Functions @@ -17,22 +17,18 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 2.10 Requires: R-core >= 2.10 BuildArch: noarch -BuildRequires: R-CRAN-BSDA BuildRequires: R-grDevices -BuildRequires: R-graphics -BuildRequires: R-CRAN-hypergeo BuildRequires: R-CRAN-ggplot2 BuildRequires: R-CRAN-Matrix BuildRequires: R-CRAN-gsl BuildRequires: R-stats -Requires: R-CRAN-BSDA +BuildRequires: R-CRAN-rlang Requires: R-grDevices -Requires: R-graphics -Requires: R-CRAN-hypergeo Requires: R-CRAN-ggplot2 Requires: R-CRAN-Matrix Requires: R-CRAN-gsl Requires: R-stats +Requires: R-CRAN-rlang %description Bayes factors represent the ratio of probabilities assigned to data by @@ -50,10 +46,9 @@ thresholds to determine "statistical significance." BFFs are available in closed form and can be easily computed from z, t, chi-squared, and F statistics. They depend on hyperparameters "r" and "tau^2", which determine the shape and scale of the prior distributions defining the -alternative hypotheses. For replicated designs, the "r" parameter in each -function can be adjusted to be greater than 1. Plots of BFFs versus effect -size provide informative summaries of hypothesis tests that can be easily -aggregated across studies. +alternative hypotheses. Plots of BFFs versus effect size provide +informative summaries of hypothesis tests that can be easily aggregated +across studies. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-CDCPLACES.spec b/specs/R-CRAN-CDCPLACES.spec index 4decd2d38..16c062385 100644 --- a/specs/R-CRAN-CDCPLACES.spec +++ b/specs/R-CRAN-CDCPLACES.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname CDCPLACES -%global packver 1.1.5 +%global packver 1.1.6 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.1.5 +Version: 1.1.6 Release: 1%{?dist}%{?buildtag} Summary: Access the 'CDC PLACES' API @@ -21,20 +21,22 @@ BuildRequires: R-CRAN-curl BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-httr BuildRequires: R-CRAN-httr2 -BuildRequires: R-CRAN-jsonlite +BuildRequires: R-CRAN-yyjsonr BuildRequires: R-CRAN-tidyr BuildRequires: R-CRAN-tigris BuildRequires: R-CRAN-sf BuildRequires: R-CRAN-usa +BuildRequires: R-CRAN-zctaCrosswalk Requires: R-CRAN-curl Requires: R-CRAN-dplyr Requires: R-CRAN-httr Requires: R-CRAN-httr2 -Requires: R-CRAN-jsonlite +Requires: R-CRAN-yyjsonr Requires: R-CRAN-tidyr Requires: R-CRAN-tigris Requires: R-CRAN-sf Requires: R-CRAN-usa +Requires: R-CRAN-zctaCrosswalk %description Allows users to seamlessly query several 'CDC PLACES' APIs diff --git a/specs/R-CRAN-DescToolsAddIns.spec b/specs/R-CRAN-DescToolsAddIns.spec index fc35fc42e..bd8599c3f 100644 --- a/specs/R-CRAN-DescToolsAddIns.spec +++ b/specs/R-CRAN-DescToolsAddIns.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname DescToolsAddIns -%global packver 1.10 +%global packver 1.11 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.10 +Version: 1.11 Release: 1%{?dist}%{?buildtag} Summary: Interactive Functions to be Used as Shortcuts in 'RStudio' diff --git a/specs/R-CRAN-HypergeoMat.spec b/specs/R-CRAN-HypergeoMat.spec new file mode 100644 index 000000000..ac2590aa1 --- /dev/null +++ b/specs/R-CRAN-HypergeoMat.spec @@ -0,0 +1,59 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname HypergeoMat +%global packver 4.0.3 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 4.0.3 +Release: 1%{?dist}%{?buildtag} +Summary: Hypergeometric Function of a Matrix Argument + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel +Requires: R-core +BuildRequires: R-CRAN-Rcpp >= 1.0.2 +BuildRequires: R-CRAN-EigenR +BuildRequires: R-CRAN-gsl +BuildRequires: R-CRAN-JuliaConnectoR +BuildRequires: R-CRAN-RcppEigen +Requires: R-CRAN-Rcpp >= 1.0.2 +Requires: R-CRAN-EigenR +Requires: R-CRAN-gsl +Requires: R-CRAN-JuliaConnectoR + +%description +Evaluates the hypergeometric functions of a matrix argument, which appear +in random matrix theory. This is an implementation of Koev & Edelman's +algorithm (2006) . + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-IDSpatialStats.spec b/specs/R-CRAN-IDSpatialStats.spec new file mode 100644 index 000000000..08e955467 --- /dev/null +++ b/specs/R-CRAN-IDSpatialStats.spec @@ -0,0 +1,61 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname IDSpatialStats +%global packver 0.4.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.4.0 +Release: 1%{?dist}%{?buildtag} +Summary: Estimate Global Clustering in Infectious Disease + +License: GPL (>= 2) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 2.10 +Requires: R-core >= 2.10 +BuildRequires: R-CRAN-doParallel +BuildRequires: R-CRAN-foreach +BuildRequires: R-parallel +BuildRequires: R-CRAN-igraph +BuildRequires: R-CRAN-spatstat.explore +BuildRequires: R-CRAN-spatstat.geom +Requires: R-CRAN-doParallel +Requires: R-CRAN-foreach +Requires: R-parallel +Requires: R-CRAN-igraph +Requires: R-CRAN-spatstat.explore +Requires: R-CRAN-spatstat.geom + +%description +Implements various novel and standard clustering statistics and other +analyses useful for understanding the spread of infectious disease. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-PatientProfiles.spec b/specs/R-CRAN-PatientProfiles.spec index aabaffe2a..88b16c0f6 100644 --- a/specs/R-CRAN-PatientProfiles.spec +++ b/specs/R-CRAN-PatientProfiles.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname PatientProfiles -%global packver 1.1.0 +%global packver 1.1.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.1.0 +Version: 1.1.1 Release: 1%{?dist}%{?buildtag} Summary: Identify Characteristics of Patients in the OMOP Common Data Model diff --git a/specs/R-CRAN-corrMCT.spec b/specs/R-CRAN-corrMCT.spec new file mode 100644 index 000000000..daf9fc15a --- /dev/null +++ b/specs/R-CRAN-corrMCT.spec @@ -0,0 +1,63 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname corrMCT +%global packver 0.1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Correlated Weighted Hochberg + +License: GPL (>= 3) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel +Requires: R-core +BuildArch: noarch +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-glue +BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-Matrix +BuildRequires: R-CRAN-tibble +Requires: R-CRAN-dplyr +Requires: R-CRAN-glue +Requires: R-CRAN-magrittr +Requires: R-CRAN-Matrix +Requires: R-CRAN-tibble + +%description +Perform additional multiple testing procedure methods to p.adjust(), such +as weighted Hochberg (Tamhane, A. C., & Liu, L., 2008) +, ICC adjusted Bonferroni method (Shi, Q., +Pavey, E. S., & Carter, R. E., 2012) and a new +correlation corrected weighted Hochberg for correlated endpoints. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-hgwrr.spec b/specs/R-CRAN-hgwrr.spec index 49f25906d..fec81bbf2 100644 --- a/specs/R-CRAN-hgwrr.spec +++ b/specs/R-CRAN-hgwrr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname hgwrr -%global packver 0.4-0 +%global packver 0.5-0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4.0 +Version: 0.5.0 Release: 1%{?dist}%{?buildtag} Summary: Hierarchical and Geographically Weighted Regression diff --git a/specs/R-CRAN-metaHelper.spec b/specs/R-CRAN-metaHelper.spec new file mode 100644 index 000000000..d44468346 --- /dev/null +++ b/specs/R-CRAN-metaHelper.spec @@ -0,0 +1,76 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname metaHelper +%global packver 1.0.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0.0 +Release: 1%{?dist}%{?buildtag} +Summary: Transforms Statistical Measures Commonly Used for Meta-Analysis + +License: MIT + file LICENSE +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel +Requires: R-core +BuildArch: noarch +BuildRequires: R-CRAN-magrittr +BuildRequires: R-stats +BuildRequires: R-CRAN-confintr +Requires: R-CRAN-magrittr +Requires: R-stats +Requires: R-CRAN-confintr + +%description +Helps calculate statistical values commonly used in meta-analysis. It +provides several methods to compute different forms of standardized mean +differences, as well as other values such as standard errors and standard +deviations. The methods used in this package are described in the +following references: Altman D G, Bland J M. (2011) + Borenstein, M., Hedges, L.V., Higgins, J.P.T. and +Rothstein, H.R. (2009) Chinn S. (2000) + +Cochrane Handbook (2011) + Cooper, H., Hedges, L. +V., & Valentine, J. C. (2009) + Cohen, J. (1977) + Ellis, P.D. (2009) + Goulet-Pelletier, J.-C., & +Cousineau, D. (2018) Hedges, L. V. (1981) + Hedges L. V., Olkin I. (1985) + Murad M H, Wang Z, Zhu Y, Saadi S, Chu H, +Lin L et al. (2023) Mayer M (2023) + +Stackoverflow (2014) + +Stackoverflow (2018) . + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-moocore.spec b/specs/R-CRAN-moocore.spec new file mode 100644 index 000000000..4e1a4894d --- /dev/null +++ b/specs/R-CRAN-moocore.spec @@ -0,0 +1,60 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname moocore +%global packver 0.1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Core Mathematical Functions for Multi-Objective Optimization + +License: LGPL (>= 2) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 4.0 +Requires: R-core >= 4.0 +BuildRequires: R-CRAN-matrixStats +BuildRequires: R-CRAN-Rdpack +Requires: R-CRAN-matrixStats +Requires: R-CRAN-Rdpack + +%description +Fast implementation of mathematical operations and performance metrics for +multi-objective optimization, including filtering and ranking of dominated +vectors according to Pareto optimality, computation of the empirical +attainment function, V.G. da Fonseca, C.M. Fonseca, A.O. Hall (2001) +, hypervolume metric, C.M. Fonseca, L. +Paquete, M. López-Ibáñez (2006) ), epsilon +indicator, inverted generational distance, and Vorob'ev threshold, +expectation and deviation, M. Binois, D. Ginsbourger, O. Roustant (2015) +, among others. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-multinet.spec b/specs/R-CRAN-multinet.spec index 9ce889807..d66c2f1b5 100644 --- a/specs/R-CRAN-multinet.spec +++ b/specs/R-CRAN-multinet.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname multinet -%global packver 4.1.2 +%global packver 4.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 4.1.2 +Version: 4.2 Release: 1%{?dist}%{?buildtag} Summary: Analysis and mining of multilayer social networks diff --git a/specs/R-CRAN-mxsem.spec b/specs/R-CRAN-mxsem.spec new file mode 100644 index 000000000..22d94ce56 --- /dev/null +++ b/specs/R-CRAN-mxsem.spec @@ -0,0 +1,63 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname mxsem +%global packver 0.1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Specify 'OpenMx' Models with a 'lavaan'-Style Syntax + +License: GPL (>= 3) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel +Requires: R-core +BuildRequires: R-CRAN-Rcpp >= 1.0.10 +BuildRequires: R-CRAN-OpenMx +BuildRequires: R-stats +BuildRequires: R-methods +BuildRequires: R-CRAN-dplyr +BuildRequires: R-utils +Requires: R-CRAN-Rcpp >= 1.0.10 +Requires: R-CRAN-OpenMx +Requires: R-stats +Requires: R-methods +Requires: R-CRAN-dplyr +Requires: R-utils + +%description +Provides a 'lavaan'-like syntax for 'OpenMx' models. The syntax supports +definition variables, bounds, and parameter transformations. This allows +for latent growth curve models with person-specific measurement occasions, +moderated nonlinear factor analysis and much more. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-neotoma2.spec b/specs/R-CRAN-neotoma2.spec new file mode 100644 index 000000000..9ecb7258d --- /dev/null +++ b/specs/R-CRAN-neotoma2.spec @@ -0,0 +1,86 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname neotoma2 +%global packver 1.0.4 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0.4 +Release: 1%{?dist}%{?buildtag} +Summary: Working with the Neotoma Paleoecology Database + +License: MIT + file LICENSE +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel +Requires: R-core +BuildArch: noarch +BuildRequires: R-CRAN-rlang +BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-sf +BuildRequires: R-CRAN-geojsonsf +BuildRequires: R-CRAN-purrr +BuildRequires: R-CRAN-lubridate +BuildRequires: R-CRAN-httr +BuildRequires: R-CRAN-jsonlite +BuildRequires: R-methods +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-gtools +BuildRequires: R-CRAN-leaflet +BuildRequires: R-CRAN-assertthat +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-progress +BuildRequires: R-CRAN-wk +BuildRequires: R-CRAN-uuid +BuildRequires: R-CRAN-tidyr +Requires: R-CRAN-rlang +Requires: R-CRAN-magrittr +Requires: R-CRAN-sf +Requires: R-CRAN-geojsonsf +Requires: R-CRAN-purrr +Requires: R-CRAN-lubridate +Requires: R-CRAN-httr +Requires: R-CRAN-jsonlite +Requires: R-methods +Requires: R-CRAN-dplyr +Requires: R-CRAN-gtools +Requires: R-CRAN-leaflet +Requires: R-CRAN-assertthat +Requires: R-CRAN-stringr +Requires: R-CRAN-progress +Requires: R-CRAN-wk +Requires: R-CRAN-uuid +Requires: R-CRAN-tidyr + +%description +Access and manipulation of data using the Neotoma Paleoecology Database. +. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-octopucs.spec b/specs/R-CRAN-octopucs.spec new file mode 100644 index 000000000..e7081532d --- /dev/null +++ b/specs/R-CRAN-octopucs.spec @@ -0,0 +1,62 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname octopucs +%global packver 0.1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Statistical Support for Hierarchical Clusters + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel +Requires: R-core +BuildArch: noarch +BuildRequires: R-CRAN-vegan +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-progress +Requires: R-CRAN-vegan +Requires: R-CRAN-stringr +Requires: R-CRAN-progress + +%description +Generates n hierarchical clustering hypotheses on subsets of classifiers +(usually species in community ecology studies). The n clustering +hypotheses are combined to generate a generalized cluster, and computes +three metrics of support. 1) The average proportion of elements conforming +the group in each of the n clusters (integrity). And 2) the contamination, +i.e., the average proportion of elements from other groups that enter a +focal group. 3) The probability of existence of the group gives the +integrity and contamination in a Bayesian approach. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-orbital.spec b/specs/R-CRAN-orbital.spec index 9bb2c5cd0..ae8e35c1e 100644 --- a/specs/R-CRAN-orbital.spec +++ b/specs/R-CRAN-orbital.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname orbital -%global packver 0.1.0 +%global packver 0.2.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.0 +Version: 0.2.0 Release: 1%{?dist}%{?buildtag} Summary: Predict with 'tidymodels' Workflows in Databases @@ -18,8 +18,10 @@ BuildRequires: R-devel Requires: R-core BuildArch: noarch BuildRequires: R-CRAN-cli +BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-rlang Requires: R-CRAN-cli +Requires: R-CRAN-dplyr Requires: R-CRAN-rlang %description diff --git a/specs/R-CRAN-ratioOfQsprays.spec b/specs/R-CRAN-ratioOfQsprays.spec index 48d7cbcab..7b1e375a7 100644 --- a/specs/R-CRAN-ratioOfQsprays.spec +++ b/specs/R-CRAN-ratioOfQsprays.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ratioOfQsprays -%global packver 1.0.0 +%global packver 1.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.1.0 Release: 1%{?dist}%{?buildtag} Summary: Fractions of Multivariate Polynomials with Rational Coefficients @@ -16,16 +16,15 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel Requires: R-core -BuildRequires: R-CRAN-qspray >= 3.0.0 +BuildRequires: R-CRAN-qspray >= 3.1.0 BuildRequires: R-CRAN-gmp BuildRequires: R-methods BuildRequires: R-CRAN-Rcpp BuildRequires: R-CRAN-Ryacas BuildRequires: R-utils BuildRequires: R-CRAN-BH -BuildRequires: R-CRAN-RcppArmadillo BuildRequires: R-CRAN-RcppCGAL -Requires: R-CRAN-qspray >= 3.0.0 +Requires: R-CRAN-qspray >= 3.1.0 Requires: R-CRAN-gmp Requires: R-methods Requires: R-CRAN-Rcpp diff --git a/specs/R-CRAN-spnaf.spec b/specs/R-CRAN-spnaf.spec index 736943d8b..fc766ca90 100644 --- a/specs/R-CRAN-spnaf.spec +++ b/specs/R-CRAN-spnaf.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname spnaf -%global packver 1.0.0 +%global packver 1.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.1.0 Release: 1%{?dist}%{?buildtag} Summary: Spatial Network Autocorrelation for Flow Data diff --git a/specs/R-CRAN-stR.spec b/specs/R-CRAN-stR.spec index 055a194bf..d114649c2 100644 --- a/specs/R-CRAN-stR.spec +++ b/specs/R-CRAN-stR.spec @@ -1,15 +1,15 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname stR -%global packver 0.6 +%global packver 0.7 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.6 +Version: 0.7 Release: 1%{?dist}%{?buildtag} -Summary: STR Decomposition +Summary: Seasonal Trend Decomposition Using Regression -License: GPL (>= 2) +License: GPL-3 URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz @@ -17,35 +17,35 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 3.5.0 Requires: R-core >= 3.5.0 BuildArch: noarch -BuildRequires: R-CRAN-Matrix -BuildRequires: R-CRAN-SparseM -BuildRequires: R-CRAN-quantreg -BuildRequires: R-CRAN-forecast BuildRequires: R-CRAN-foreach -BuildRequires: R-stats -BuildRequires: R-methods +BuildRequires: R-CRAN-forecast BuildRequires: R-graphics BuildRequires: R-grDevices -Requires: R-CRAN-Matrix -Requires: R-CRAN-SparseM -Requires: R-CRAN-quantreg -Requires: R-CRAN-forecast +BuildRequires: R-CRAN-Matrix +BuildRequires: R-methods +BuildRequires: R-CRAN-quantreg +BuildRequires: R-CRAN-SparseM +BuildRequires: R-stats Requires: R-CRAN-foreach -Requires: R-stats -Requires: R-methods +Requires: R-CRAN-forecast Requires: R-graphics Requires: R-grDevices +Requires: R-CRAN-Matrix +Requires: R-methods +Requires: R-CRAN-quantreg +Requires: R-CRAN-SparseM +Requires: R-stats %description -Methods for decomposing seasonal data: STR (a Seasonal-Trend decomposition -procedure based on Regression) and Robust STR. In some ways, STR is -similar to Ridge Regression and Robust STR can be related to LASSO. They -allow for multiple seasonal components, multiple linear covariates with -constant, flexible and seasonal influence. Seasonal patterns (for both -seasonal components and seasonal covariates) can be fractional and +Methods for decomposing seasonal data: STR (a Seasonal-Trend time series +decomposition procedure based on Regression) and Robust STR. In some ways, +STR is similar to Ridge Regression and Robust STR can be related to LASSO. +They allow for multiple seasonal components, multiple linear covariates +with constant, flexible and seasonal influence. Seasonal patterns (for +both seasonal components and seasonal covariates) can be fractional and flexible over time; moreover they can be either strictly periodic or have a more complex topology. The methods provide confidence intervals for the -estimated components. The methods can be used for forecasting. +estimated components. The methods can also be used for forecasting. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-symbolicQspray.spec b/specs/R-CRAN-symbolicQspray.spec index c2a0357a4..45663dd49 100644 --- a/specs/R-CRAN-symbolicQspray.spec +++ b/specs/R-CRAN-symbolicQspray.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname symbolicQspray -%global packver 1.0.0 +%global packver 1.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.1.0 Release: 1%{?dist}%{?buildtag} Summary: Multivariate Polynomials with Symbolic Parameters in their Coefficients @@ -16,17 +16,16 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel Requires: R-core -BuildRequires: R-CRAN-qspray >= 3.0.0 -BuildRequires: R-CRAN-ratioOfQsprays +BuildRequires: R-CRAN-qspray >= 3.1.0 +BuildRequires: R-CRAN-ratioOfQsprays >= 1.1.0 BuildRequires: R-CRAN-gmp BuildRequires: R-methods BuildRequires: R-CRAN-Rcpp BuildRequires: R-utils BuildRequires: R-CRAN-BH -BuildRequires: R-CRAN-RcppArmadillo BuildRequires: R-CRAN-RcppCGAL -Requires: R-CRAN-qspray >= 3.0.0 -Requires: R-CRAN-ratioOfQsprays +Requires: R-CRAN-qspray >= 3.1.0 +Requires: R-CRAN-ratioOfQsprays >= 1.1.0 Requires: R-CRAN-gmp Requires: R-methods Requires: R-CRAN-Rcpp