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cran4linux · Nov 6, 2024 · 9defda3 · 9defda3
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diff --git a/specs/R-CRAN-CRF.spec b/specs/R-CRAN-CRF.spec
diff --git a/specs/R-CRAN-CausalQueries.spec b/specs/R-CRAN-CausalQueries.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  CausalQueries
-%global packver   1.1.1
+%global packver   1.2.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.1.1
+Version:          1.2.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Make, Update, and Query Binary Causal Models
 
@@ -14,54 +14,49 @@ URL:              https://cran.r-project.org/package=%{packname}
 Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
 
 
-BuildRequires:    R-devel >= 3.4.0
-Requires:         R-core >= 3.4.0
+BuildRequires:    R-devel >= 3.5.0
+Requires:         R-core >= 3.5.0
 BuildRequires:    R-stats >= 4.1.1
 BuildRequires:    R-CRAN-ggplot2 >= 3.3.5
 BuildRequires:    R-CRAN-rstan >= 2.26.0
 BuildRequires:    R-CRAN-StanHeaders >= 2.26.0
+BuildRequires:    R-CRAN-ggraph >= 2.2.0
 BuildRequires:    R-CRAN-rstantools >= 2.0.0
 BuildRequires:    R-CRAN-BH >= 1.66.0
 BuildRequires:    R-CRAN-knitr >= 1.45
 BuildRequires:    R-CRAN-stringr >= 1.4.0
 BuildRequires:    R-CRAN-lifecycle >= 1.0.1
 BuildRequires:    R-CRAN-latex2exp >= 0.9.4
 BuildRequires:    R-CRAN-RcppEigen >= 0.3.3.3.0
-BuildRequires:    R-CRAN-dagitty >= 0.3.1
-BuildRequires:    R-CRAN-ggdag >= 0.2.4
 BuildRequires:    R-CRAN-rlang >= 0.2.0
 BuildRequires:    R-CRAN-Rcpp >= 0.12.0
 BuildRequires:    R-CRAN-dirmult >= 0.1.3.4
-BuildRequires:    R-CRAN-dplyr 
 BuildRequires:    R-methods 
+BuildRequires:    R-CRAN-dplyr 
 BuildRequires:    R-CRAN-RcppArmadillo 
 BuildRequires:    R-CRAN-rstantools
 Requires:         R-stats >= 4.1.1
 Requires:         R-CRAN-ggplot2 >= 3.3.5
 Requires:         R-CRAN-rstan >= 2.26.0
+Requires:         R-CRAN-ggraph >= 2.2.0
 Requires:         R-CRAN-rstantools >= 2.0.0
 Requires:         R-CRAN-knitr >= 1.45
 Requires:         R-CRAN-stringr >= 1.4.0
 Requires:         R-CRAN-lifecycle >= 1.0.1
 Requires:         R-CRAN-latex2exp >= 0.9.4
-Requires:         R-CRAN-dagitty >= 0.3.1
-Requires:         R-CRAN-ggdag >= 0.2.4
 Requires:         R-CRAN-rlang >= 0.2.0
 Requires:         R-CRAN-Rcpp >= 0.12.0
 Requires:         R-CRAN-dirmult >= 0.1.3.4
-Requires:         R-CRAN-dplyr 
 Requires:         R-methods 
+Requires:         R-CRAN-dplyr 
 Requires:         R-CRAN-rstantools
 
 %description
-Users can declare binary causal models, update beliefs about causal types
-given data and calculate arbitrary estimands.  Model definition makes use
-of 'dagitty' functionality. Updating is implemented in 'stan'. The
-approach used in 'CausalQueries' is a generalization of the 'biqq' models
-described in "Mixing Methods: A Bayesian Approach" (Humphreys and Jacobs,
-2015, <DOI:10.1017/S0003055415000453>). The conceptual extension makes use
-of work on probabilistic causal models described in Pearl's Causality
-(Pearl, 2009, <DOI:10.1017/CBO9780511803161>).
+Users can declare causal models over binary nodes, update beliefs about
+causal types given data, and calculate arbitrary queries.  Updating is
+implemented in 'stan'. See Humphreys and Jacobs, 2023, Integrated
+Inferences (<DOI: 10.1017/9781316718636>) and Pearl, 2009 Causality
+(<DOI:10.1017/CBO9780511803161>).
 
 %prep
 %setup -q -c -n %{packname}

diff --git a/specs/R-CRAN-CollocInfer.spec b/specs/R-CRAN-CollocInfer.spec
@@ -1,30 +1,31 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  CollocInfer
-%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
-Release:          3%{?dist}%{?buildtag}
+Version:          1.0.5
+Release:          1%{?dist}%{?buildtag}
 Summary:          Collocation Inference for Dynamic Systems
 
 License:          GPL (>= 2)
 URL:              https://cran.r-project.org/package=%{packname}
 Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
 
 
-BuildRequires:    R-devel >= 2.4.0
-Requires:         R-core >= 2.4.0
+BuildRequires:    R-devel >= 4.3.0
+Requires:         R-core >= 4.3.0
 BuildArch:        noarch
 BuildRequires:    R-CRAN-fda 
-BuildRequires:    R-MASS 
-BuildRequires:    R-Matrix 
+BuildRequires:    R-CRAN-MASS 
+BuildRequires:    R-CRAN-Matrix 
 BuildRequires:    R-CRAN-spam 
 BuildRequires:    R-CRAN-deSolve 
 BuildRequires:    R-methods 
 Requires:         R-CRAN-fda 
-Requires:         R-MASS 
-Requires:         R-Matrix 
+Requires:         R-CRAN-MASS 
+Requires:         R-CRAN-Matrix 
 Requires:         R-CRAN-spam 
 Requires:         R-CRAN-deSolve 
 Requires:         R-methods 
@@ -38,6 +39,15 @@ methods.
 %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
 
@@ -47,6 +57,8 @@ 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-KODAMA.spec b/specs/R-CRAN-KODAMA.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  KODAMA
-%global packver   2.4
+%global packver   2.4.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.4
+Version:          2.4.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Knowledge Discovery by Accuracy Maximization
 

diff --git a/specs/R-CRAN-LMest.spec b/specs/R-CRAN-LMest.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  LMest
-%global packver   3.2.2
+%global packver   3.2.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          3.2.2
+Version:          3.2.3
 Release:          1%{?dist}%{?buildtag}
 Summary:          Generalized Latent Markov Models
 

diff --git a/specs/R-CRAN-MVar.pt.spec b/specs/R-CRAN-MVar.pt.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  MVar.pt
-%global packver   2.2.2
+%global packver   2.2.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.2.2
+Version:          2.2.3
 Release:          1%{?dist}%{?buildtag}
 Summary:          Analise multivariada (brazilian portuguese)
 

diff --git a/specs/R-CRAN-MVar.spec b/specs/R-CRAN-MVar.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  MVar
-%global packver   2.2.2
+%global packver   2.2.3
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.2.2
+Version:          2.2.3
 Release:          1%{?dist}%{?buildtag}
 Summary:          Multivariate Analysis
 

diff --git a/specs/R-CRAN-RaceID.spec b/specs/R-CRAN-RaceID.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  RaceID
-%global packver   0.3.7
+%global packver   0.3.8
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.3.7
+Version:          0.3.8
 Release:          1%{?dist}%{?buildtag}
 Summary:          Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
 

diff --git a/specs/R-CRAN-TrialSize.spec b/specs/R-CRAN-TrialSize.spec
@@ -1,12 +1,13 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  TrialSize
-%global packver   1.4
+%global packver   1.4.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.4
-Release:          2%{?dist}%{?buildtag}
-Summary:          R Functions for Chapter 3,4,6,7,9,10,11,12,14,15 of Sample SizeCalculation in Clinical Research
+Version:          1.4.1
+Release:          1%{?dist}%{?buildtag}
+Summary:          R Functions for Chapter 3,4,6,7,9,10,11,12,14,15 of Sample Size Calculation in Clinical Research
 
 License:          GPL (>= 2.15.1)
 URL:              https://cran.r-project.org/package=%{packname}
@@ -22,9 +23,15 @@ Functions and Examples in Sample Size Calculation in Clinical Research.
 %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
 
@@ -34,6 +41,7 @@ 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

diff --git a/specs/R-CRAN-WeightIt.spec b/specs/R-CRAN-WeightIt.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  WeightIt
-%global packver   1.3.1
+%global packver   1.3.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.3.1
+Version:          1.3.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Weighting for Covariate Balance in Observational Studies
 

diff --git a/specs/R-CRAN-XNomial.spec b/specs/R-CRAN-XNomial.spec
@@ -1,12 +1,13 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  XNomial
-%global packver   1.0.4
+%global packver   1.0.4.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.0.4
-Release:          3%{?dist}%{?buildtag}
-Summary:          Exact Goodness-of-Fit Test for Multinomial Data with FixedProbabilities
+Version:          1.0.4.1
+Release:          1%{?dist}%{?buildtag}
+Summary:          Exact Goodness-of-Fit Test for Multinomial Data with Fixed Probabilities
 
 License:          GPL
 URL:              https://cran.r-project.org/package=%{packname}
@@ -31,6 +32,15 @@ plotted and compared with the asymptotic curve.
 %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
 
@@ -40,6 +50,8 @@ 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-admix.spec b/specs/R-CRAN-admix.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  admix
-%global packver   2.3.1
+%global packver   2.3.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.3.1
+Version:          2.3.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Package Admix for Admixture (aka Contamination) Models
 

diff --git a/specs/R-CRAN-animint2.spec b/specs/R-CRAN-animint2.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  animint2
-%global packver   2024.1.24
+%global packver   2024.11.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2024.1.24
+Version:          2024.11.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Animated Interactive Grammar of Graphics