From 2a0984ad22eee4e824d941a7d6ccb84f23ab4f5e Mon Sep 17 00:00:00 2001 From: Github Action Date: Wed, 4 Dec 2024 01:50:19 +0000 Subject: [PATCH] sync --- specs/R-CRAN-BANAM.spec | 4 +- specs/R-CRAN-BFpack.spec | 22 ++-- specs/R-CRAN-MazamaCoreUtils.spec | 4 +- specs/R-CRAN-RCNA.spec | 70 +++++++++++ specs/R-CRAN-RSQLite.spec | 4 +- specs/R-CRAN-RcppEnsmallen.spec | 10 +- specs/R-CRAN-SSDforR.spec | 4 +- specs/R-CRAN-abc.spec | 5 +- specs/R-CRAN-aphylo.spec | 4 +- specs/R-CRAN-basicspace.spec | 62 ++++++++++ specs/R-CRAN-bayesGAM.spec | 110 ------------------ specs/R-CRAN-bit.spec | 4 +- specs/R-CRAN-breathtestcore.spec | 4 +- specs/R-CRAN-breathteststan.spec | 18 +-- specs/R-CRAN-cir.spec | 4 +- specs/R-CRAN-csmGmm.spec | 69 +++++++++++ specs/R-CRAN-dbarts.spec | 4 +- specs/R-CRAN-deeptrafo.spec | 21 ++-- ...yStatTraEOO.spec => R-CRAN-extractox.spec} | 45 ++++--- specs/R-CRAN-gasanalyzer.spec | 4 +- specs/R-CRAN-geocausal.spec | 7 +- specs/R-CRAN-ggfun.spec | 4 +- specs/R-CRAN-googleCloudRunner.spec | 83 ------------- specs/R-CRAN-harbinger.spec | 4 +- specs/R-CRAN-ipd.spec | 4 +- specs/R-CRAN-iq.spec | 4 +- specs/R-CRAN-klassR.spec | 8 +- specs/R-CRAN-knfi.spec | 4 +- ...-CRAN-W4MRUtils.spec => R-CRAN-messy.spec} | 29 ++--- specs/R-CRAN-mongolite.spec | 4 +- specs/R-CRAN-npclust.spec | 4 +- specs/R-CRAN-opendataformat.spec | 4 +- specs/R-CRAN-parallelly.spec | 4 +- specs/R-CRAN-particles.spec | 24 ++-- specs/R-CRAN-pkgmaker.spec | 81 ------------- specs/R-CRAN-processmapR.spec | 4 +- ...idysynth.spec => R-CRAN-resourcecode.spec} | 66 ++++++----- specs/R-CRAN-simdata.spec | 4 +- specs/R-CRAN-sivirep.spec | 36 +++--- specs/R-CRAN-spmoran.spec | 4 +- ...RAN-wooldridge.spec => R-CRAN-sshicm.spec} | 41 ++++--- specs/R-CRAN-tibbletime.spec | 4 +- 42 files changed, 430 insertions(+), 469 deletions(-) create mode 100644 specs/R-CRAN-RCNA.spec create mode 100644 specs/R-CRAN-basicspace.spec delete mode 100644 specs/R-CRAN-bayesGAM.spec create mode 100644 specs/R-CRAN-csmGmm.spec rename specs/{R-CRAN-FuzzyStatTraEOO.spec => R-CRAN-extractox.spec} (53%) delete mode 100644 specs/R-CRAN-googleCloudRunner.spec rename specs/{R-CRAN-W4MRUtils.spec => R-CRAN-messy.spec} (67%) delete mode 100644 specs/R-CRAN-pkgmaker.spec rename specs/{R-CRAN-tidysynth.spec => R-CRAN-resourcecode.spec} (55%) rename specs/{R-CRAN-wooldridge.spec => R-CRAN-sshicm.spec} (55%) diff --git a/specs/R-CRAN-BANAM.spec b/specs/R-CRAN-BANAM.spec index 200e98a57f..cc520a57cb 100644 --- a/specs/R-CRAN-BANAM.spec +++ b/specs/R-CRAN-BANAM.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname BANAM -%global packver 0.2.1 +%global packver 0.2.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.1 +Version: 0.2.2 Release: 1%{?dist}%{?buildtag} Summary: Bayesian Analysis of the Network Autocorrelation Model diff --git a/specs/R-CRAN-BFpack.spec b/specs/R-CRAN-BFpack.spec index b3e6c8a5f2..1ad2402cb8 100644 --- a/specs/R-CRAN-BFpack.spec +++ b/specs/R-CRAN-BFpack.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname BFpack -%global packver 1.3.0 +%global packver 1.4.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.3.0 +Version: 1.4.0 Release: 1%{?dist}%{?buildtag} Summary: Flexible Bayes Factor Testing of Scientific Expectations @@ -28,6 +28,9 @@ BuildRequires: R-CRAN-ergm BuildRequires: R-CRAN-Bergm BuildRequires: R-CRAN-sandwich BuildRequires: R-CRAN-QRM +BuildRequires: R-CRAN-coda +BuildRequires: R-CRAN-metaBMA +BuildRequires: R-methods Requires: R-CRAN-bain Requires: R-stats Requires: R-utils @@ -40,6 +43,9 @@ Requires: R-CRAN-ergm Requires: R-CRAN-Bergm Requires: R-CRAN-sandwich Requires: R-CRAN-QRM +Requires: R-CRAN-coda +Requires: R-CRAN-metaBMA +Requires: R-methods %description Implementation of default Bayes factors for testing statistical hypotheses @@ -53,17 +59,17 @@ that can be tested are location parameters (e.g., group means, regression coefficients), variances (e.g., group variances), and measures of association (e.g,. polychoric/polyserial/biserial/tetrachoric/product moments correlations), among others. The statistical underpinnings are -described in Mulder and Xin (2019) , +described in Mulder and Xin (2022) , Mulder and Gelissen (2019) , Mulder (2016) , Mulder and Fox (2019) , Mulder and Fox (2013) , Boeing-Messing, van Assen, Hofman, Hoijtink, and Mulder (2017) , Hoijtink, Mulder, -van Lissa, and Gu, (2018) , Gu, Mulder, and -Hoijtink, (2018) , Hoijtink, Gu, and Mulder, -(2018) , and Hoijtink, Gu, Mulder, and Rosseel, -(2018) . When using the packages, please refer to -Mulder et al. (2021) . +van Lissa, and Gu (2018) , Gu, Mulder, and +Hoijtink (2018) , Hoijtink, Gu, and Mulder (2018) +, and Hoijtink, Gu, Mulder, and Rosseel (2018) +. When using the packages, please refer to Mulder +et al. (2021) . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-MazamaCoreUtils.spec b/specs/R-CRAN-MazamaCoreUtils.spec index d432523bc2..ee59e0a9b6 100644 --- a/specs/R-CRAN-MazamaCoreUtils.spec +++ b/specs/R-CRAN-MazamaCoreUtils.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname MazamaCoreUtils -%global packver 0.5.2 +%global packver 0.5.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.5.2 +Version: 0.5.3 Release: 1%{?dist}%{?buildtag} Summary: Utility Functions for Production R Code diff --git a/specs/R-CRAN-RCNA.spec b/specs/R-CRAN-RCNA.spec new file mode 100644 index 0000000000..20dfd732f6 --- /dev/null +++ b/specs/R-CRAN-RCNA.spec @@ -0,0 +1,70 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname RCNA +%global packver 1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Robust Copy Number Alteration Detection (RCNA) + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +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-doParallel +BuildRequires: R-methods +BuildRequires: R-utils +BuildRequires: R-CRAN-modeest +BuildRequires: R-CRAN-data.table +BuildRequires: R-CRAN-foreach +BuildRequires: R-CRAN-R.utils +Requires: R-CRAN-doParallel +Requires: R-methods +Requires: R-utils +Requires: R-CRAN-modeest +Requires: R-CRAN-data.table +Requires: R-CRAN-foreach +Requires: R-CRAN-R.utils + +%description +Detects copy number alteration events in targeted exon sequencing data for +tumor samples without matched normal controls. The advantage of this +method is that it can be applied to smaller sequencing panels including +evaluations of exon, transcript, gene, or even user specified genetic +regions of interest. Functions in the package include steps for GC-content +correction, calculation of quantile based normal karyotype ranges, and +calculation of feature score. Cutoffs for "normal" quantile and score are +user-adjustable. + +%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-RSQLite.spec b/specs/R-CRAN-RSQLite.spec index 9d016793ca..cc333ba359 100644 --- a/specs/R-CRAN-RSQLite.spec +++ b/specs/R-CRAN-RSQLite.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname RSQLite -%global packver 2.3.8 +%global packver 2.3.9 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.3.8 +Version: 2.3.9 Release: 1%{?dist}%{?buildtag} Summary: SQLite Interface for R diff --git a/specs/R-CRAN-RcppEnsmallen.spec b/specs/R-CRAN-RcppEnsmallen.spec index 0bed18e3fb..3ef126400a 100644 --- a/specs/R-CRAN-RcppEnsmallen.spec +++ b/specs/R-CRAN-RcppEnsmallen.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname RcppEnsmallen -%global packver 0.2.21.1.1 +%global packver 0.2.22.1.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.21.1.1 +Version: 0.2.22.1.1 Release: 1%{?dist}%{?buildtag} Summary: Header-Only C++ Mathematical Optimization Library for 'Armadillo' @@ -16,7 +16,7 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 4.0.0 Requires: R-core >= 4.0.0 -BuildRequires: R-CRAN-RcppArmadillo >= 0.9.800.0.0 +BuildRequires: R-CRAN-RcppArmadillo >= 0.10.8.2.0 BuildRequires: R-CRAN-Rcpp Requires: R-CRAN-Rcpp @@ -34,8 +34,8 @@ Note that 'Ensmallen' is licensed under 3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2, 'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under similar -terms. Note that 'Ensmallen' requires a compiler that supports 'C++11' and -'Armadillo' 9.800 or later. +terms. Note that 'Ensmallen' requires a compiler that supports 'C++14' and +'Armadillo' 10.8.2 or later. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-SSDforR.spec b/specs/R-CRAN-SSDforR.spec index b77486e024..a783343cd0 100644 --- a/specs/R-CRAN-SSDforR.spec +++ b/specs/R-CRAN-SSDforR.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname SSDforR -%global packver 1.5.35 +%global packver 1.5.36 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.5.35 +Version: 1.5.36 Release: 1%{?dist}%{?buildtag} Summary: Functions to Analyze Single System Data diff --git a/specs/R-CRAN-abc.spec b/specs/R-CRAN-abc.spec index b62e06f520..660f934971 100644 --- a/specs/R-CRAN-abc.spec +++ b/specs/R-CRAN-abc.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname abc -%global packver 2.2.1 +%global packver 2.2.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.2.1 +Version: 2.2.2 Release: 1%{?dist}%{?buildtag} Summary: Tools for Approximate Bayesian Computation (ABC) diff --git a/specs/R-CRAN-aphylo.spec b/specs/R-CRAN-aphylo.spec index 22fa633430..e275285e4a 100644 --- a/specs/R-CRAN-aphylo.spec +++ b/specs/R-CRAN-aphylo.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname aphylo -%global packver 0.3-3 +%global packver 0.3-4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.3.3 +Version: 0.3.4 Release: 1%{?dist}%{?buildtag} Summary: Statistical Inference and Prediction of Annotations in Phylogenetic Trees diff --git a/specs/R-CRAN-basicspace.spec b/specs/R-CRAN-basicspace.spec new file mode 100644 index 0000000000..2bd4ec8157 --- /dev/null +++ b/specs/R-CRAN-basicspace.spec @@ -0,0 +1,62 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname basicspace +%global packver 0.25 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.25 +Release: 1%{?dist}%{?buildtag} +Summary: Recovering a Basic Space from Issue Scales + +License: GPL-2 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.0.0 +Requires: R-core >= 3.0.0 +BuildRequires: R-tools +Requires: R-tools + +%description +Provides functions to estimate latent dimensions of choice and judgment +using Aldrich-McKelvey and Blackbox scaling methods, as described in Poole +et al. (2016, ). These techniques allow +researchers (particularly those analyzing political attitudes, public +opinion, and legislative behavior) to recover spatial estimates of +political actors' ideal points and stimuli from issue scale data, +accounting for perceptual bias, multidimensional spaces, and missing data. +The package uses singular value decomposition and alternating least +squares (ALS) procedures to scale self-placement and perceptual data into +a common latent space for the analysis of ideological or evaluative +dimensions. Functionality also include tools for assessing model fit, +handling complex survey data structures, and reproducing simulated +datasets for methodological validation. + +%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-bayesGAM.spec b/specs/R-CRAN-bayesGAM.spec deleted file mode 100644 index 369edc0f82..0000000000 --- a/specs/R-CRAN-bayesGAM.spec +++ /dev/null @@ -1,110 +0,0 @@ -%global __brp_check_rpaths %{nil} -%global packname bayesGAM -%global packver 0.0.2 -%global rlibdir /usr/local/lib/R/library - -Name: R-CRAN-%{packname} -Version: 0.0.2 -Release: 1%{?dist}%{?buildtag} -Summary: Fit Multivariate Response Generalized Additive Models using Hamiltonian Monte Carlo - -License: GPL-3 -URL: https://cran.r-project.org/package=%{packname} -Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz - - -BuildRequires: R-devel >= 3.6 -Requires: R-core >= 3.6 -BuildRequires: R-CRAN-RcppParallel >= 5.0.1 -BuildRequires: R-CRAN-rstan >= 2.18.1 -BuildRequires: R-CRAN-StanHeaders >= 2.18.0 -BuildRequires: R-CRAN-rstantools >= 2.1.0.9000 -BuildRequires: R-CRAN-BH >= 1.66.0 -BuildRequires: R-CRAN-RcppEigen >= 0.3.3.3.0 -BuildRequires: R-CRAN-Rcpp >= 0.12.0 -BuildRequires: R-CRAN-bayesplot -BuildRequires: R-CRAN-boot -BuildRequires: R-CRAN-cluster -BuildRequires: R-CRAN-corrplot -BuildRequires: R-CRAN-ggplot2 -BuildRequires: R-graphics -BuildRequires: R-CRAN-gridExtra -BuildRequires: R-CRAN-loo -BuildRequires: R-methods -BuildRequires: R-CRAN-mlbench -BuildRequires: R-CRAN-SemiPar -BuildRequires: R-stats -BuildRequires: R-CRAN-geometry -BuildRequires: R-CRAN-MASS -BuildRequires: R-CRAN-rstantools -Requires: R-CRAN-RcppParallel >= 5.0.1 -Requires: R-CRAN-rstan >= 2.18.1 -Requires: R-CRAN-rstantools >= 2.1.0.9000 -Requires: R-CRAN-Rcpp >= 0.12.0 -Requires: R-CRAN-bayesplot -Requires: R-CRAN-boot -Requires: R-CRAN-cluster -Requires: R-CRAN-corrplot -Requires: R-CRAN-ggplot2 -Requires: R-graphics -Requires: R-CRAN-gridExtra -Requires: R-CRAN-loo -Requires: R-methods -Requires: R-CRAN-mlbench -Requires: R-CRAN-SemiPar -Requires: R-stats -Requires: R-CRAN-geometry -Requires: R-CRAN-MASS -Requires: R-CRAN-rstantools - -%description -The 'bayesGAM' package is designed to provide a user friendly option to -fit univariate and multivariate response Generalized Additive Models (GAM) -using Hamiltonian Monte Carlo (HMC) with few technical burdens. The -functions in this package use 'rstan' (Stan Development Team 2020) to call -'Stan' routines that run the HMC simulations. The 'Stan' code for these -models is already pre-compiled for the user. The programming formulation -for models in 'bayesGAM' is designed to be familiar to analysts who fit -statistical models in 'R'. Carpenter, B., Gelman, A., Hoffman, M. D., Lee, -D., Goodrich, B., Betancourt, M., ... & Riddell, A. (2017). Stan: A -probabilistic programming language. Journal of statistical software, -76(1). Stan Development Team. 2018. RStan: the R interface to Stan. R -package version 2.17.3. Neal, Radford (2011) -"Handbook of Markov Chain Monte Carlo" ISBN: 978-1420079418. Betancourt, -Michael, and Mark Girolami. "Hamiltonian Monte Carlo for hierarchical -models." Current trends in Bayesian methodology with applications 79.30 -(2015): 2-4. Thomas, S., Tu, W. (2020) "Learning Hamiltonian Monte Carlo -in R" , Gelman, A., Carlin, J. B., Stern, H. S., Dunson, -D. B., Vehtari, A., & Rubin, D. B. (2013) "Bayesian Data Analysis" ISBN: -978-1439840955, Agresti, Alan (2015) "Foundations of Linear and -Generalized Linear Models ISBN: 978-1118730034, Pinheiro, J., Bates, D. -(2006) "Mixed-effects Models in S and S-Plus" ISBN: 978-1441903174. -Ruppert, D., Wand, M. P., & Carroll, R. J. (2003). Semiparametric -regression (No. 12). Cambridge university press. ISBN: 978-0521785167. - -%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-bit.spec b/specs/R-CRAN-bit.spec index 91a38fd92b..ee591b863f 100644 --- a/specs/R-CRAN-bit.spec +++ b/specs/R-CRAN-bit.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname bit -%global packver 4.5.0 +%global packver 4.5.0.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 4.5.0 +Version: 4.5.0.1 Release: 1%{?dist}%{?buildtag} Summary: Classes and Methods for Fast Memory-Efficient Boolean Selections diff --git a/specs/R-CRAN-breathtestcore.spec b/specs/R-CRAN-breathtestcore.spec index 58e19bd99c..52282ddabb 100644 --- a/specs/R-CRAN-breathtestcore.spec +++ b/specs/R-CRAN-breathtestcore.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname breathtestcore -%global packver 0.8.7 +%global packver 0.8.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.8.7 +Version: 0.8.8 Release: 1%{?dist}%{?buildtag} Summary: Core Functions to Read and Fit 13c Time Series from Breath Tests diff --git a/specs/R-CRAN-breathteststan.spec b/specs/R-CRAN-breathteststan.spec index 36b7d8aac0..c222d42ec7 100644 --- a/specs/R-CRAN-breathteststan.spec +++ b/specs/R-CRAN-breathteststan.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname breathteststan -%global packver 0.8.5 +%global packver 0.8.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.8.5 +Version: 0.8.8 Release: 1%{?dist}%{?buildtag} Summary: Stan-Based Fit to Gastric Emptying Curves @@ -17,23 +17,23 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz Recommends: pandoc BuildRequires: R-devel >= 4.0.0 Requires: R-core >= 4.0.0 -BuildRequires: R-CRAN-rstan >= 2.26.0 +BuildRequires: R-CRAN-rstantools >= 2.4.0 +BuildRequires: R-CRAN-rstan >= 2.32.0 BuildRequires: R-CRAN-StanHeaders >= 2.26.0 -BuildRequires: R-CRAN-rstantools >= 2.1.1 BuildRequires: R-CRAN-BH >= 1.72 BuildRequires: R-CRAN-Rcpp >= 1.0.6 -BuildRequires: R-CRAN-breathtestcore >= 0.8.4 +BuildRequires: R-CRAN-breathtestcore >= 0.8.7 +BuildRequires: R-CRAN-RcppEigen >= 0.3.4 BuildRequires: R-methods BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-purrr BuildRequires: R-CRAN-stringr BuildRequires: R-CRAN-tidyr -BuildRequires: R-CRAN-RcppEigen BuildRequires: R-CRAN-rstantools -Requires: R-CRAN-rstan >= 2.26.0 -Requires: R-CRAN-rstantools >= 2.1.1 +Requires: R-CRAN-rstantools >= 2.4.0 +Requires: R-CRAN-rstan >= 2.32.0 Requires: R-CRAN-Rcpp >= 1.0.6 -Requires: R-CRAN-breathtestcore >= 0.8.4 +Requires: R-CRAN-breathtestcore >= 0.8.7 Requires: R-methods Requires: R-CRAN-dplyr Requires: R-CRAN-purrr diff --git a/specs/R-CRAN-cir.spec b/specs/R-CRAN-cir.spec index cfce88ac08..62e6eb073b 100644 --- a/specs/R-CRAN-cir.spec +++ b/specs/R-CRAN-cir.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname cir -%global packver 2.3.1 +%global packver 2.5.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.3.1 +Version: 2.5.0 Release: 1%{?dist}%{?buildtag} Summary: Centered Isotonic Regression and Dose-Response Utilities diff --git a/specs/R-CRAN-csmGmm.spec b/specs/R-CRAN-csmGmm.spec new file mode 100644 index 0000000000..72f19e92da --- /dev/null +++ b/specs/R-CRAN-csmGmm.spec @@ -0,0 +1,69 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname csmGmm +%global packver 0.3.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.3.0 +Release: 1%{?dist}%{?buildtag} +Summary: Conditionally Symmetric Multidimensional Gaussian Mixture Model + +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-mvtnorm +BuildRequires: R-CRAN-rlang +BuildRequires: R-CRAN-magrittr +Requires: R-CRAN-dplyr +Requires: R-CRAN-mvtnorm +Requires: R-CRAN-rlang +Requires: R-CRAN-magrittr + +%description +Implements the conditionally symmetric multidimensional Gaussian mixture +model (csmGmm) for large-scale testing of composite null hypotheses in +genetic association applications such as mediation analysis, pleiotropy +analysis, and replication analysis. In such analyses, we typically have J +sets of K test statistics where K is a small number (e.g. 2 or 3) and J is +large (e.g. 1 million). For each one of the J sets, we want to know if we +can reject all K individual nulls. Please see the vignette for a +quickstart guide. The paper describing these methods is "Testing a Large +Number of Composite Null Hypotheses Using Conditionally Symmetric +Multidimensional Gaussian Mixtures in Genome-Wide Studies" by Sun R, McCaw +Z, & Lin X (2024, ). The paper is +accepted and published online (but not yet in print) in the Journal of the +American Statistical Association as of Dec 1 2024. + +%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-dbarts.spec b/specs/R-CRAN-dbarts.spec index c1d49ef2e2..e2037f02c0 100644 --- a/specs/R-CRAN-dbarts.spec +++ b/specs/R-CRAN-dbarts.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname dbarts -%global packver 0.9-28 +%global packver 0.9-30 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.9.28 +Version: 0.9.30 Release: 1%{?dist}%{?buildtag} Summary: Discrete Bayesian Additive Regression Trees Sampler diff --git a/specs/R-CRAN-deeptrafo.spec b/specs/R-CRAN-deeptrafo.spec index 95d4236088..30f013593a 100644 --- a/specs/R-CRAN-deeptrafo.spec +++ b/specs/R-CRAN-deeptrafo.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname deeptrafo -%global packver 0.1-1 +%global packver 1.0-0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.1 +Version: 1.0.0 Release: 1%{?dist}%{?buildtag} Summary: Fitting Deep Conditional Transformation Models @@ -19,27 +19,29 @@ Requires: R-core >= 4.0.0 BuildArch: noarch BuildRequires: R-CRAN-tensorflow >= 2.2.0 BuildRequires: R-CRAN-keras >= 2.2.0 +BuildRequires: R-CRAN-deepregression >= 2.2.0 BuildRequires: R-CRAN-tfprobability >= 0.15 -BuildRequires: R-CRAN-Formula -BuildRequires: R-CRAN-deepregression BuildRequires: R-CRAN-mlt +BuildRequires: R-CRAN-data.table BuildRequires: R-CRAN-variables BuildRequires: R-stats BuildRequires: R-CRAN-purrr BuildRequires: R-CRAN-survival BuildRequires: R-CRAN-R6 +BuildRequires: R-CRAN-Formula BuildRequires: R-CRAN-reticulate Requires: R-CRAN-tensorflow >= 2.2.0 Requires: R-CRAN-keras >= 2.2.0 +Requires: R-CRAN-deepregression >= 2.2.0 Requires: R-CRAN-tfprobability >= 0.15 -Requires: R-CRAN-Formula -Requires: R-CRAN-deepregression Requires: R-CRAN-mlt +Requires: R-CRAN-data.table Requires: R-CRAN-variables Requires: R-stats Requires: R-CRAN-purrr Requires: R-CRAN-survival Requires: R-CRAN-R6 +Requires: R-CRAN-Formula Requires: R-CRAN-reticulate %description @@ -47,9 +49,10 @@ Allows for the specification of deep conditional transformation models (DCTMs) and ordinal neural network transformation models, as described in Baumann et al (2021) and Kook et al (2022) . Extensions such as -autoregressive DCTMs (Ruegamer et al, 2022, -) and transformation ensembles (Kook et al, -2022, ) are implemented. +autoregressive DCTMs (Ruegamer et al, 2023, +) and transformation ensembles (Kook et +al, 2022, ) are implemented. The software +package is described in Kook et al (2024, ). %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-FuzzyStatTraEOO.spec b/specs/R-CRAN-extractox.spec similarity index 53% rename from specs/R-CRAN-FuzzyStatTraEOO.spec rename to specs/R-CRAN-extractox.spec index 7b8a93704a..902666dec1 100644 --- a/specs/R-CRAN-FuzzyStatTraEOO.spec +++ b/specs/R-CRAN-extractox.spec @@ -1,15 +1,15 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi -%global packname FuzzyStatTraEOO -%global packver 1.0 +%global packname extractox +%global packver 0.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0 +Version: 0.1.0 Release: 1%{?dist}%{?buildtag} -Summary: Package 'FuzzyStatTra' in Encapsulated Object Oriented Programming +Summary: Extract Tox Info from Various Databases -License: LGPL (>= 3) +License: MIT + file LICENSE URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz @@ -17,21 +17,30 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 4.1 Requires: R-core >= 4.1 BuildArch: noarch -BuildRequires: R-CRAN-R6 -Requires: R-CRAN-R6 +BuildRequires: R-CRAN-cli +BuildRequires: R-CRAN-httr2 +BuildRequires: R-CRAN-janitor +BuildRequires: R-CRAN-pingr +BuildRequires: R-CRAN-readxl +BuildRequires: R-CRAN-rvest +BuildRequires: R-CRAN-webchem +Requires: R-CRAN-cli +Requires: R-CRAN-httr2 +Requires: R-CRAN-janitor +Requires: R-CRAN-pingr +Requires: R-CRAN-readxl +Requires: R-CRAN-rvest +Requires: R-CRAN-webchem %description -The aim of the package is to contain the package 'FuzzyStatTra' in -Encapsulated Object Oriented Programming using R6. 'FuzzyStatTra' contains -Statistical Methods for Trapezoidal Fuzzy Numbers, whose aim is to provide -some basic functions for doing statistical analysis with trapezoidal fuzzy -numbers. For more details, you can visit the website of the SMIRE+CoDiRE -(Statistical Methods with Imprecise Random Elements and Comparison of -Distributions of Random Elements) Research Group -(). The most related -paper can be found in References. Now, those functions are organized in -specific classes and methods. This object-based approach is an important -step in making statistical computing more accessible to users. +Extract toxicological and chemical information from databases maintained +by scientific agencies and resources, including the Comparative +Toxicogenomics Database , the Integrated Chemical +Environment , the Integrated Risk +Information System , the CompTox +Chemicals Dashboard Resource Hub +, +and PubChem . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-gasanalyzer.spec b/specs/R-CRAN-gasanalyzer.spec index 1e06cb6833..4f27a83d3b 100644 --- a/specs/R-CRAN-gasanalyzer.spec +++ b/specs/R-CRAN-gasanalyzer.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname gasanalyzer -%global packver 0.4.1 +%global packver 0.4.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4.1 +Version: 0.4.2 Release: 1%{?dist}%{?buildtag} Summary: Import, Recompute and Analyze Data from Portable Gas Analyzers diff --git a/specs/R-CRAN-geocausal.spec b/specs/R-CRAN-geocausal.spec index 1d31e71c64..05c2107d65 100644 --- a/specs/R-CRAN-geocausal.spec +++ b/specs/R-CRAN-geocausal.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname geocausal -%global packver 0.3.2 +%global packver 0.3.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.3.2 +Version: 0.3.3 Release: 1%{?dist}%{?buildtag} Summary: Causal Inference with Spatio-Temporal Data @@ -59,7 +59,8 @@ Spatio-temporal causal inference based on point process data. You provide the raw data of locations and timings of treatment and outcome events, specify counterfactual scenarios, and the package estimates causal effects over specified spatial and temporal windows. See Papadogeorgou, et al. -(2022) . +(2022) and Mukaigawara, et al. (2024) +. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-ggfun.spec b/specs/R-CRAN-ggfun.spec index a3123a74f0..81eb09d7ef 100644 --- a/specs/R-CRAN-ggfun.spec +++ b/specs/R-CRAN-ggfun.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ggfun -%global packver 0.1.7 +%global packver 0.1.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.7 +Version: 0.1.8 Release: 1%{?dist}%{?buildtag} Summary: Miscellaneous Functions for 'ggplot2' diff --git a/specs/R-CRAN-googleCloudRunner.spec b/specs/R-CRAN-googleCloudRunner.spec deleted file mode 100644 index e5a838e9eb..0000000000 --- a/specs/R-CRAN-googleCloudRunner.spec +++ /dev/null @@ -1,83 +0,0 @@ -%global __brp_check_rpaths %{nil} -%global __requires_exclude ^libmpi -%global packname googleCloudRunner -%global packver 0.5.0 -%global rlibdir /usr/local/lib/R/library - -Name: R-CRAN-%{packname} -Version: 0.5.0 -Release: 1%{?dist}%{?buildtag} -Summary: R Scripts in the Google Cloud via Cloud Run, Cloud Build and Cloud Scheduler - -License: MIT + file LICENSE -URL: https://cran.r-project.org/package=%{packname} -Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz - - -BuildRequires: R-devel >= 3.3.0 -Requires: R-core >= 3.3.0 -BuildArch: noarch -BuildRequires: R-CRAN-curl >= 4.3 -BuildRequires: R-CRAN-yaml >= 2.2.0 -BuildRequires: R-CRAN-cli >= 2.0.2 -BuildRequires: R-CRAN-googleAuthR >= 2.0.0 -BuildRequires: R-CRAN-usethis >= 1.6.0 -BuildRequires: R-CRAN-jsonlite >= 1.5 -BuildRequires: R-CRAN-httr >= 1.4.1 -BuildRequires: R-CRAN-openssl >= 1.4.1 -BuildRequires: R-CRAN-plumber >= 1.0.0 -BuildRequires: R-CRAN-jose >= 1.0 -BuildRequires: R-CRAN-googleCloudStorageR >= 0.7.0 -BuildRequires: R-CRAN-assertthat >= 0.2.0 -BuildRequires: R-CRAN-googlePubsubR >= 0.0.2 -BuildRequires: R-utils -BuildRequires: R-CRAN-withr -Requires: R-CRAN-curl >= 4.3 -Requires: R-CRAN-yaml >= 2.2.0 -Requires: R-CRAN-cli >= 2.0.2 -Requires: R-CRAN-googleAuthR >= 2.0.0 -Requires: R-CRAN-usethis >= 1.6.0 -Requires: R-CRAN-jsonlite >= 1.5 -Requires: R-CRAN-httr >= 1.4.1 -Requires: R-CRAN-openssl >= 1.4.1 -Requires: R-CRAN-plumber >= 1.0.0 -Requires: R-CRAN-jose >= 1.0 -Requires: R-CRAN-googleCloudStorageR >= 0.7.0 -Requires: R-CRAN-assertthat >= 0.2.0 -Requires: R-CRAN-googlePubsubR >= 0.0.2 -Requires: R-utils -Requires: R-CRAN-withr - -%description -Tools to easily enable R scripts in the Google Cloud Platform. Utilise -cloud services such as Cloud Run for R -over HTTP, Cloud Build for Continuous -Delivery and Integration services and Cloud Scheduler - for scheduled scripts. - -%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-harbinger.spec b/specs/R-CRAN-harbinger.spec index cba349a3ea..d899b7dc34 100644 --- a/specs/R-CRAN-harbinger.spec +++ b/specs/R-CRAN-harbinger.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname harbinger -%global packver 1.0.787 +%global packver 1.1.707 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.787 +Version: 1.1.707 Release: 1%{?dist}%{?buildtag} Summary: A Unified Time Series Event Detection Framework diff --git a/specs/R-CRAN-ipd.spec b/specs/R-CRAN-ipd.spec index 5985dc98ed..9f1d8010b6 100644 --- a/specs/R-CRAN-ipd.spec +++ b/specs/R-CRAN-ipd.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ipd -%global packver 0.1.2 +%global packver 0.1.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.2 +Version: 0.1.3 Release: 1%{?dist}%{?buildtag} Summary: Inference on Predicted Data diff --git a/specs/R-CRAN-iq.spec b/specs/R-CRAN-iq.spec index 11e067decf..1ce669bbc2 100644 --- a/specs/R-CRAN-iq.spec +++ b/specs/R-CRAN-iq.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname iq -%global packver 1.9.12 +%global packver 1.10 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.9.12 +Version: 1.10 Release: 1%{?dist}%{?buildtag} Summary: Protein Quantification in Mass Spectrometry-Based Proteomics diff --git a/specs/R-CRAN-klassR.spec b/specs/R-CRAN-klassR.spec index 8b75a72653..a807aeee6a 100644 --- a/specs/R-CRAN-klassR.spec +++ b/specs/R-CRAN-klassR.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname klassR -%global packver 1.0.0 +%global packver 1.0.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.0.1 Release: 1%{?dist}%{?buildtag} Summary: Classifications and Codelists for Statistics Norway @@ -17,15 +17,15 @@ 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-igraph >= 2.1.1 BuildRequires: R-CRAN-tm BuildRequires: R-CRAN-httr BuildRequires: R-CRAN-jsonlite -BuildRequires: R-CRAN-igraph BuildRequires: R-methods +Requires: R-CRAN-igraph >= 2.1.1 Requires: R-CRAN-tm Requires: R-CRAN-httr Requires: R-CRAN-jsonlite -Requires: R-CRAN-igraph Requires: R-methods %description diff --git a/specs/R-CRAN-knfi.spec b/specs/R-CRAN-knfi.spec index aea97b7e85..c2e2cf69af 100644 --- a/specs/R-CRAN-knfi.spec +++ b/specs/R-CRAN-knfi.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname knfi -%global packver 1.0.1 +%global packver 1.0.1.9 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.1 +Version: 1.0.1.9 Release: 1%{?dist}%{?buildtag} Summary: Analysis of Korean National Forest Inventory Database diff --git a/specs/R-CRAN-W4MRUtils.spec b/specs/R-CRAN-messy.spec similarity index 67% rename from specs/R-CRAN-W4MRUtils.spec rename to specs/R-CRAN-messy.spec index 5ce344aa51..f82583ddc2 100644 --- a/specs/R-CRAN-W4MRUtils.spec +++ b/specs/R-CRAN-messy.spec @@ -1,33 +1,34 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi -%global packname W4MRUtils -%global packver 1.0.0 +%global packname messy +%global packver 0.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 0.1.0 Release: 1%{?dist}%{?buildtag} -Summary: Utils List for W4M - Workflow for Metabolomics +Summary: Create Messy Data from Clean Data Frames -License: AGPL (>= 3) +License: CC BY 4.0 URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz -BuildRequires: R-devel -Requires: R-core +BuildRequires: R-devel >= 4.1 +Requires: R-core >= 4.1 BuildArch: noarch -BuildRequires: R-methods +BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-rlang -Requires: R-methods +BuildRequires: R-CRAN-stringr +Requires: R-CRAN-dplyr Requires: R-CRAN-rlang +Requires: R-CRAN-stringr %description -Provides a set of utility function to prevent the spread of utilities -script in W4M (Workflow4Metabolomics) scripts, and centralize them in a -single package. Some are meant to be replaced by real packages in a near -future, like the parse_args() function: it is here only to prepare the -ground for more global changes in W4M scripts and tools. +For the purposes of teaching, it is often desirable to show examples of +working with messy data and how to clean it. This R package creates messy +data from clean, tidy data frames so that students have a clean example to +work towards. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-mongolite.spec b/specs/R-CRAN-mongolite.spec index d54b6291b0..1beb88d884 100644 --- a/specs/R-CRAN-mongolite.spec +++ b/specs/R-CRAN-mongolite.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname mongolite -%global packver 2.8.1 +%global packver 2.8.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.8.1 +Version: 2.8.2 Release: 1%{?dist}%{?buildtag} Summary: Fast and Simple 'MongoDB' Client for R diff --git a/specs/R-CRAN-npclust.spec b/specs/R-CRAN-npclust.spec index 24c79da51c..66da4108e7 100644 --- a/specs/R-CRAN-npclust.spec +++ b/specs/R-CRAN-npclust.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname npclust -%global packver 0.1.0 +%global packver 0.1.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.0 +Version: 0.1.1 Release: 1%{?dist}%{?buildtag} Summary: Nonparametric Tests for Incomplete Clustered Data diff --git a/specs/R-CRAN-opendataformat.spec b/specs/R-CRAN-opendataformat.spec index 79cc630332..0735e9731e 100644 --- a/specs/R-CRAN-opendataformat.spec +++ b/specs/R-CRAN-opendataformat.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname opendataformat -%global packver 2.0.0 +%global packver 2.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.0.0 +Version: 2.1.0 Release: 1%{?dist}%{?buildtag} Summary: Reading and Writing Open Data Format Files diff --git a/specs/R-CRAN-parallelly.spec b/specs/R-CRAN-parallelly.spec index 59eba85112..b87ac695a7 100644 --- a/specs/R-CRAN-parallelly.spec +++ b/specs/R-CRAN-parallelly.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname parallelly -%global packver 1.39.0 +%global packver 1.40.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.39.0 +Version: 1.40.0 Release: 1%{?dist}%{?buildtag} Summary: Enhancing the 'parallel' Package diff --git a/specs/R-CRAN-particles.spec b/specs/R-CRAN-particles.spec index 5e748311f7..385aac8e1a 100644 --- a/specs/R-CRAN-particles.spec +++ b/specs/R-CRAN-particles.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname particles -%global packver 0.2.3 +%global packver 0.2.4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.3 +Version: 0.2.4 Release: 1%{?dist}%{?buildtag} Summary: A Graph Based Particle Simulator Based on D3-Force @@ -16,21 +16,21 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel Requires: R-core -BuildRequires: R-CRAN-tidygraph -BuildRequires: R-CRAN-rlang -BuildRequires: R-CRAN-igraph -BuildRequires: R-stats -BuildRequires: R-CRAN-mgcv BuildRequires: R-CRAN-digest BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-igraph +BuildRequires: R-CRAN-mgcv +BuildRequires: R-CRAN-rlang +BuildRequires: R-stats +BuildRequires: R-CRAN-tidygraph BuildRequires: R-CRAN-cpp11 -Requires: R-CRAN-tidygraph -Requires: R-CRAN-rlang -Requires: R-CRAN-igraph -Requires: R-stats -Requires: R-CRAN-mgcv Requires: R-CRAN-digest Requires: R-CRAN-dplyr +Requires: R-CRAN-igraph +Requires: R-CRAN-mgcv +Requires: R-CRAN-rlang +Requires: R-stats +Requires: R-CRAN-tidygraph %description Simulating particle movement in 2D space has many application. The diff --git a/specs/R-CRAN-pkgmaker.spec b/specs/R-CRAN-pkgmaker.spec deleted file mode 100644 index f26e4e5475..0000000000 --- a/specs/R-CRAN-pkgmaker.spec +++ /dev/null @@ -1,81 +0,0 @@ -%global __brp_check_rpaths %{nil} -%global __requires_exclude ^libmpi -%global packname pkgmaker -%global packver 0.32.10 -%global rlibdir /usr/local/lib/R/library - -Name: R-CRAN-%{packname} -Version: 0.32.10 -Release: 1%{?dist}%{?buildtag} -Summary: Development Utilities for R Packages - -License: GPL (>= 2) -URL: https://cran.r-project.org/package=%{packname} -Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz - - -BuildRequires: R-devel >= 3.0.0 -Requires: R-core >= 3.0.0 -BuildArch: noarch -BuildRequires: R-methods -BuildRequires: R-stats -BuildRequires: R-CRAN-registry -BuildRequires: R-tools -BuildRequires: R-grDevices -BuildRequires: R-utils -BuildRequires: R-graphics -BuildRequires: R-CRAN-codetools -BuildRequires: R-CRAN-digest -BuildRequires: R-CRAN-stringr -BuildRequires: R-CRAN-xtable -BuildRequires: R-CRAN-withr -BuildRequires: R-CRAN-assertthat -Requires: R-methods -Requires: R-stats -Requires: R-CRAN-registry -Requires: R-tools -Requires: R-grDevices -Requires: R-utils -Requires: R-graphics -Requires: R-CRAN-codetools -Requires: R-CRAN-digest -Requires: R-CRAN-stringr -Requires: R-CRAN-xtable -Requires: R-CRAN-withr -Requires: R-CRAN-assertthat - -%description -Provides some low-level utilities to use for package development. It -currently provides managers for multiple package specific options and -registries, vignette, unit test and bibtex related utilities. It serves as -a base package for packages like 'NMF', 'RcppOctave', 'doRNG', and as an -incubator package for other general purposes utilities, that will -eventually be packaged separately. It is still under heavy development and -changes in the interface(s) are more than likely to happen. - -%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-processmapR.spec b/specs/R-CRAN-processmapR.spec index ce01cd5d22..4cec494200 100644 --- a/specs/R-CRAN-processmapR.spec +++ b/specs/R-CRAN-processmapR.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname processmapR -%global packver 0.5.5 +%global packver 0.5.6 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.5.5 +Version: 0.5.6 Release: 1%{?dist}%{?buildtag} Summary: Construct Process Maps Using Event Data diff --git a/specs/R-CRAN-tidysynth.spec b/specs/R-CRAN-resourcecode.spec similarity index 55% rename from specs/R-CRAN-tidysynth.spec rename to specs/R-CRAN-resourcecode.spec index 2ecd7badb6..6710951ff2 100644 --- a/specs/R-CRAN-tidysynth.spec +++ b/specs/R-CRAN-resourcecode.spec @@ -1,53 +1,57 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi -%global packname tidysynth -%global packver 0.2.0 +%global packname resourcecode +%global packver 0.2.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.0 +Version: 0.2.1 Release: 1%{?dist}%{?buildtag} -Summary: A Tidy Implementation of the Synthetic Control Method +Summary: Access to the 'RESOURCECODE' Hindcast Database -License: MIT + file LICENSE +License: GPL (>= 3) URL: https://cran.r-project.org/package=%{packname} 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-magrittr -BuildRequires: R-CRAN-tibble -BuildRequires: R-CRAN-dplyr +BuildRequires: R-devel >= 3.6 +Requires: R-core >= 3.6 +BuildRequires: R-CRAN-abind +BuildRequires: R-CRAN-curl +BuildRequires: R-CRAN-geosphere BuildRequires: R-CRAN-ggplot2 -BuildRequires: R-CRAN-tidyr -BuildRequires: R-CRAN-forcats +BuildRequires: R-CRAN-jsonlite +BuildRequires: R-CRAN-ncdf4 +BuildRequires: R-CRAN-pracma +BuildRequires: R-CRAN-Rcpp BuildRequires: R-CRAN-rlang -BuildRequires: R-CRAN-kernlab -BuildRequires: R-CRAN-rgenoud -BuildRequires: R-CRAN-optimx +BuildRequires: R-CRAN-sf BuildRequires: R-stats -Requires: R-CRAN-magrittr -Requires: R-CRAN-tibble -Requires: R-CRAN-dplyr +BuildRequires: R-CRAN-tibble +BuildRequires: R-CRAN-tidyr +BuildRequires: R-CRAN-RcppArmadillo +Requires: R-CRAN-abind +Requires: R-CRAN-curl +Requires: R-CRAN-geosphere Requires: R-CRAN-ggplot2 -Requires: R-CRAN-tidyr -Requires: R-CRAN-forcats +Requires: R-CRAN-jsonlite +Requires: R-CRAN-ncdf4 +Requires: R-CRAN-pracma +Requires: R-CRAN-Rcpp Requires: R-CRAN-rlang -Requires: R-CRAN-kernlab -Requires: R-CRAN-rgenoud -Requires: R-CRAN-optimx +Requires: R-CRAN-sf Requires: R-stats +Requires: R-CRAN-tibble +Requires: R-CRAN-tidyr %description -A synthetic control offers a way of evaluating the effect of an -intervention in comparative case studies. The package makes a number of -improvements when implementing the method in R. These improvements allow -users to inspect, visualize, and tune the synthetic control more easily. A -key benefit of a tidy implementation is that the entire preparation -process for building the synthetic control can be accomplished in a single -pipe. +Utility functions to download data from the 'RESOURCECODE' hindcast +database of sea-states, time series of sea-state parameters and time +series of 1D and 2D wave spectra. See +for more details about the available data. Also provides facilities to +plot and analyse downloaded data, such as computing the sea-state +parameters from both the 1D and 2D surface elevation variance spectral +density. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-simdata.spec b/specs/R-CRAN-simdata.spec index 04251b0641..6a84ba68a9 100644 --- a/specs/R-CRAN-simdata.spec +++ b/specs/R-CRAN-simdata.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname simdata -%global packver 0.4.0 +%global packver 0.4.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4.0 +Version: 0.4.1 Release: 1%{?dist}%{?buildtag} Summary: Generate Simulated Datasets diff --git a/specs/R-CRAN-sivirep.spec b/specs/R-CRAN-sivirep.spec index a90273c06c..1863fe729b 100644 --- a/specs/R-CRAN-sivirep.spec +++ b/specs/R-CRAN-sivirep.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname sivirep -%global packver 1.0.0 +%global packver 1.0.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.0.1 Release: 1%{?dist}%{?buildtag} Summary: Data Wrangling and Automated Reports from 'SIVIGILA' Source @@ -19,32 +19,36 @@ Requires: R-core >= 4.0.0 BuildArch: noarch BuildRequires: R-CRAN-config BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-epitrix BuildRequires: R-CRAN-ggplot2 BuildRequires: R-CRAN-httr2 -BuildRequires: R-CRAN-stringr -BuildRequires: R-CRAN-xml2 -BuildRequires: R-CRAN-epitrix -BuildRequires: R-CRAN-sf +BuildRequires: R-CRAN-kableExtra BuildRequires: R-CRAN-readxl BuildRequires: R-CRAN-rlang -BuildRequires: R-tools -BuildRequires: R-CRAN-sysfonts +BuildRequires: R-CRAN-sf BuildRequires: R-CRAN-showtext -BuildRequires: R-CRAN-kableExtra +BuildRequires: R-stats +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-sysfonts +BuildRequires: R-tools +BuildRequires: R-utils +BuildRequires: R-CRAN-xml2 Requires: R-CRAN-config Requires: R-CRAN-dplyr +Requires: R-CRAN-epitrix Requires: R-CRAN-ggplot2 Requires: R-CRAN-httr2 -Requires: R-CRAN-stringr -Requires: R-CRAN-xml2 -Requires: R-CRAN-epitrix -Requires: R-CRAN-sf +Requires: R-CRAN-kableExtra Requires: R-CRAN-readxl Requires: R-CRAN-rlang -Requires: R-tools -Requires: R-CRAN-sysfonts +Requires: R-CRAN-sf Requires: R-CRAN-showtext -Requires: R-CRAN-kableExtra +Requires: R-stats +Requires: R-CRAN-stringr +Requires: R-CRAN-sysfonts +Requires: R-tools +Requires: R-utils +Requires: R-CRAN-xml2 %description Data wrangling, pre-processing, and generating automated reports from diff --git a/specs/R-CRAN-spmoran.spec b/specs/R-CRAN-spmoran.spec index 8f21247fbd..bf34553fd6 100644 --- a/specs/R-CRAN-spmoran.spec +++ b/specs/R-CRAN-spmoran.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname spmoran -%global packver 0.3.1 +%global packver 0.3.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.3.1 +Version: 0.3.2 Release: 1%{?dist}%{?buildtag} Summary: Fast Spatial and Spatio-Temporal Regression using Moran Eigenvectors diff --git a/specs/R-CRAN-wooldridge.spec b/specs/R-CRAN-sshicm.spec similarity index 55% rename from specs/R-CRAN-wooldridge.spec rename to specs/R-CRAN-sshicm.spec index 01729ac3c5..58cdccb716 100644 --- a/specs/R-CRAN-wooldridge.spec +++ b/specs/R-CRAN-sshicm.spec @@ -1,35 +1,40 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi -%global packname wooldridge -%global packver 1.4-3 +%global packname sshicm +%global packver 0.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.4.3 +Version: 0.1.0 Release: 1%{?dist}%{?buildtag} -Summary: 115 Data Sets from "Introductory Econometrics: A Modern Approach, 7e" by Jeffrey M. Wooldridge +Summary: Information Consistency-Based Measures for Spatial Stratified Heterogeneity License: GPL-3 URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz -BuildRequires: R-devel >= 3.5.0 -Requires: R-core >= 3.5.0 -BuildArch: noarch +BuildRequires: R-devel >= 4.1.0 +Requires: R-core >= 4.1.0 +BuildRequires: R-CRAN-sdsfun >= 0.5.0 +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-purrr +BuildRequires: R-CRAN-sf +BuildRequires: R-CRAN-Rcpp +BuildRequires: R-CRAN-RcppThread +Requires: R-CRAN-sdsfun >= 0.5.0 +Requires: R-CRAN-dplyr +Requires: R-CRAN-purrr +Requires: R-CRAN-sf %description -Students learning both econometrics and R may find the introduction to -both challenging. The wooldridge data package aims to lighten the task by -efficiently loading any data set found in the text with a single command. -Data sets have been compressed to a fraction of their original size. -Documentation files contain page numbers, the original source, time of -publication, and notes from the author suggesting avenues for further -analysis and research. If one needs an introduction to R model syntax, a -vignette contains solutions to examples from chapters of the text. Data -sets are from the 7th edition (Wooldridge 2020, ISBN-13 -978-1-337-55886-0), and are backwards compatible with all previous -versions of the text. +Spatial stratified heterogeneity (SSH) denotes the coexistence of +within-strata homogeneity and between-strata heterogeneity. Information +consistency-based methods provide a rigorous approach to quantify SSH and +evaluate its role in spatial processes, grounded in principles of +geographical stratification and information theory (Bai, H. et al. (2023) +; Wang, J. et al. (2024) +). %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-tibbletime.spec b/specs/R-CRAN-tibbletime.spec index 0619e219cf..e14bec8cc7 100644 --- a/specs/R-CRAN-tibbletime.spec +++ b/specs/R-CRAN-tibbletime.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname tibbletime -%global packver 0.1.8 +%global packver 0.1.9 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.8 +Version: 0.1.9 Release: 1%{?dist}%{?buildtag} Summary: Time Aware Tibbles