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cran4linux · Nov 13, 2024 · 58ac838 · 58ac838
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diff --git a/specs/R-CRAN-BayesGP.spec b/specs/R-CRAN-BayesGP.spec
@@ -0,0 +1,79 @@
+%global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
+%global packname  BayesGP
+%global packver   0.1.3
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          0.1.3
+Release:          1%{?dist}%{?buildtag}
+Summary:          Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models
+
+License:          GPL (>= 3)
+URL:              https://cran.r-project.org/package=%{packname}
+Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
+
+
+BuildRequires:    R-devel >= 3.6.0
+Requires:         R-core >= 3.6.0
+BuildRequires:    R-CRAN-TMB >= 1.9.7
+BuildRequires:    R-CRAN-Matrix >= 1.6.3
+BuildRequires:    R-CRAN-aghq >= 0.4.1
+BuildRequires:    R-CRAN-numDeriv 
+BuildRequires:    R-CRAN-rstan 
+BuildRequires:    R-CRAN-sfsmisc 
+BuildRequires:    R-CRAN-fda 
+BuildRequires:    R-CRAN-tmbstan 
+BuildRequires:    R-CRAN-LaplacesDemon 
+BuildRequires:    R-methods 
+BuildRequires:    R-CRAN-RcppEigen 
+BuildRequires:    R-CRAN-rstantools
+Requires:         R-CRAN-TMB >= 1.9.7
+Requires:         R-CRAN-Matrix >= 1.6.3
+Requires:         R-CRAN-aghq >= 0.4.1
+Requires:         R-CRAN-numDeriv 
+Requires:         R-CRAN-rstan 
+Requires:         R-CRAN-sfsmisc 
+Requires:         R-CRAN-fda 
+Requires:         R-CRAN-tmbstan 
+Requires:         R-CRAN-LaplacesDemon 
+Requires:         R-methods 
+Requires:         R-CRAN-rstantools
+
+%description
+Implements Bayesian hierarchical models with flexible Gaussian process
+priors, focusing on Extended Latent Gaussian Models and incorporating
+various Gaussian process priors for Bayesian smoothing. Computations
+leverage finite element approximations and adaptive quadrature for
+efficient inference. Methods are detailed in Zhang, Stringer, Brown, and
+Stafford (2023) <doi:10.1177/09622802221134172>; Zhang, Stringer, Brown,
+and Stafford (2024) <doi:10.1080/10618600.2023.2289532>; Zhang, Brown, and
+Stafford (2023) <doi:10.48550/arXiv.2305.09914>; and Stringer, Brown, and
+Stafford (2021) <doi:10.1111/biom.13329>.
+
+%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-Bolstad.spec b/specs/R-CRAN-Bolstad.spec
@@ -1,10 +1,11 @@
 %global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
 %global packname  Bolstad
-%global packver   0.2-41
+%global packver   0.2.42
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.2.41
+Version:          0.2.42
 Release:          1%{?dist}%{?buildtag}
 Summary:          Functions for Elementary Bayesian Inference
 
@@ -13,11 +14,13 @@ 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 >= 4.2.0
+Requires:         R-core >= 4.2.0
 BuildArch:        noarch
 BuildRequires:    R-CRAN-mvtnorm 
+BuildRequires:    R-methods 
 Requires:         R-CRAN-mvtnorm 
+Requires:         R-methods 
 
 %description
 A set of R functions and data sets for the book Introduction to Bayesian
@@ -32,6 +35,8 @@ 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' {} \;
 

diff --git a/specs/R-CRAN-CIMPLE.spec b/specs/R-CRAN-CIMPLE.spec
@@ -0,0 +1,75 @@
+%global __brp_check_rpaths %{nil}
+%global __requires_exclude ^libmpi
+%global packname  CIMPLE
+%global packver   0.1.0
+%global rlibdir   /usr/local/lib/R/library
+
+Name:             R-CRAN-%{packname}
+Version:          0.1.0
+Release:          1%{?dist}%{?buildtag}
+Summary:          Analysis of Longitudinal Electronic Health Record (EHR) Data with Possibly Informative Observational Time
+
+License:          GPL (>= 3)
+URL:              https://cran.r-project.org/package=%{packname}
+Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz
+
+
+BuildRequires:    R-devel >= 2.10
+Requires:         R-core >= 2.10
+BuildArch:        noarch
+BuildRequires:    R-CRAN-dplyr 
+BuildRequires:    R-CRAN-JMbayes2 
+BuildRequires:    R-CRAN-lme4 
+BuildRequires:    R-CRAN-mice 
+BuildRequires:    R-CRAN-nleqslv 
+BuildRequires:    R-CRAN-nlme 
+BuildRequires:    R-CRAN-statmod 
+BuildRequires:    R-stats 
+BuildRequires:    R-CRAN-survival 
+BuildRequires:    R-utils 
+Requires:         R-CRAN-dplyr 
+Requires:         R-CRAN-JMbayes2 
+Requires:         R-CRAN-lme4 
+Requires:         R-CRAN-mice 
+Requires:         R-CRAN-nleqslv 
+Requires:         R-CRAN-nlme 
+Requires:         R-CRAN-statmod 
+Requires:         R-stats 
+Requires:         R-CRAN-survival 
+Requires:         R-utils 
+
+%description
+Analyzes longitudinal Electronic Health Record (EHR) data with possibly
+informative observational time. These methods are grouped into two classes
+depending on the inferential task. One group focuses on estimating the
+effect of an exposure on a longitudinal biomarker while the other group
+assesses the impact of a longitudinal biomarker on time-to-diagnosis
+outcomes. The accompanying paper is Du et al (2024)
+<doi:10.48550/arXiv.2410.13113>.
+
+%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-DiceView.spec b/specs/R-CRAN-DiceView.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  DiceView
-%global packver   2.2-0
+%global packver   3.1-0
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.2.0
+Version:          3.1.0
 Release:          1%{?dist}%{?buildtag}
 Summary:          Methods for Visualization of Computer Experiments Design and Surrogate
 

diff --git a/specs/R-CRAN-Ecfun.spec b/specs/R-CRAN-Ecfun.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  Ecfun
-%global packver   0.3-2
+%global packver   0.3-6
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.3.2
+Version:          0.3.6
 Release:          1%{?dist}%{?buildtag}
 Summary:          Functions for 'Ecdat'
 
@@ -21,24 +21,26 @@ BuildRequires:    R-CRAN-fda
 BuildRequires:    R-CRAN-tis 
 BuildRequires:    R-CRAN-jpeg 
 BuildRequires:    R-CRAN-MASS 
-BuildRequires:    R-CRAN-TeachingDemos 
 BuildRequires:    R-CRAN-stringi 
 BuildRequires:    R-methods 
 BuildRequires:    R-CRAN-xml2 
 BuildRequires:    R-CRAN-BMA 
 BuildRequires:    R-CRAN-mvtnorm 
 BuildRequires:    R-CRAN-rvest 
+BuildRequires:    R-CRAN-readr 
+BuildRequires:    R-CRAN-rworldmap 
 Requires:         R-CRAN-fda 
 Requires:         R-CRAN-tis 
 Requires:         R-CRAN-jpeg 
 Requires:         R-CRAN-MASS 
-Requires:         R-CRAN-TeachingDemos 
 Requires:         R-CRAN-stringi 
 Requires:         R-methods 
 Requires:         R-CRAN-xml2 
 Requires:         R-CRAN-BMA 
 Requires:         R-CRAN-mvtnorm 
 Requires:         R-CRAN-rvest 
+Requires:         R-CRAN-readr 
+Requires:         R-CRAN-rworldmap 
 
 %description
 Functions and vignettes to update data sets in 'Ecdat' and to create,

diff --git a/specs/R-CRAN-FishResp.spec b/specs/R-CRAN-FishResp.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  FishResp
-%global packver   1.1.1
+%global packver   1.1.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          1.1.1
+Version:          1.1.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Analytical Tool for Aquatic Respirometry
 

diff --git a/specs/R-CRAN-GeneNMF.spec b/specs/R-CRAN-GeneNMF.spec
@@ -1,11 +1,11 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  GeneNMF
-%global packver   0.6.0
+%global packver   0.6.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          0.6.0
+Version:          0.6.2
 Release:          1%{?dist}%{?buildtag}
 Summary:          Non-Negative Matrix Factorization for Single-Cell Omics
 
@@ -27,6 +27,7 @@ BuildRequires:    R-CRAN-cluster
 BuildRequires:    R-CRAN-lsa 
 BuildRequires:    R-CRAN-irlba 
 BuildRequires:    R-CRAN-pheatmap 
+BuildRequires:    R-CRAN-dendextend 
 BuildRequires:    R-CRAN-viridis 
 Requires:         R-CRAN-Seurat >= 4.3.0
 Requires:         R-CRAN-RcppML 
@@ -38,6 +39,7 @@ Requires:         R-CRAN-cluster
 Requires:         R-CRAN-lsa 
 Requires:         R-CRAN-irlba 
 Requires:         R-CRAN-pheatmap 
+Requires:         R-CRAN-dendextend 
 Requires:         R-CRAN-viridis 
 
 %description

diff --git a/specs/R-CRAN-GitStats.spec b/specs/R-CRAN-GitStats.spec
@@ -1,13 +1,13 @@
 %global __brp_check_rpaths %{nil}
 %global __requires_exclude ^libmpi
 %global packname  GitStats
-%global packver   2.1.1
+%global packver   2.1.2
 %global rlibdir   /usr/local/lib/R/library
 
 Name:             R-CRAN-%{packname}
-Version:          2.1.1
+Version:          2.1.2
 Release:          1%{?dist}%{?buildtag}
-Summary:          Get Statistics from 'GitHub' and 'GitLab'
+Summary:          Standardized Git Repository Data
 
 License:          MIT + file LICENSE
 URL:              https://cran.r-project.org/package=%{packname}
@@ -39,10 +39,10 @@ Requires:         R-CRAN-R6
 Requires:         R-CRAN-stringr 
 
 %description
-Obtain statistics in a standardized way from multiple 'Git' services:
-'GitHub' and 'GitLab' for the time-being. Its main purpose is to help
-teams, whose activities are spread across multiple git platforms, get
-their repository metadata in a standardized way from all these platforms.
+Obtain standardized data from multiple 'Git' services, including 'GitHub'
+and 'GitLab'. Designed to be 'Git' service-agnostic, this package assists
+teams with activities spread across various 'Git' platforms by providing a
+unified way to access repository data.
 
 %prep
 %setup -q -c -n %{packname}