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cran4linux · Nov 17, 2024 · c5436e9 · c5436e9
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Showing 16 changed files with 213 additions and 47 deletions.
diff --git a/specs/R-CRAN-DFA.CANCOR.spec b/specs/R-CRAN-DFA.CANCOR.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  DFA.CANCOR
-%global packver   0.2.8
+%global packver   0.3.6
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.2.8
+Version:          0.3.6
 Release:          1%{?dist}%{?buildtag}
 Summary:          Linear Discriminant Function and Canonical Correlation Analysis
 
@@ -19,14 +19,20 @@ Requires:         R-core
 BuildArch:        noarch
 BuildRequires:    R-graphics 
 BuildRequires:    R-stats 
+BuildRequires:    R-utils 
+BuildRequires:    R-grDevices 
 BuildRequires:    R-CRAN-BayesFactor 
+BuildRequires:    R-CRAN-MASS 
+BuildRequires:    R-CRAN-mvoutlier 
 BuildRequires:    R-CRAN-MVN 
-BuildRequires:    R-utils 
 Requires:         R-graphics 
 Requires:         R-stats 
+Requires:         R-utils 
+Requires:         R-grDevices 
 Requires:         R-CRAN-BayesFactor 
+Requires:         R-CRAN-MASS 
+Requires:         R-CRAN-mvoutlier 
 Requires:         R-CRAN-MVN 
-Requires:         R-utils 
 
 %description
 Produces SPSS- and SAS-like output for linear discriminant function

diff --git a/specs/R-CRAN-Epi.spec b/specs/R-CRAN-Epi.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  Epi
-%global packver   2.56
+%global packver   2.57
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.56
+Version:          2.57
 Release:          1%{?dist}%{?buildtag}
 Summary:          Statistical Analysis in Epidemiology
 

diff --git a/specs/R-CRAN-HGNChelper.spec b/specs/R-CRAN-HGNChelper.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  HGNChelper
-%global packver   0.8.14
+%global packver   0.8.15
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.8.14
+Version:          0.8.15
 Release:          1%{?dist}%{?buildtag}
 Summary:          Identify and Correct Invalid HGNC Human Gene Symbols and MGI Mouse Gene Symbols
 

diff --git a/specs/R-CRAN-MortCast.spec b/specs/R-CRAN-MortCast.spec
@@ -1,10 +1,11 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  MortCast
-%global packver   2.7-0
+%global packver   2.8-0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.7.0
+Version:          2.8.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Estimation and Projection of Age-Specific Mortality Rates
 

diff --git a/specs/R-CRAN-ReliaGrowR.spec b/specs/R-CRAN-ReliaGrowR.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  ReliaGrowR
-%global packver   0.1.1
+%global packver   0.1.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.1.1
+Version:          0.1.3
 Release:          1%{?dist}%{?buildtag}
 Summary:          Reliability Growth Analysis
 

diff --git a/specs/R-CRAN-cchs.spec b/specs/R-CRAN-cchs.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  cchs
-%global packver   0.4.4
+%global packver   0.4.5
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.4.4
+Version:          0.4.5
 Release:          1%{?dist}%{?buildtag}
 Summary:          Cox Model for Case-Cohort Data with Stratified Subcohort-Selection
 

diff --git a/specs/R-CRAN-dfr.spec b/specs/R-CRAN-dfr.spec
@@ -0,0 +1,76 @@
+%global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
+%global packname  dfr
+%global packver   0.1.1
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          0.1.1
+Release:          1%{?dist}%{?buildtag}
+Summary:          Dual Feature Reduction for SGL
+
+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-sgs 
+BuildRequires:    R-CRAN-caret 
+BuildRequires:    R-CRAN-MASS 
+BuildRequires:    R-methods 
+BuildRequires:    R-stats 
+BuildRequires:    R-grDevices 
+BuildRequires:    R-graphics 
+BuildRequires:    R-CRAN-Matrix 
+Requires:         R-CRAN-sgs 
+Requires:         R-CRAN-caret 
+Requires:         R-CRAN-MASS 
+Requires:         R-methods 
+Requires:         R-stats 
+Requires:         R-grDevices 
+Requires:         R-graphics 
+Requires:         R-CRAN-Matrix 
+
+%description
+Implementation of the Dual Feature Reduction (DFR) approach for the Sparse
+Group Lasso (SGL) and the Adaptive Sparse Group Lasso (aSGL) (Feser and
+Evangelou (2024) <doi:10.48550/arXiv.2405.17094>). The DFR approach is a
+feature reduction approach that applies strong screening to reduce the
+feature space before optimisation, leading to speed-up improvements for
+fitting SGL (Simon et al. (2013) <doi:10.1080/10618600.2012.681250>) and
+aSGL (Mendez-Civieta et al. (2020) <doi:10.1007/s11634-020-00413-8> and
+Poignard (2020) <doi:10.1007/s10463-018-0692-7>) models. DFR is
+implemented using the Adaptive Three Operator Splitting (ATOS) (Pedregosa
+and Gidel (2018) <doi:10.48550/arXiv.1804.02339>) algorithm, with linear
+and logistic SGL models supported, both of which can be fit using k-fold
+cross-validation. Dense and sparse input matrices are supported.
+
+%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-fontawesome.spec b/specs/R-CRAN-fontawesome.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  fontawesome
-%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:          Easily Work with 'Font Awesome' Icons
 

diff --git a/specs/R-CRAN-forsearch.spec b/specs/R-CRAN-forsearch.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  forsearch
-%global packver   6.2.0
+%global packver   6.3.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          6.2.0
+Version:          6.3.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Diagnostic Analysis Using Forward Search Procedure for Various Models
 
@@ -34,11 +34,13 @@ Requires:         R-CRAN-Cairo >= 1.6.0
 
 %description
 Identifies potential data outliers and their impact on estimates and
-analyses. Uses the forward search approach of Atkinson and Riani, "Robust
-Diagnostic Regression Analysis", 2000,<ISBN: o-387-95017-6> to prepare
-descriptive statistics of a dataset that is to be analyzed by stats::lm(),
-stats::glm(), stats::nls(), nlme::lme() or survival::coxph().  Includes
-graphics functions to display the descriptive statistics.
+analyses. Tool for evaluation of study credibility. Uses the forward
+search approach of Atkinson and Riani, "Robust Diagnostic Regression
+Analysis", 2000,<ISBN: o-387-95017-6> to prepare descriptive statistics of
+a dataset that is to be analyzed by functions lm {stats}, glm {stats}, nls
+{stats}, lme {nlme}, or coxph {survival}, or their equivalent in another
+language.  Includes graphics functions to display the descriptive
+statistics.
 
 %prep
 %setup -q -c -n %{packname}

diff --git a/specs/R-CRAN-gdverse.spec b/specs/R-CRAN-gdverse.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  gdverse
-%global packver   1.2
+%global packver   1.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.2
+Version:          1.3
 Release:          1%{?dist}%{?buildtag}
 Summary:          Analysis of Spatial Stratified Heterogeneity
 
@@ -16,10 +16,9 @@ Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
 
 BuildRequires:    R-devel >= 4.1.0
 Requires:         R-core >= 4.1.0
-BuildRequires:    R-CRAN-sdsfun >= 0.4.0
+BuildRequires:    R-CRAN-sdsfun >= 0.4.3
 BuildRequires:    R-CRAN-dplyr 
 BuildRequires:    R-CRAN-forcats 
-BuildRequires:    R-CRAN-geosphere 
 BuildRequires:    R-CRAN-ggplot2 
 BuildRequires:    R-CRAN-magrittr 
 BuildRequires:    R-parallel 
@@ -34,10 +33,9 @@ BuildRequires:    R-CRAN-tibble
 BuildRequires:    R-CRAN-tidyr 
 BuildRequires:    R-utils 
 BuildRequires:    R-CRAN-Rcpp 
-Requires:         R-CRAN-sdsfun >= 0.4.0
+Requires:         R-CRAN-sdsfun >= 0.4.3
 Requires:         R-CRAN-dplyr 
 Requires:         R-CRAN-forcats 
-Requires:         R-CRAN-geosphere 
 Requires:         R-CRAN-ggplot2 
 Requires:         R-CRAN-magrittr 
 Requires:         R-parallel 
@@ -54,10 +52,11 @@ Requires:         R-utils
 
 %description
 Analyzing spatial factors and exploring spatial associations based on the
-concept of spatial stratified heterogeneity, and also takes into account
-local spatial dependencies, spatial interpretability, potential spatial
-interactions, and robust spatial stratification. Additionally, it supports
-geographical detector models established in academic literature.
+concept of spatial stratified heterogeneity, while also taking into
+account local spatial dependencies, spatial interpretability, complex
+spatial interactions, and robust spatial stratification. Additionally, it
+supports the spatial stratified heterogeneity family established in
+academic literature.
 
 %prep
 %setup -q -c -n %{packname}

diff --git a/specs/R-CRAN-geostan.spec b/specs/R-CRAN-geostan.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  geostan
-%global packver   0.7.0
+%global packver   0.8.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.7.0
+Version:          0.8.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Bayesian Spatial Analysis
 
@@ -30,6 +30,7 @@ BuildRequires:    R-CRAN-Rcpp >= 0.12.0
 BuildRequires:    R-methods 
 BuildRequires:    R-graphics 
 BuildRequires:    R-stats 
+BuildRequires:    R-CRAN-spData 
 BuildRequires:    R-CRAN-MASS 
 BuildRequires:    R-CRAN-truncnorm 
 BuildRequires:    R-CRAN-signs 
@@ -47,6 +48,7 @@ Requires:         R-CRAN-Rcpp >= 0.12.0
 Requires:         R-methods 
 Requires:         R-graphics 
 Requires:         R-stats 
+Requires:         R-CRAN-spData 
 Requires:         R-CRAN-MASS 
 Requires:         R-CRAN-truncnorm 
 Requires:         R-CRAN-signs 
@@ -56,10 +58,10 @@ Requires:         R-CRAN-rstantools
 
 %description
 For spatial data analysis; provides exploratory spatial analysis tools,
-spatial regression models, disease mapping models, model diagnostics, and
-special methods for inference with small area survey data (e.g., the
-America Community Survey (ACS)) and censored population health
-surveillance data. Models are pre-specified using the Stan programming
+spatial regression, spatial econometric, and disease mapping models, model
+diagnostics, and special methods for inference with small area survey data
+(e.g., the America Community Survey (ACS)) and censored population health
+monitoring data. Models are pre-specified using the Stan programming
 language, a platform for Bayesian inference using Markov chain Monte Carlo
 (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
 Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022)

diff --git 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   0.6-0
+%global packver   0.6-1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.6.0
+Version:          0.6.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Hierarchical and Geographically Weighted Regression
 

diff --git a/specs/R-CRAN-pargasite.spec b/specs/R-CRAN-pargasite.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  pargasite
-%global packver   2.1.0
+%global packver   2.1.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.1.0
+Version:          2.1.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Pollution-Associated Risk Geospatial Analysis Site
 

diff --git a/specs/R-CRAN-rgl.spec b/specs/R-CRAN-rgl.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  rgl
-%global packver   1.3.12
+%global packver   1.3.14
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.3.12
+Version:          1.3.14
 Release:          1%{?dist}%{?buildtag}
 Summary:          3D Visualization Using OpenGL