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cran4linux · Nov 19, 2024 · 9c6fade · 9c6fade
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diff --git a/specs/R-CRAN-APackOfTheClones.spec b/specs/R-CRAN-APackOfTheClones.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  APackOfTheClones
-%global packver   1.2.1
+%global packver   1.2.4
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.2.1
+Version:          1.2.4
 Release:          1%{?dist}%{?buildtag}
 Summary:          Visualization of Clonal Expansion for Single Cell Immune Profiles
 

diff --git a/specs/R-CRAN-BalancedSampling.spec b/specs/R-CRAN-BalancedSampling.spec
@@ -1,24 +1,24 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  BalancedSampling
-%global packver   2.0.6
+%global packver   2.1.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.0.6
+Version:          2.1.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Balanced and Spatially Balanced Sampling
 
-License:          GPL (>= 2)
+License:          AGPL-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 >= 1.0.12
+BuildRequires:    R-CRAN-Rcpp >= 1.0.13
 BuildRequires:    R-CRAN-RcppArmadillo 
-Requires:         R-CRAN-Rcpp >= 1.0.12
+Requires:         R-CRAN-Rcpp >= 1.0.13
 
 %description
 Select balanced and spatially balanced probability samples in

diff --git a/specs/R-CRAN-COR.spec b/specs/R-CRAN-COR.spec
@@ -1,10 +1,11 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  COR
-%global packver   0.0.1
+%global packver   0.1.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.0.1
+Version:          0.1.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          The COR for Optimal Subset Selection in Distributed Estimation
 

diff --git a/specs/R-CRAN-pmlbr.spec → specs/R-CRAN-CareDensity.spec b/specs/R-CRAN-pmlbr.spec → specs/R-CRAN-CareDensity.spec
@@ -1,38 +1,38 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
-%global packname  pmlbr
-%global packver   0.2.2
+%global packname  CareDensity
+%global packver   0.1.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.2.2
+Version:          0.1.0
 Release:          1%{?dist}%{?buildtag}
-Summary:          Interface to the Penn Machine Learning Benchmarks Data Repository
+Summary:          Calculate the Care Density or Fragmented Care Density Given a Patient-Sharing Network
 
-License:          GPL-2 | file LICENSE
+License:          GPL (>= 3)
 URL:              https://cran.r-project.org/package=%{packname}
 Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
 
 
-BuildRequires:    R-devel >= 3.2.0
-Requires:         R-core >= 3.2.0
+BuildRequires:    R-devel
+Requires:         R-core
 BuildArch:        noarch
+BuildRequires:    R-CRAN-igraph >= 2.0.0
+BuildRequires:    R-CRAN-MatrixExtra 
+BuildRequires:    R-CRAN-data.table 
 BuildRequires:    R-utils 
-BuildRequires:    R-CRAN-FNN 
-BuildRequires:    R-stats 
+Requires:         R-CRAN-igraph >= 2.0.0
+Requires:         R-CRAN-MatrixExtra 
+Requires:         R-CRAN-data.table 
 Requires:         R-utils 
-Requires:         R-CRAN-FNN 
-Requires:         R-stats 
 
 %description
-Check available classification and regression data sets from the PMLB
-repository and download them. The PMLB repository
-(<https://github.com/EpistasisLab/pmlbr>) contains a curated collection of
-data sets for evaluating and comparing machine learning algorithms. These
-data sets cover a range of applications, and include binary/multi-class
-classification problems and regression problems, as well as combinations
-of categorical, ordinal, and continuous features. There are currently over
-150 datasets included in the PMLB repository.
+Given a patient-sharing network, calculate either the classic care density
+as proposed by Pollack et al. (2013) <doi:10.1007/s11606-012-2104-7> or
+the fragmented care density as proposed by Engels et al. (2024)
+<doi:10.1186/s12874-023-02106-0>. By utilizing the 'igraph' and
+'data.table' packages, the provided functions scale well for very large
+graphs.
 
 %prep
 %setup -q -c -n %{packname}

diff --git a/specs/R-CRAN-DRIP.spec b/specs/R-CRAN-DRIP.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  DRIP
-%global packver   2.0
+%global packver   2.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.0
+Version:          2.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Discontinuous Regression and Image Processing
 

diff --git a/specs/R-CRAN-GPvam.spec b/specs/R-CRAN-GPvam.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  GPvam
-%global packver   3.1-1
+%global packver   3.1-2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          3.1.1
+Version:          3.1.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Maximum Likelihood Estimation of Multiple Membership Mixed Models Used in Value-Added Modeling
 
@@ -19,6 +19,7 @@ Requires:         R-core >= 3.2.0
 BuildRequires:    R-CRAN-Rcpp >= 0.11.2
 BuildRequires:    R-CRAN-Matrix 
 BuildRequires:    R-CRAN-numDeriv 
+BuildRequires:    R-CRAN-rlang 
 BuildRequires:    R-graphics 
 BuildRequires:    R-grDevices 
 BuildRequires:    R-methods 
@@ -31,6 +32,7 @@ BuildRequires:    R-CRAN-RcppArmadillo
 Requires:         R-CRAN-Rcpp >= 0.11.2
 Requires:         R-CRAN-Matrix 
 Requires:         R-CRAN-numDeriv 
+Requires:         R-CRAN-rlang 
 Requires:         R-graphics 
 Requires:         R-grDevices 
 Requires:         R-methods 

diff --git a/specs/R-CRAN-Jaya.spec b/specs/R-CRAN-Jaya.spec
@@ -1,45 +1,57 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  Jaya
-%global packver   0.1.9
+%global packver   1.0.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.1.9
-Release:          3%{?dist}%{?buildtag}
-Summary:          Jaya, a Gradient-Free Optimization Algorithm
+Version:          1.0.3
+Release:          1%{?dist}%{?buildtag}
+Summary:          Gradient-Free Optimization Algorithm for Single and Multi-Objective Problems
 
-License:          GPL (>= 2)
+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
+BuildRequires:    R-devel >= 3.5.0
+Requires:         R-core >= 3.5.0
 BuildArch:        noarch
-BuildRequires:    R-CRAN-GA 
-Requires:         R-CRAN-GA 
+BuildRequires:    R-parallel 
+Requires:         R-parallel 
 
 %description
-Maximization or Minimization of a fitness function using Jaya Algorithm
-(JA). A population based method which repeatedly modifies a population of
-individual solutions. Capable of solving both constrained and
-unconstrained optimization problems. It does not contain any
-hyperparameters. For further details: R.V. Rao (2016)
-<doi:10.5267/j.ijiec.2015.8.004> .
+An implementation of the Jaya optimization algorithm for both
+single-objective and multi-objective problems. Jaya is a population-based,
+gradient-free optimization algorithm capable of solving constrained and
+unconstrained optimization problems without hyperparameters. This package
+includes features such as multi-objective Pareto optimization, adaptive
+population adjustment, and early stopping. For further details, see R.V.
+Rao (2016) <doi:10.5267/j.ijiec.2015.8.004>.
 
 %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-Luminescence.spec b/specs/R-CRAN-Luminescence.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  Luminescence
-%global packver   0.9.25
+%global packver   0.9.26
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.9.25
+Version:          0.9.26
 Release:          1%{?dist}%{?buildtag}
 Summary:          Comprehensive Luminescence Dating Data Analysis
 

diff --git a/specs/R-CRAN-RMariaDB.spec b/specs/R-CRAN-RMariaDB.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  RMariaDB
-%global packver   1.3.2
+%global packver   1.3.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.3.2
+Version:          1.3.3
 Release:          1%{?dist}%{?buildtag}
 Summary:          Database Interface and MariaDB Driver
 

diff --git a/specs/R-CRAN-RadEro.spec b/specs/R-CRAN-RadEro.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  RadEro
-%global packver   1.0.4
+%global packver   1.0.5
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.0.4
+Version:          1.0.5
 Release:          1%{?dist}%{?buildtag}
 Summary:          Cs-137 Conversion Model
 
@@ -51,9 +51,10 @@ density, effective volume) to accurately capture the 137Cs distribution
 within the soil profile. The model simulates annual 137Cs fallout,
 radioactive decay, and vertical diffusion, with the diffusion coefficient
 calculated from 137Cs reference inventory profiles. Additionally, it
-allows users to input custom parameters as calibration coefficients. This
-tool and its code are openly accessible, facilitating usage in soil
-erosion studies.
+allows users to input custom parameters as calibration coefficients. The
+RadEro user manual and protocol, including detailed instructions on how to
+format input data and configuration files, can be found at the following
+link: <https://github.com/eead-csic-eesa/RadEro>.
 
 %prep
 %setup -q -c -n %{packname}

diff --git a/specs/R-CRAN-RcppArmadillo.spec b/specs/R-CRAN-RcppArmadillo.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  RcppArmadillo
-%global packver   14.0.2-1
+%global packver   14.2.0-1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          14.0.2.1
+Version:          14.2.0.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
 
@@ -16,11 +16,11 @@ Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
 
 BuildRequires:    R-devel >= 3.3.0
 Requires:         R-core >= 3.3.0
-BuildRequires:    R-CRAN-Rcpp >= 1.0.8
+BuildRequires:    R-CRAN-Rcpp >= 1.0.12
 BuildRequires:    R-stats 
 BuildRequires:    R-utils 
 BuildRequires:    R-methods 
-Requires:         R-CRAN-Rcpp >= 1.0.8
+Requires:         R-CRAN-Rcpp >= 1.0.12
 Requires:         R-stats 
 Requires:         R-utils 
 Requires:         R-methods 

diff --git a/specs/R-CRAN-Rmpfr.spec b/specs/R-CRAN-Rmpfr.spec
@@ -1,13 +1,13 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  Rmpfr
-%global packver   0.9-5
+%global packver   1.0-0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.9.5
+Version:          1.0.0
 Release:          1%{?dist}%{?buildtag}
-Summary:          R MPFR - Multiple Precision Floating-Point Reliable
+Summary:          Interface R to MPFR - Multiple Precision Floating-Point Reliable
 
 License:          GPL (>= 2)
 URL:              https://cran.r-project.org/package=%{packname}

diff --git a/specs/R-CRAN-atime.spec b/specs/R-CRAN-atime.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  atime
-%global packver   2024.10.5
+%global packver   2024.11.15
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2024.10.5
+Version:          2024.11.15
 Release:          1%{?dist}%{?buildtag}
 Summary:          Asymptotic Timing
 

diff --git a/specs/R-CRAN-autovi.spec b/specs/R-CRAN-autovi.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  autovi
-%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:          Auto Visual Inference with Computer Vision Models
 

diff --git a/specs/R-CRAN-bWGR.spec b/specs/R-CRAN-bWGR.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  bWGR
-%global packver   2.2.11
+%global packver   2.2.12
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.2.11
+Version:          2.2.12
 Release:          1%{?dist}%{?buildtag}
 Summary:          Bayesian Whole-Genome Regression
 
@@ -25,8 +25,9 @@ Requires:         R-CRAN-Rcpp
 %description
 Whole-genome regression methods on Bayesian framework fitted via EM or
 Gibbs sampling, single step (<doi:10.1534/g3.119.400728>), univariate and
-multivariate (<doi:10.1186/s12711-022-00730-w>), with optional kernel term
-and sampling techniques (<doi:10.1186/s12859-017-1582-3>).
+multivariate (<doi:10.1186/s12711-022-00730-w>,
+<doi:10.1093/genetics/iyae179>), with optional kernel term and sampling
+techniques (<doi:10.1186/s12859-017-1582-3>).
 
 %prep
 %setup -q -c -n %{packname}