sync

specs/R-CRAN-IPEDSuploadables.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  IPEDSuploadables
-%global packver   2.9.0
+%global packver   2.10.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.9.0
+Version:          2.10.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload
 

specs/R-CRAN-MF.beta4.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  MF.beta4
-%global packver   1.1.0
+%global packver   1.1.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.1.0
+Version:          1.1.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Measuring Ecosystem Multi-Functionality and Its Decomposition
 

specs/R-CRAN-MapperAlgo.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  MapperAlgo
-%global packver   1.0
+%global packver   1.0.1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.0
+Version:          1.0.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          Topological Data Analysis: Mapper Algorithm
 

specs/R-CRAN-SparseChol.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  SparseChol
-%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:          Sparse Matrix C++ Classes Including Sparse Cholesky LDL Decomposition of Symmetric Matrices
 

specs/R-CRAN-SurrogateParadoxTest.spec

@@ -0,0 +1,57 @@
+%global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
+%global packname  SurrogateParadoxTest
+%global packver   1.0
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          1.0
+Release:          1%{?dist}%{?buildtag}
+Summary:          Empirical Testing of Surrogate Paradox Assumptions
+
+License:          GPL
+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-stats 
+BuildRequires:    R-parallel 
+Requires:         R-stats 
+Requires:         R-parallel 
+
+%description
+Provides functions to nonparametrically assess assumptions necessary to
+prevent the surrogate paradox through hypothesis tests of stochastic
+dominance, monotonicity of regression functions, and non-negative residual
+treatment effects. More details are available in Hsiao et al 2024 (under
+review).
+
+%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}

specs/R-CRAN-TraMineR.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  TraMineR
-%global packver   2.2-10
+%global packver   2.2-11
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.2.10
+Version:          2.2.11
 Release:          1%{?dist}%{?buildtag}
 Summary:          Trajectory Miner: a Sequence Analysis Toolkit
 

specs/R-CRAN-admisc.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  admisc
-%global packver   0.36
+%global packver   0.37
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.36
+Version:          0.37
 Release:          1%{?dist}%{?buildtag}
 Summary:          Adrian Dusa's Miscellaneous
 

specs/R-CRAN-bolasso.spec

@@ -1,10 +1,11 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  bolasso
-%global packver   0.2.0
+%global packver   0.3.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.2.0
+Version:          0.3.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Model Consistent Lasso Estimation Through the Bootstrap
 
@@ -20,26 +21,26 @@ BuildRequires:    R-CRAN-glmnet >= 3.0
 BuildRequires:    R-CRAN-future.apply >= 1.1.0
 BuildRequires:    R-CRAN-Matrix >= 1.0.6
 BuildRequires:    R-CRAN-gamlr >= 1.0
+BuildRequires:    R-CRAN-generics 
 BuildRequires:    R-CRAN-ggplot2 
 BuildRequires:    R-CRAN-progressr 
-BuildRequires:    R-CRAN-Rdpack 
 BuildRequires:    R-stats 
 BuildRequires:    R-CRAN-tibble 
 Requires:         R-CRAN-glmnet >= 3.0
 Requires:         R-CRAN-future.apply >= 1.1.0
 Requires:         R-CRAN-Matrix >= 1.0.6
 Requires:         R-CRAN-gamlr >= 1.0
+Requires:         R-CRAN-generics 
 Requires:         R-CRAN-ggplot2 
 Requires:         R-CRAN-progressr 
-Requires:         R-CRAN-Rdpack 
 Requires:         R-stats 
 Requires:         R-CRAN-tibble 
 
 %description
 Implements the bolasso algorithm for consistent variable selection and
 estimation accuracy. Includes support for many parallel backends via the
 future package. For details see: Bach (2008), 'Bolasso: model consistent
-Lasso estimation through the bootstrap', <arXiv:0804.1302>.
+Lasso estimation through the bootstrap', <doi:10.48550/arXiv.0804.1302>.
 
 %prep
 %setup -q -c -n %{packname}

specs/R-CRAN-cluster.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  cluster
-%global packver   2.1.6
+%global packver   2.1.7
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.1.6
+Version:          2.1.7
 Release:          1%{?dist}%{?buildtag}
 Summary:          "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.
 

specs/R-CRAN-depower.spec

@@ -0,0 +1,72 @@
+%global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
+%global packname  depower
+%global packver   2024.12.4
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          2024.12.4
+Release:          1%{?dist}%{?buildtag}
+Summary:          Power Analysis for Differential Expression Studies
+
+License:          MIT + file LICENSE
+URL:              https://cran.r-project.org/package=%{packname}
+Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
+
+
+BuildRequires:    R-devel >= 4.2.0
+Requires:         R-core >= 4.2.0
+BuildArch:        noarch
+BuildRequires:    R-CRAN-Rdpack 
+BuildRequires:    R-stats 
+BuildRequires:    R-CRAN-mvnfast 
+BuildRequires:    R-CRAN-glmmTMB 
+BuildRequires:    R-CRAN-dplyr 
+BuildRequires:    R-CRAN-multidplyr 
+BuildRequires:    R-CRAN-ggplot2 
+BuildRequires:    R-CRAN-scales 
+Requires:         R-CRAN-Rdpack 
+Requires:         R-stats 
+Requires:         R-CRAN-mvnfast 
+Requires:         R-CRAN-glmmTMB 
+Requires:         R-CRAN-dplyr 
+Requires:         R-CRAN-multidplyr 
+Requires:         R-CRAN-ggplot2 
+Requires:         R-CRAN-scales 
+
+%description
+Provides a convenient framework to simulate, test, power, and visualize
+data for differential expression studies with lognormal or negative
+binomial outcomes. Supported designs are two-sample comparisons of
+independent or dependent outcomes. Power may be summarized in the context
+of controlling the per-family error rate or family-wise error rate.
+Negative binomial methods are described in Yu, Fernandez, and Brock (2017)
+<doi:10.1186/s12859-017-1648-2> and Yu, Fernandez, and Brock (2020)
+<doi:10.1186/s12859-020-3541-7>.
+
+%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}

specs/R-CRAN-duckdb.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  duckdb
-%global packver   1.1.3
+%global packver   1.1.3-1
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.1.3
+Version:          1.1.3.1
 Release:          1%{?dist}%{?buildtag}
 Summary:          DBI Package for the DuckDB Database Management System
 

specs/R-CRAN-flashr.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  flashr
-%global packver   0.1.2
+%global packver   0.2.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.1.2
+Version:          0.2.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Create Flashcards of Terms and Definitions
 
@@ -25,6 +25,7 @@ BuildRequires:    R-CRAN-memoise
 BuildRequires:    R-CRAN-revealjs 
 BuildRequires:    R-CRAN-rmarkdown 
 BuildRequires:    R-CRAN-testthat 
+BuildRequires:    R-utils 
 Requires:         R-CRAN-cli 
 Requires:         R-CRAN-curl 
 Requires:         R-CRAN-gh 
@@ -33,6 +34,7 @@ Requires:         R-CRAN-memoise
 Requires:         R-CRAN-revealjs 
 Requires:         R-CRAN-rmarkdown 
 Requires:         R-CRAN-testthat 
+Requires:         R-utils 
 
 %description
 Provides functions for creating flashcard decks of terms and definitions.

specs/R-CRAN-imuf.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  imuf
-%global packver   0.3.0
+%global packver   0.4.0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.3.0
+Version:          0.4.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Estimate Orientation of an Inertial Measurement Unit
 
@@ -14,8 +14,8 @@ 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 >= 2.10
+Requires:         R-core >= 2.10
 BuildRequires:    R-CRAN-Rcpp 
 BuildRequires:    R-CRAN-RcppEigen 
 Requires:         R-CRAN-Rcpp 

specs/R-CRAN-lessR.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  lessR
-%global packver   4.3.8
+%global packver   4.3.9
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          4.3.8
+Version:          4.3.9
 Release:          1%{?dist}%{?buildtag}
 Summary:          Less Code, More Results
 

specs/R-CRAN-lubridate.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  lubridate
-%global packver   1.9.3
+%global packver   1.9.4
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.9.3
+Version:          1.9.4
 Release:          1%{?dist}%{?buildtag}
 Summary:          Make Dealing with Dates a Little Easier
 
@@ -16,10 +16,10 @@ Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
 
 BuildRequires:    R-devel >= 3.2
 Requires:         R-core >= 3.2
-BuildRequires:    R-CRAN-timechange >= 0.1.1
+BuildRequires:    R-CRAN-timechange >= 0.3.0
 BuildRequires:    R-methods 
 BuildRequires:    R-CRAN-generics 
-Requires:         R-CRAN-timechange >= 0.1.1
+Requires:         R-CRAN-timechange >= 0.3.0
 Requires:         R-methods 
 Requires:         R-CRAN-generics 
 

specs/R-CRAN-manymome.spec

@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  manymome
-%global packver   0.2.4
+%global packver   0.2.5
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.2.4
+Version:          0.2.5
 Release:          1%{?dist}%{?buildtag}
 Summary:          Mediation, Moderation and Moderated-Mediation After Model Fitting