diff --git a/specs/R-CRAN-Argentum.spec b/specs/R-CRAN-Argentum.spec new file mode 100644 index 000000000..6e15a9b7d --- /dev/null +++ b/specs/R-CRAN-Argentum.spec @@ -0,0 +1,62 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname Argentum +%global packver 0.5.1 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.5.1 +Release: 1%{?dist}%{?buildtag} +Summary: Access and Import WMS and WFS Data from Argentine Organizations + +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 +BuildArch: noarch +BuildRequires: R-CRAN-httr +BuildRequires: R-CRAN-xml2 +BuildRequires: R-CRAN-sf +BuildRequires: R-CRAN-readr +Requires: R-CRAN-httr +Requires: R-CRAN-xml2 +Requires: R-CRAN-sf +Requires: R-CRAN-readr + +%description +Provides functions to retrieve information from Web Feature Service (WFS) +and Web Map Service (WMS) layers from various Argentine organizations and +import them into R for further analysis. WFS and WMS are standardized +protocols for serving georeferenced map data over the internet. For more +information on these services, see and +. + +%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-BGVAR.spec b/specs/R-CRAN-BGVAR.spec index f4d015d68..a5c4ee542 100644 --- a/specs/R-CRAN-BGVAR.spec +++ b/specs/R-CRAN-BGVAR.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname BGVAR -%global packver 2.5.7 +%global packver 2.5.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.5.7 +Version: 2.5.8 Release: 1%{?dist}%{?buildtag} Summary: Bayesian Global Vector Autoregressions diff --git a/specs/R-CRAN-CholWishart.spec b/specs/R-CRAN-CholWishart.spec index 079a46d30..c2c911db0 100644 --- a/specs/R-CRAN-CholWishart.spec +++ b/specs/R-CRAN-CholWishart.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname CholWishart -%global packver 1.1.2.1 +%global packver 1.1.4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.1.2.1 +Version: 1.1.4 Release: 1%{?dist}%{?buildtag} Summary: Cholesky Decomposition of the Wishart Distribution diff --git a/specs/R-CRAN-CohortGenerator.spec b/specs/R-CRAN-CohortGenerator.spec index f43668e5e..6b9b9cd33 100644 --- a/specs/R-CRAN-CohortGenerator.spec +++ b/specs/R-CRAN-CohortGenerator.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname CohortGenerator -%global packver 0.11.1 +%global packver 0.11.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.11.1 +Version: 0.11.2 Release: 1%{?dist}%{?buildtag} Summary: Cohort Generation for the OMOP Common Data Model diff --git a/specs/R-CRAN-EmpiricalCalibration.spec b/specs/R-CRAN-EmpiricalCalibration.spec index fd12416df..3da6bae03 100644 --- a/specs/R-CRAN-EmpiricalCalibration.spec +++ b/specs/R-CRAN-EmpiricalCalibration.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname EmpiricalCalibration -%global packver 3.1.2 +%global packver 3.1.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.1.2 +Version: 3.1.3 Release: 1%{?dist}%{?buildtag} Summary: Routines for Performing Empirical Calibration of Observational Study Estimates diff --git a/specs/R-CRAN-IGC.CSM.spec b/specs/R-CRAN-IGC.CSM.spec new file mode 100644 index 000000000..d6ba7b452 --- /dev/null +++ b/specs/R-CRAN-IGC.CSM.spec @@ -0,0 +1,54 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname IGC.CSM +%global packver 0.2.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.2.0 +Release: 1%{?dist}%{?buildtag} +Summary: Simulate Impact of Different Urban Policies Through a General Equilibrium Model + +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 +BuildArch: noarch + +%description +Develops a General Equilibrium (GE) Model, which estimates key variables +such as wages, the number of residents and workers, the prices of the +floor space, and its distribution between commercial and residential use, +as in Ahlfeldt et al., (2015) . By doing so, the +model allows understanding the economic influence of different urban +policies. + +%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-MAMS.spec b/specs/R-CRAN-MAMS.spec index e937885de..468cd20fa 100644 --- a/specs/R-CRAN-MAMS.spec +++ b/specs/R-CRAN-MAMS.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname MAMS -%global packver 2.0.2 +%global packver 3.0.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.0.2 +Version: 3.0.0 Release: 1%{?dist}%{?buildtag} Summary: Designing Multi-Arm Multi-Stage Studies @@ -20,12 +20,12 @@ BuildRequires: R-CRAN-mvtnorm BuildRequires: R-methods BuildRequires: R-CRAN-future BuildRequires: R-CRAN-future.apply -BuildRequires: R-CRAN-knitr +BuildRequires: R-CRAN-cli Requires: R-CRAN-mvtnorm Requires: R-methods Requires: R-CRAN-future Requires: R-CRAN-future.apply -Requires: R-CRAN-knitr +Requires: R-CRAN-cli %description Designing multi-arm multi-stage studies with (asymptotically) normal diff --git a/specs/R-CRAN-MethodOpt.spec b/specs/R-CRAN-MethodOpt.spec new file mode 100644 index 000000000..5e4b8d6d3 --- /dev/null +++ b/specs/R-CRAN-MethodOpt.spec @@ -0,0 +1,94 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname MethodOpt +%global packver 1.0.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0.0 +Release: 1%{?dist}%{?buildtag} +Summary: Advanced Method Optimization for Spectra-Generating Sampling and Analysis Instrumentation + +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-stats >= 4.3.2 +BuildRequires: R-CRAN-gtools >= 3.9.5 +BuildRequires: R-CRAN-ggplot2 >= 3.4.4 +BuildRequires: R-CRAN-tibble >= 3.2.1 +BuildRequires: R-CRAN-shinyalert >= 3.0.0 +BuildRequires: R-CRAN-FrF2 >= 2.3.3 +BuildRequires: R-CRAN-zip >= 2.3.0 +BuildRequires: R-CRAN-shinyjs >= 2.1.0 +BuildRequires: R-CRAN-magrittr >= 2.0.3 +BuildRequires: R-CRAN-zoo >= 1.8.12 +BuildRequires: R-CRAN-shiny >= 1.7.5.1 +BuildRequires: R-CRAN-glue >= 1.6.2 +BuildRequires: R-CRAN-dplyr >= 1.1.3 +BuildRequires: R-CRAN-rlang >= 1.1.2 +BuildRequires: R-CRAN-purrr >= 1.0.2 +BuildRequires: R-CRAN-shinyBS >= 0.61.1 +BuildRequires: R-CRAN-htmltools >= 0.5.8.1 +BuildRequires: R-CRAN-shinyFeedback >= 0.4.0 +BuildRequires: R-CRAN-DT >= 0.30 +BuildRequires: R-CRAN-DoE.wrapper >= 0.12 +Requires: R-stats >= 4.3.2 +Requires: R-CRAN-gtools >= 3.9.5 +Requires: R-CRAN-ggplot2 >= 3.4.4 +Requires: R-CRAN-tibble >= 3.2.1 +Requires: R-CRAN-shinyalert >= 3.0.0 +Requires: R-CRAN-FrF2 >= 2.3.3 +Requires: R-CRAN-zip >= 2.3.0 +Requires: R-CRAN-shinyjs >= 2.1.0 +Requires: R-CRAN-magrittr >= 2.0.3 +Requires: R-CRAN-zoo >= 1.8.12 +Requires: R-CRAN-shiny >= 1.7.5.1 +Requires: R-CRAN-glue >= 1.6.2 +Requires: R-CRAN-dplyr >= 1.1.3 +Requires: R-CRAN-rlang >= 1.1.2 +Requires: R-CRAN-purrr >= 1.0.2 +Requires: R-CRAN-shinyBS >= 0.61.1 +Requires: R-CRAN-htmltools >= 0.5.8.1 +Requires: R-CRAN-shinyFeedback >= 0.4.0 +Requires: R-CRAN-DT >= 0.30 +Requires: R-CRAN-DoE.wrapper >= 0.12 + +%description +A graphical user interface to apply an advanced method optimization +algorithm to various sampling and analysis instruments. This includes +generating experimental designs, uploading and viewing data, and +performing various analyses to determine the optimal method. Details of +the techniques used in this package are published in Gamble, Granger, & +Mannion (2024) . + +%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-MixMatrix.spec b/specs/R-CRAN-MixMatrix.spec index eac217617..0e0460b9a 100644 --- a/specs/R-CRAN-MixMatrix.spec +++ b/specs/R-CRAN-MixMatrix.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname MixMatrix -%global packver 0.2.6 +%global packver 0.2.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.6 +Version: 0.2.8 Release: 1%{?dist}%{?buildtag} Summary: Classification with Matrix Variate Normal and t Distributions @@ -18,10 +19,12 @@ Requires: R-core >= 3.5.0 BuildRequires: R-stats BuildRequires: R-CRAN-CholWishart BuildRequires: R-CRAN-Rcpp +BuildRequires: R-CRAN-glue BuildRequires: R-CRAN-RcppArmadillo Requires: R-stats Requires: R-CRAN-CholWishart Requires: R-CRAN-Rcpp +Requires: R-CRAN-glue %description Provides sampling and density functions for matrix variate normal, t, and diff --git a/specs/R-CRAN-ModTools.spec b/specs/R-CRAN-ModTools.spec new file mode 100644 index 000000000..55ff4fb39 --- /dev/null +++ b/specs/R-CRAN-ModTools.spec @@ -0,0 +1,98 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname ModTools +%global packver 0.9.13 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.9.13 +Release: 1%{?dist}%{?buildtag} +Summary: Building Regression and Classification Models + +License: GPL (>= 2) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.5.0 +Requires: R-core >= 3.5.0 +BuildArch: noarch +BuildRequires: R-CRAN-DescTools +BuildRequires: R-CRAN-MASS +BuildRequires: R-CRAN-nnet +BuildRequires: R-CRAN-survival +BuildRequires: R-CRAN-e1071 +BuildRequires: R-CRAN-C50 +BuildRequires: R-CRAN-rpart +BuildRequires: R-CRAN-randomForest +BuildRequires: R-CRAN-pROC +BuildRequires: R-methods +BuildRequires: R-CRAN-relaimpo +BuildRequires: R-CRAN-rpart.plot +BuildRequires: R-CRAN-lattice +BuildRequires: R-CRAN-lmtest +BuildRequires: R-CRAN-car +BuildRequires: R-CRAN-robustbase +BuildRequires: R-CRAN-class +BuildRequires: R-CRAN-NeuralNetTools +BuildRequires: R-CRAN-naivebayes +BuildRequires: R-CRAN-sandwich +BuildRequires: R-CRAN-AER +BuildRequires: R-CRAN-boot +BuildRequires: R-CRAN-pscl +Requires: R-CRAN-DescTools +Requires: R-CRAN-MASS +Requires: R-CRAN-nnet +Requires: R-CRAN-survival +Requires: R-CRAN-e1071 +Requires: R-CRAN-C50 +Requires: R-CRAN-rpart +Requires: R-CRAN-randomForest +Requires: R-CRAN-pROC +Requires: R-methods +Requires: R-CRAN-relaimpo +Requires: R-CRAN-rpart.plot +Requires: R-CRAN-lattice +Requires: R-CRAN-lmtest +Requires: R-CRAN-car +Requires: R-CRAN-robustbase +Requires: R-CRAN-class +Requires: R-CRAN-NeuralNetTools +Requires: R-CRAN-naivebayes +Requires: R-CRAN-sandwich +Requires: R-CRAN-AER +Requires: R-CRAN-boot +Requires: R-CRAN-pscl + +%description +Consistent user interface to the most common regression and classification +algorithms, such as random forest, neural networks, C5 trees and support +vector machines, complemented with a handful of auxiliary functions, such +as variable importance and a tuning function for the parameters. + +%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-MorphoTools2.spec b/specs/R-CRAN-MorphoTools2.spec index bfcba6eca..0b2961cbd 100644 --- a/specs/R-CRAN-MorphoTools2.spec +++ b/specs/R-CRAN-MorphoTools2.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname MorphoTools2 -%global packver 1.0.1.1 +%global packver 1.0.2.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.1.1 +Version: 1.0.2.0 Release: 1%{?dist}%{?buildtag} Summary: Multivariate Morphometric Analysis diff --git a/specs/R-CRAN-RHRV.spec b/specs/R-CRAN-RHRV.spec index f11a92f6d..15dba32b8 100644 --- a/specs/R-CRAN-RHRV.spec +++ b/specs/R-CRAN-RHRV.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname RHRV -%global packver 4.2.7 +%global packver 5.0.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 4.2.7 +Version: 5.0.0 Release: 1%{?dist}%{?buildtag} Summary: Heart Rate Variability Analysis of ECG Data @@ -18,10 +18,36 @@ BuildRequires: R-devel >= 3.0.0 Requires: R-core >= 3.0.0 BuildRequires: R-CRAN-waveslim >= 1.6.4 BuildRequires: R-CRAN-lomb >= 1.0 -BuildRequires: R-CRAN-nonlinearTseries >= 0.2.3 +BuildRequires: R-CRAN-nonlinearTseries >= 0.3.0 +BuildRequires: R-CRAN-boot +BuildRequires: R-CRAN-broom +BuildRequires: R-CRAN-doParallel +BuildRequires: R-CRAN-foreach +BuildRequires: R-CRAN-iterators +BuildRequires: R-parallel +BuildRequires: R-CRAN-plotrix +BuildRequires: R-CRAN-PMCMRplus +BuildRequires: R-CRAN-segmented +BuildRequires: R-stats +BuildRequires: R-CRAN-tibble +BuildRequires: R-CRAN-tidyr +BuildRequires: R-CRAN-writexl Requires: R-CRAN-waveslim >= 1.6.4 Requires: R-CRAN-lomb >= 1.0 -Requires: R-CRAN-nonlinearTseries >= 0.2.3 +Requires: R-CRAN-nonlinearTseries >= 0.3.0 +Requires: R-CRAN-boot +Requires: R-CRAN-broom +Requires: R-CRAN-doParallel +Requires: R-CRAN-foreach +Requires: R-CRAN-iterators +Requires: R-parallel +Requires: R-CRAN-plotrix +Requires: R-CRAN-PMCMRplus +Requires: R-CRAN-segmented +Requires: R-stats +Requires: R-CRAN-tibble +Requires: R-CRAN-tidyr +Requires: R-CRAN-writexl %description Allows users to import data files containing heartbeat positions in the diff --git a/specs/R-CRAN-RNiftyReg.spec b/specs/R-CRAN-RNiftyReg.spec index af96f816c..12fab27a9 100644 --- a/specs/R-CRAN-RNiftyReg.spec +++ b/specs/R-CRAN-RNiftyReg.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname RNiftyReg -%global packver 2.8.3 +%global packver 2.8.4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.8.3 +Version: 2.8.4 Release: 1%{?dist}%{?buildtag} Summary: Image Registration Using the 'NiftyReg' Library @@ -18,11 +18,9 @@ BuildRequires: R-devel Requires: R-core BuildRequires: R-CRAN-Rcpp BuildRequires: R-CRAN-RNifti -BuildRequires: R-CRAN-ore BuildRequires: R-CRAN-RcppEigen Requires: R-CRAN-Rcpp Requires: R-CRAN-RNifti -Requires: R-CRAN-ore %description Provides an 'R' interface to the 'NiftyReg' image registration tools diff --git a/specs/R-CRAN-RPostgreSQL.spec b/specs/R-CRAN-RPostgreSQL.spec index 4d254d8f7..489dbd946 100644 --- a/specs/R-CRAN-RPostgreSQL.spec +++ b/specs/R-CRAN-RPostgreSQL.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname RPostgreSQL -%global packver 0.7-6 +%global packver 0.7-7 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.7.6 +Version: 0.7.7 Release: 1%{?dist}%{?buildtag} Summary: R Interface to the 'PostgreSQL' Database System @@ -15,8 +15,8 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: libpq-devel -BuildRequires: R-devel >= 2.9.0 -Requires: R-core >= 2.9.0 +BuildRequires: R-devel >= 3.4.0 +Requires: R-core >= 3.4.0 BuildRequires: R-CRAN-DBI >= 0.3 BuildRequires: R-methods Requires: R-CRAN-DBI >= 0.3 diff --git a/specs/R-CRAN-STICr.spec b/specs/R-CRAN-STICr.spec new file mode 100644 index 000000000..05a398a9c --- /dev/null +++ b/specs/R-CRAN-STICr.spec @@ -0,0 +1,63 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname STICr +%global packver 1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Process Stream Temperature, Intermittency, and Conductivity (STIC) Sensor Data + +License: AGPL (>= 3) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 4.2 +Requires: R-core >= 4.2 +BuildArch: noarch +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-lubridate +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-tidyr +BuildRequires: R-methods +Requires: R-CRAN-dplyr +Requires: R-CRAN-lubridate +Requires: R-CRAN-stringr +Requires: R-CRAN-tidyr +Requires: R-methods + +%description +A collection of functions for processing raw data from Stream Temperature, +Intermittency, and Conductivity (STIC) loggers. 'STICr' (pronounced +"sticker") includes functions for tidying, calibrating, classifying, and +doing quality checks on data from STIC sensors. Some package functionality +is described in Wheeler/Zipper et al. (2023) . + +%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-SpaCCI.spec b/specs/R-CRAN-SpaCCI.spec new file mode 100644 index 000000000..c739af818 --- /dev/null +++ b/specs/R-CRAN-SpaCCI.spec @@ -0,0 +1,84 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname SpaCCI +%global packver 1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0 +Release: 1%{?dist}%{?buildtag} +Summary: Spatially Aware Cell-Cell Interaction Analysis + +License: GPL (>= 2) +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.5.0 +Requires: R-core >= 3.5.0 +BuildRequires: R-CRAN-Seurat >= 4.0.0 +BuildRequires: R-CRAN-Rcpp >= 1.0.13 +BuildRequires: R-CRAN-circlize >= 0.4.12 +BuildRequires: R-CRAN-nnls +BuildRequires: R-CRAN-ggrepel +BuildRequires: R-CRAN-pheatmap +BuildRequires: R-CRAN-Matrix +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-patchwork +BuildRequires: R-grDevices +BuildRequires: R-CRAN-reshape2 +BuildRequires: R-graphics +BuildRequires: R-CRAN-ggplot2 +BuildRequires: R-CRAN-RcppArmadillo +Requires: R-CRAN-Seurat >= 4.0.0 +Requires: R-CRAN-Rcpp >= 1.0.13 +Requires: R-CRAN-circlize >= 0.4.12 +Requires: R-CRAN-nnls +Requires: R-CRAN-ggrepel +Requires: R-CRAN-pheatmap +Requires: R-CRAN-Matrix +Requires: R-CRAN-dplyr +Requires: R-CRAN-patchwork +Requires: R-grDevices +Requires: R-CRAN-reshape2 +Requires: R-graphics +Requires: R-CRAN-ggplot2 + +%description +Provides tools for analyzing spatial cell-cell interactions based on +ligand-receptor pairs, including functions for local, regional, and global +analysis using spatial transcriptomics data. Integrates with databases +like 'CellChat' , 'CellPhoneDB' +, 'Cellinker' +, 'ICELLNET' +, and 'ConnectomeDB' + to identify +ligand-receptor pairs, visualize interactions through heatmaps, chord +diagrams, and infer interactions on different spatial scales. + +%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-WMWssp.spec b/specs/R-CRAN-WMWssp.spec deleted file mode 100644 index fd7818b62..000000000 --- a/specs/R-CRAN-WMWssp.spec +++ /dev/null @@ -1,45 +0,0 @@ -%global __brp_check_rpaths %{nil} -%global packname WMWssp -%global packver 0.4.0 -%global rlibdir /usr/local/lib/R/library - -Name: R-CRAN-%{packname} -Version: 0.4.0 -Release: 3%{?dist}%{?buildtag} -Summary: Wilcoxon-Mann-Whitney Sample Size Planning - -License: GPL-3 -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 -BuildArch: noarch - -%description -Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test that -is needed for a given power and two sided type I error rate. The method -works for metric data with and without ties, count data, ordered -categorical data, and even dichotomous data. But data is needed for the -reference group to generate synthetic data for the treatment group based -on a relevant effect. For details, see Brunner, E., Bathke A. C. and -Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - -Using R and SAS, Springer Verlag, to appear. - -%prep -%setup -q -c -n %{packname} - - -%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 - -%files -%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-adepro.spec b/specs/R-CRAN-adepro.spec index d4ba26399..a9783eb6f 100644 --- a/specs/R-CRAN-adepro.spec +++ b/specs/R-CRAN-adepro.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname adepro -%global packver 4.1.0 +%global packver 4.1.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 4.1.0 +Version: 4.1.2 Release: 1%{?dist}%{?buildtag} Summary: A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles @@ -37,6 +37,7 @@ BuildRequires: R-CRAN-tidyr BuildRequires: R-CRAN-haven BuildRequires: R-stats BuildRequires: R-CRAN-shinyWidgets +BuildRequires: R-CRAN-DT Requires: R-CRAN-seriation >= 1.2.9 Requires: R-CRAN-shinyBS Requires: R-graphics @@ -57,6 +58,7 @@ Requires: R-CRAN-tidyr Requires: R-CRAN-haven Requires: R-stats Requires: R-CRAN-shinyWidgets +Requires: R-CRAN-DT %description Contains a 'shiny' application called AdEPro (Animation of Adverse Event diff --git a/specs/R-CRAN-aws.spec b/specs/R-CRAN-aws.spec index c97dec37a..3d9960e8a 100644 --- a/specs/R-CRAN-aws.spec +++ b/specs/R-CRAN-aws.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname aws -%global packver 2.5-5 +%global packver 2.5-6 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.5.5 +Version: 2.5.6 Release: 1%{?dist}%{?buildtag} Summary: Adaptive Weights Smoothing diff --git a/specs/R-CRAN-bayesreg.spec b/specs/R-CRAN-bayesreg.spec index 4e4db9db0..c537bda73 100644 --- a/specs/R-CRAN-bayesreg.spec +++ b/specs/R-CRAN-bayesreg.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname bayesreg -%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: Bayesian Regression Models with Global-Local Shrinkage Priors @@ -17,8 +18,12 @@ BuildRequires: R-devel Requires: R-core BuildArch: noarch BuildRequires: R-stats >= 3.0 +BuildRequires: R-CRAN-foreach >= 1.5.1 +BuildRequires: R-CRAN-doParallel >= 1.0.16 BuildRequires: R-CRAN-pgdraw >= 1.0 Requires: R-stats >= 3.0 +Requires: R-CRAN-foreach >= 1.5.1 +Requires: R-CRAN-doParallel >= 1.0.16 Requires: R-CRAN-pgdraw >= 1.0 %description @@ -28,7 +33,7 @@ global-local shrinkage prior hierarchies as described in Polson and Scott efficient implementation of ridge, lasso, horseshoe and horseshoe+ regression with logistic, Gaussian, Laplace, Student-t, Poisson or geometric distributed targets using the algorithms summarized in Makalic -and Schmidt (2016) . +and Schmidt (2016) . %prep %setup -q -c -n %{packname} @@ -38,6 +43,8 @@ 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-cmsafvis.spec b/specs/R-CRAN-cmsafvis.spec index 591b5c47e..0608b2c8c 100644 --- a/specs/R-CRAN-cmsafvis.spec +++ b/specs/R-CRAN-cmsafvis.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname cmsafvis -%global packver 1.2.8 +%global packver 1.2.9 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.2.8 +Version: 1.2.9 Release: 1%{?dist}%{?buildtag} Summary: Tools to Visualize CM SAF NetCDF Data diff --git a/specs/R-CRAN-coRanking.spec b/specs/R-CRAN-coRanking.spec index 136388e92..07450c4cf 100644 --- a/specs/R-CRAN-coRanking.spec +++ b/specs/R-CRAN-coRanking.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname coRanking -%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: Co-Ranking Matrix diff --git a/specs/R-CRAN-crosstable.spec b/specs/R-CRAN-crosstable.spec index f4b54aca9..89eced3c7 100644 --- a/specs/R-CRAN-crosstable.spec +++ b/specs/R-CRAN-crosstable.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname crosstable -%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: Crosstables for Descriptive Analyses diff --git a/specs/R-CRAN-dampack.spec b/specs/R-CRAN-dampack.spec new file mode 100644 index 000000000..bf40a98f5 --- /dev/null +++ b/specs/R-CRAN-dampack.spec @@ -0,0 +1,78 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname dampack +%global packver 1.0.2.1000 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0.2.1000 +Release: 1%{?dist}%{?buildtag} +Summary: Decision-Analytic Modeling Package + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.5 +Requires: R-core >= 3.5 +BuildArch: noarch +BuildRequires: R-CRAN-ggplot2 >= 3.3.0 +BuildRequires: R-CRAN-ellipse +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-scales +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-mgcv +BuildRequires: R-CRAN-truncnorm +BuildRequires: R-CRAN-triangle +BuildRequires: R-CRAN-ggrepel +BuildRequires: R-CRAN-tidyr +BuildRequires: R-CRAN-rlang +Requires: R-CRAN-ggplot2 >= 3.3.0 +Requires: R-CRAN-ellipse +Requires: R-CRAN-dplyr +Requires: R-CRAN-scales +Requires: R-CRAN-stringr +Requires: R-CRAN-mgcv +Requires: R-CRAN-truncnorm +Requires: R-CRAN-triangle +Requires: R-CRAN-ggrepel +Requires: R-CRAN-tidyr +Requires: R-CRAN-rlang + +%description +A suite of functions for analyzing and visualizing the health economic +outputs of mathematical models. This package was developed with funding +from the National Institutes of Allergy and Infectious Diseases of the +National Institutes of Health under award no. R01AI138783. The content of +this package is solely the responsibility of the authors and does not +necessarily represent the official views of the National Institutes of +Health. The theoretical underpinnings of 'dampack''s functionality are +detailed in Hunink et al. (2014) . + +%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-ddalpha.spec b/specs/R-CRAN-ddalpha.spec index 28e6c1dea..8a64c82a2 100644 --- a/specs/R-CRAN-ddalpha.spec +++ b/specs/R-CRAN-ddalpha.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ddalpha -%global packver 1.3.15 +%global packver 1.3.16 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.3.15 +Version: 1.3.16 Release: 1%{?dist}%{?buildtag} Summary: Depth-Based Classification and Calculation of Data Depth diff --git a/specs/R-CRAN-dfcomb.spec b/specs/R-CRAN-dfcomb.spec index c2f6eecb6..2064c8fcb 100644 --- a/specs/R-CRAN-dfcomb.spec +++ b/specs/R-CRAN-dfcomb.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname dfcomb -%global packver 3.1-1 +%global packver 3.1-4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.1.1 +Version: 3.1.4 Release: 1%{?dist}%{?buildtag} Summary: Phase I/II Adaptive Dose-Finding Design for Combination Studies diff --git a/specs/R-CRAN-dfmta.spec b/specs/R-CRAN-dfmta.spec index 6ca4fc250..fa3d51308 100644 --- a/specs/R-CRAN-dfmta.spec +++ b/specs/R-CRAN-dfmta.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname dfmta -%global packver 1.7-3 +%global packver 1.7-6 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.7.3 +Version: 1.7.6 Release: 1%{?dist}%{?buildtag} Summary: Phase I/II Adaptive Dose-Finding Design for MTA diff --git a/specs/R-CRAN-explainer.spec b/specs/R-CRAN-explainer.spec index 1a0bd5ee9..e4578f39e 100644 --- a/specs/R-CRAN-explainer.spec +++ b/specs/R-CRAN-explainer.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname explainer -%global packver 1.0.1 +%global packver 1.0.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.1 +Version: 1.0.2 Release: 1%{?dist}%{?buildtag} Summary: Machine Learning Model Explainer @@ -29,6 +29,8 @@ BuildRequires: R-CRAN-plotly BuildRequires: R-CRAN-tibble BuildRequires: R-CRAN-tidyr BuildRequires: R-CRAN-writexl +BuildRequires: R-CRAN-gridExtra +BuildRequires: R-CRAN-scales Requires: R-CRAN-cvms Requires: R-CRAN-data.table Requires: R-CRAN-dplyr @@ -41,6 +43,8 @@ Requires: R-CRAN-plotly Requires: R-CRAN-tibble Requires: R-CRAN-tidyr Requires: R-CRAN-writexl +Requires: R-CRAN-gridExtra +Requires: R-CRAN-scales %description It enables detailed interpretation of complex classification and diff --git a/specs/R-CRAN-fctutils.spec b/specs/R-CRAN-fctutils.spec index fd5a81f11..38c19f835 100644 --- a/specs/R-CRAN-fctutils.spec +++ b/specs/R-CRAN-fctutils.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname fctutils -%global packver 0.0.6 +%global packver 0.0.7 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.0.6 +Version: 0.0.7 Release: 1%{?dist}%{?buildtag} Summary: Advanced Factor Manipulation Utilities diff --git a/specs/R-CRAN-fields.spec b/specs/R-CRAN-fields.spec index 5bccea436..a62a05c83 100644 --- a/specs/R-CRAN-fields.spec +++ b/specs/R-CRAN-fields.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname fields -%global packver 16.2 +%global packver 16.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 16.2 +Version: 16.3 Release: 1%{?dist}%{?buildtag} Summary: Tools for Spatial Data diff --git a/specs/R-CRAN-ganGenerativeData.spec b/specs/R-CRAN-ganGenerativeData.spec index 484b80472..375667d8c 100644 --- a/specs/R-CRAN-ganGenerativeData.spec +++ b/specs/R-CRAN-ganGenerativeData.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ganGenerativeData -%global packver 2.0.2 +%global packver 2.1.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.0.2 +Version: 2.1.2 Release: 1%{?dist}%{?buildtag} Summary: Generate Generative Data for a Data Source @@ -29,10 +29,9 @@ for a data source. A generative model consisting of a generator and a discriminator network is trained. During iterative training the distribution of generated data is converging to that of the data source. Direct applications of generative data are the created functions for data -classifying and missing data completion. A software service for -accelerated training of generative models on graphics processing units is -available. Reference: Goodfellow et al. (2014) -. +evaluation and missing data completion. A software service for accelerated +training of generative models on graphics processing units is available. +Reference: Goodfellow et al. (2014) . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-gdverse.spec b/specs/R-CRAN-gdverse.spec index 7f9f30a6d..d68c2aaa2 100644 --- 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 1.0-2 +%global packver 1.0-3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.2 +Version: 1.0.3 Release: 1%{?dist}%{?buildtag} Summary: Analysis of Spatial Stratified Heterogeneity diff --git a/specs/R-CRAN-glue.spec b/specs/R-CRAN-glue.spec index a408ce15c..eba195973 100644 --- a/specs/R-CRAN-glue.spec +++ b/specs/R-CRAN-glue.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname glue -%global packver 1.7.0 +%global packver 1.8.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.7.0 +Version: 1.8.0 Release: 1%{?dist}%{?buildtag} Summary: Interpreted String Literals diff --git a/specs/R-CRAN-gmoTree.spec b/specs/R-CRAN-gmoTree.spec index a9349d141..ca8f330f0 100644 --- a/specs/R-CRAN-gmoTree.spec +++ b/specs/R-CRAN-gmoTree.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname gmoTree -%global packver 1.1.0 +%global packver 1.2.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.1.0 +Version: 1.2.0 Release: 1%{?dist}%{?buildtag} Summary: Get and Modify 'oTree' Data @@ -17,31 +17,36 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 4.4.0 Requires: R-core >= 4.4.0 BuildArch: noarch -BuildRequires: R-stats >= 4.4.1 BuildRequires: R-CRAN-openxlsx >= 4.2.5.2 +BuildRequires: R-CRAN-rmarkdown >= 2.27 BuildRequires: R-CRAN-plyr >= 1.8.9 BuildRequires: R-CRAN-stringr >= 1.5.1 +BuildRequires: R-CRAN-knitr >= 1.47 BuildRequires: R-CRAN-data.table >= 1.15.4 BuildRequires: R-CRAN-dplyr >= 1.1.4 BuildRequires: R-CRAN-rlang >= 1.1.4 +BuildRequires: R-CRAN-pander >= 0.6.5 BuildRequires: R-CRAN-rlist >= 0.4.6.2 -Requires: R-stats >= 4.4.1 Requires: R-CRAN-openxlsx >= 4.2.5.2 +Requires: R-CRAN-rmarkdown >= 2.27 Requires: R-CRAN-plyr >= 1.8.9 Requires: R-CRAN-stringr >= 1.5.1 +Requires: R-CRAN-knitr >= 1.47 Requires: R-CRAN-data.table >= 1.15.4 Requires: R-CRAN-dplyr >= 1.1.4 Requires: R-CRAN-rlang >= 1.1.4 +Requires: R-CRAN-pander >= 0.6.5 Requires: R-CRAN-rlist >= 0.4.6.2 %description -Manage data from 'oTree' experiments. Import 'oTree' data and clean them -by using functions to deal with messy data, dropouts, and other -problematic cases. Create IDs, calculate the time, transfer variables -between app data frames, and delete sensitive information. You can also -check your experimental data before running the experiment. Information on -'oTree' is found in Chen, D. L., Schonger, M., & Wickens, C. (2016) -. +Efficiently manage and process data from 'oTree' experiments. Import +'oTree' data and clean them by using functions that handle messy data, +dropouts, and other problematic cases. Create IDs, calculate the time, +transfer variables between app data frames, and delete sensitive +information. Review your experimental data prior to running the experiment +and automatically generate a detailed summary of the variables used in +your 'oTree' code. Information on 'oTree' is found in Chen, D. L., +Schonger, M., & Wickens, C. (2016) . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-ibawds.spec b/specs/R-CRAN-ibawds.spec index 6d8741ff9..f0d7f9224 100644 --- a/specs/R-CRAN-ibawds.spec +++ b/specs/R-CRAN-ibawds.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ibawds -%global packver 0.6.0 +%global packver 1.0.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.6.0 +Version: 1.0.0 Release: 1%{?dist}%{?buildtag} Summary: Functions and Datasets for the Data Science Course at IBAW @@ -22,25 +22,29 @@ BuildRequires: R-CRAN-dslabs BuildRequires: R-stats BuildRequires: R-grDevices BuildRequires: R-CRAN-rlang +BuildRequires: R-CRAN-rstudioapi BuildRequires: R-CRAN-remotes BuildRequires: R-CRAN-ggplot2 BuildRequires: R-CRAN-scales BuildRequires: R-CRAN-stringr BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-cli Requires: R-CRAN-dplyr >= 1.1.0 Requires: R-CRAN-dslabs Requires: R-stats Requires: R-grDevices Requires: R-CRAN-rlang +Requires: R-CRAN-rstudioapi Requires: R-CRAN-remotes Requires: R-CRAN-ggplot2 Requires: R-CRAN-scales Requires: R-CRAN-stringr Requires: R-CRAN-magrittr +Requires: R-CRAN-cli %description A collection of useful functions and datasets for the Data Science Course -at IBAW in Lucerne. +at IBAW. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-kappaGold.spec b/specs/R-CRAN-kappaGold.spec new file mode 100644 index 000000000..890a01b51 --- /dev/null +++ b/specs/R-CRAN-kappaGold.spec @@ -0,0 +1,64 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname kappaGold +%global packver 0.3.2 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.3.2 +Release: 1%{?dist}%{?buildtag} +Summary: Agreement of Nominal Scale Raters with a Gold Standard + +License: MIT + file LICENSE +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 4.0 +Requires: R-core >= 4.0 +BuildArch: noarch +BuildRequires: R-CRAN-future.apply >= 1.6 +BuildRequires: R-CRAN-purrr >= 0.3 +BuildRequires: R-stats +BuildRequires: R-CRAN-tibble +BuildRequires: R-CRAN-tidyr +Requires: R-CRAN-future.apply >= 1.6 +Requires: R-CRAN-purrr >= 0.3 +Requires: R-stats +Requires: R-CRAN-tibble +Requires: R-CRAN-tidyr + +%description +Estimate agreement of a group of raters with a gold standard rating on a +nominal scale. For a single gold standard rater the average pairwise +agreement of raters with this gold standard is provided. For a group of +gold standard raters the approach of S. Vanbelle, A. Albert (2009) + is implemented. Bias and standard error +are estimated via delete-1 jackknife. + +%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-lmom.spec b/specs/R-CRAN-lmom.spec index f2aa70697..5e77490f8 100644 --- a/specs/R-CRAN-lmom.spec +++ b/specs/R-CRAN-lmom.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname lmom -%global packver 3.0 +%global packver 3.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.0 +Version: 3.2 Release: 1%{?dist}%{?buildtag} Summary: L-Moments diff --git a/specs/R-CRAN-lmomRFA.spec b/specs/R-CRAN-lmomRFA.spec index 4ac40505c..a377b3e27 100644 --- a/specs/R-CRAN-lmomRFA.spec +++ b/specs/R-CRAN-lmomRFA.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname lmomRFA -%global packver 3.6 +%global packver 3.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.6 +Version: 3.8 Release: 1%{?dist}%{?buildtag} Summary: Regional Frequency Analysis using L-Moments diff --git a/specs/R-CRAN-lulab.utils.spec b/specs/R-CRAN-lulab.utils.spec index 2ff0c2072..cf36cc57a 100644 --- a/specs/R-CRAN-lulab.utils.spec +++ b/specs/R-CRAN-lulab.utils.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname lulab.utils -%global packver 0.0.2 +%global packver 0.0.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.0.2 +Version: 0.0.3 Release: 1%{?dist}%{?buildtag} Summary: Supporting Functions Maintained by Zhen Lu diff --git a/specs/R-CRAN-multiplex.spec b/specs/R-CRAN-multiplex.spec index 471f02892..08a68fedd 100644 --- a/specs/R-CRAN-multiplex.spec +++ b/specs/R-CRAN-multiplex.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname multiplex -%global packver 3.4 +%global packver 3.7 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.4 +Version: 3.7 Release: 1%{?dist}%{?buildtag} Summary: Algebraic Tools for the Analysis of Multiple Social Networks diff --git a/specs/R-CRAN-nichetools.spec b/specs/R-CRAN-nichetools.spec index cda69e938..fde8f64c7 100644 --- a/specs/R-CRAN-nichetools.spec +++ b/specs/R-CRAN-nichetools.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname nichetools -%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: Complementary Package to 'nicheROVER' and 'SIBER' diff --git a/specs/R-CRAN-pMEM.spec b/specs/R-CRAN-pMEM.spec new file mode 100644 index 000000000..9c044848c --- /dev/null +++ b/specs/R-CRAN-pMEM.spec @@ -0,0 +1,60 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname pMEM +%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: Predictive Moran's Eigenvector Maps + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.5.0 +Requires: R-core >= 3.5.0 +BuildRequires: R-CRAN-Rcpp >= 1.0.11 +BuildRequires: R-CRAN-sf +Requires: R-CRAN-Rcpp >= 1.0.11 +Requires: R-CRAN-sf + +%description +Calculation of Predictive Moran's eigenvector maps (pMEM), as defined by +Guénard and Legendre (In Press) "Spatially-explicit predictions using +spatial eigenvector maps" . Methods in +Ecology and Evolution. This method enables scientists to predict the +values of spatially-structured environmental variables. Multiple types of +pMEM are defined, each one implemented on the basis of spatial weighting +function taking a range parameter, and sometimes also a shape parameter. +The code's modular nature enables programers to implement new pMEM by +defining new spatial weighting functions. + +%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-pdfetch.spec b/specs/R-CRAN-pdfetch.spec index fa96a96e5..f4823eb46 100644 --- a/specs/R-CRAN-pdfetch.spec +++ b/specs/R-CRAN-pdfetch.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname pdfetch -%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: Fetch Economic and Financial Time Series Data from Public Sources @@ -23,26 +23,26 @@ BuildRequires: R-CRAN-xts BuildRequires: R-CRAN-XML BuildRequires: R-CRAN-lubridate BuildRequires: R-CRAN-jsonlite -BuildRequires: R-CRAN-curl BuildRequires: R-CRAN-xml2 BuildRequires: R-CRAN-stringr BuildRequires: R-CRAN-magrittr BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-tidyr BuildRequires: R-CRAN-readr +BuildRequires: R-CRAN-quantmod Requires: R-CRAN-httr Requires: R-CRAN-zoo Requires: R-CRAN-xts Requires: R-CRAN-XML Requires: R-CRAN-lubridate Requires: R-CRAN-jsonlite -Requires: R-CRAN-curl Requires: R-CRAN-xml2 Requires: R-CRAN-stringr Requires: R-CRAN-magrittr Requires: R-CRAN-dplyr Requires: R-CRAN-tidyr Requires: R-CRAN-readr +Requires: R-CRAN-quantmod %description Download economic and financial time series from public sources, including diff --git a/specs/R-CRAN-phylolm.spec b/specs/R-CRAN-phylolm.spec index 069f0a5e1..9194e855b 100644 --- a/specs/R-CRAN-phylolm.spec +++ b/specs/R-CRAN-phylolm.spec @@ -1,11 +1,12 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname phylolm -%global packver 2.6.2 +%global packver 2.6.5 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.6.2 -Release: 2%{?dist}%{?buildtag} +Version: 2.6.5 +Release: 1%{?dist}%{?buildtag} Summary: Phylogenetic Linear Regression License: GPL (>= 2) | file LICENSE @@ -13,8 +14,8 @@ URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz -BuildRequires: R-devel >= 4.0 -Requires: R-core >= 4.0 +BuildRequires: R-devel >= 3.0 +Requires: R-core >= 3.0 BuildRequires: R-CRAN-ape BuildRequires: R-CRAN-future.apply Requires: R-CRAN-ape @@ -30,9 +31,15 @@ tools include functions to test the adequacy of a population tree. %prep %setup -q -c -n %{packname} +# fix end of executable files find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping [ -d %{packname}/src ] && find %{packname}/src -type f -exec \ sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; %build @@ -40,9 +47,10 @@ find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; 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-pikchr.spec b/specs/R-CRAN-pikchr.spec new file mode 100644 index 000000000..1d51dfd42 --- /dev/null +++ b/specs/R-CRAN-pikchr.spec @@ -0,0 +1,70 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname pikchr +%global packver 0.97 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.97 +Release: 1%{?dist}%{?buildtag} +Summary: R Wrapper for 'pikchr' (PIC) Diagram Language + +License: GPL (>= 2) +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-knitr +BuildRequires: R-CRAN-brio +BuildRequires: R-CRAN-htmltools +BuildRequires: R-CRAN-rlang +BuildRequires: R-CRAN-purrr +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-rsvg +Requires: R-CRAN-knitr +Requires: R-CRAN-brio +Requires: R-CRAN-htmltools +Requires: R-CRAN-rlang +Requires: R-CRAN-purrr +Requires: R-CRAN-stringr +Requires: R-CRAN-rsvg + +%description +An 'R' interface to 'pikchr' (, pronounced “picture”), +a 'PIC'-like markup language for creating diagrams within technical +documentation. Originally developed by Brian Kernighan, 'PIC' has been +adapted into 'pikchr' by D. Richard Hipp, the creator of 'SQLite'. +'pikchr' is designed to be embedded in fenced code blocks of Markdown or +other documentation markup languages, making it ideal for generating +diagrams in text-based formats. This package allows R users to seamlessly +integrate the descriptive syntax of 'pikchr' for diagram creation directly +within the 'R' environment. + +%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-plpoisson.spec b/specs/R-CRAN-plpoisson.spec index 698aab962..1d45b99b9 100644 --- a/specs/R-CRAN-plpoisson.spec +++ b/specs/R-CRAN-plpoisson.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname plpoisson -%global packver 0.3.0 +%global packver 0.3.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.3.0 +Version: 0.3.1 Release: 1%{?dist}%{?buildtag} Summary: Prediction Limits for Poisson Distribution diff --git a/specs/R-CRAN-postdoc.spec b/specs/R-CRAN-postdoc.spec index 1ff10a493..f08399c61 100644 --- a/specs/R-CRAN-postdoc.spec +++ b/specs/R-CRAN-postdoc.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname postdoc -%global packver 1.2.2 +%global packver 1.4.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.2.2 +Version: 1.4.0 Release: 1%{?dist}%{?buildtag} Summary: Minimal and Uncluttered Package Documentation @@ -17,14 +17,14 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel Requires: R-core BuildArch: noarch +BuildRequires: R-CRAN-katex >= 1.5.0 BuildRequires: R-CRAN-curl BuildRequires: R-CRAN-jsonlite -BuildRequires: R-CRAN-katex BuildRequires: R-CRAN-prismjs BuildRequires: R-CRAN-xml2 +Requires: R-CRAN-katex >= 1.5.0 Requires: R-CRAN-curl Requires: R-CRAN-jsonlite -Requires: R-CRAN-katex Requires: R-CRAN-prismjs Requires: R-CRAN-xml2 diff --git a/specs/R-CRAN-powerPLS.spec b/specs/R-CRAN-powerPLS.spec index fb2c47ef5..12b5d0f35 100644 --- a/specs/R-CRAN-powerPLS.spec +++ b/specs/R-CRAN-powerPLS.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname powerPLS -%global packver 0.1.0 +%global packver 0.2.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.0 +Version: 0.2.0 Release: 1%{?dist}%{?buildtag} Summary: Power Analysis for PLS Classification @@ -18,23 +18,27 @@ BuildRequires: R-devel >= 2.10 Requires: R-core >= 2.10 BuildArch: noarch BuildRequires: R-CRAN-compositions -BuildRequires: R-CRAN-ks -BuildRequires: R-CRAN-mvtnorm -BuildRequires: R-CRAN-simukde +BuildRequires: R-CRAN-FKSUM BuildRequires: R-CRAN-nipals BuildRequires: R-CRAN-MASS BuildRequires: R-CRAN-foreach +BuildRequires: R-parallel +BuildRequires: R-CRAN-simukde +BuildRequires: R-CRAN-ks +BuildRequires: R-CRAN-mvtnorm Requires: R-CRAN-compositions -Requires: R-CRAN-ks -Requires: R-CRAN-mvtnorm -Requires: R-CRAN-simukde +Requires: R-CRAN-FKSUM Requires: R-CRAN-nipals Requires: R-CRAN-MASS Requires: R-CRAN-foreach +Requires: R-parallel +Requires: R-CRAN-simukde +Requires: R-CRAN-ks +Requires: R-CRAN-mvtnorm %description It estimates power and sample size for Partial Least Squares-based methods -described in Andreella, et al., (2024) . +described in Andreella, et al., (2024), . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-rYWAASB.spec b/specs/R-CRAN-rYWAASB.spec index 7be111d18..5e821523c 100644 --- a/specs/R-CRAN-rYWAASB.spec +++ b/specs/R-CRAN-rYWAASB.spec @@ -1,13 +1,13 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname rYWAASB -%global packver 0.1 +%global packver 0.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1 +Version: 0.2 Release: 1%{?dist}%{?buildtag} -Summary: Simultaneous Selection of Trait and WAASB Index +Summary: Simultaneous Selection by Trait and WAASB Index License: GPL-3 URL: https://cran.r-project.org/package=%{packname} @@ -19,21 +19,33 @@ Requires: R-core >= 3.5 BuildArch: noarch BuildRequires: R-CRAN-ggplot2 BuildRequires: R-graphics +BuildRequires: R-CRAN-factoextra +BuildRequires: R-CRAN-FactoMineR +BuildRequires: R-CRAN-lifecycle +BuildRequires: R-CRAN-mathjaxr Requires: R-CRAN-ggplot2 Requires: R-graphics +Requires: R-CRAN-factoextra +Requires: R-CRAN-FactoMineR +Requires: R-CRAN-lifecycle +Requires: R-CRAN-mathjaxr %description -Proposes a new ranking algorithm that utilizes a "Y*WAASB" biplot -generated from the 'metan' package. The aim of the package is to -effectively distinguish the top-ranked genotypes. For a detailed -explanation of the process of obtaining a "Y*WAASB" biplot and the related -data, please refer to the manual included in this package as well as the -study by Olivoto & Lúcio (2020) . In this -context, "WAASB" refers to the "Weighted Average of Absolute Scores" -provided by Olivoto et al. (2019) , which -quantifies the stability of genotypes across different environments using -linear mixed-effect models. In order to run the package, it is necessary -to extract the "WAASB" coefficients using the 'metan' package. +This tool proposes a new ranking algorithm that utilizes a "Y*WAASB" +biplot generated by the 'metan'. The aim of the current package is to +effectively distinguish the top-ranked genotypes in MET +(Multi-Environmental Trials). For a detailed explanation of the process of +obtaining "WAASB", "WAASBY" indices, and a "Y*WAASB" biplot, refer to the +manual included in this package as well as the study by Olivoto & Lúcio +(2020) . In this context, "WAASB" refers to +the "Weighted Average of Absolute Scores" provided by Olivoto et al. +(2019) , which quantifies the stability of +genotypes across different environments using linear mixed-effect models. +To run the package, you need to extract the "WAASB" and "WAASBY" +coefficients using the 'metan' and apply them. This tool utilizes PCA +(Principal Component Analysis) and differentiates the entries which may be +genotypes, hybrids, varieties, etc using "WAASB", "WAASBY", and a +combination of the specified trait and WAASB index. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-rapiclient.spec b/specs/R-CRAN-rapiclient.spec index 5ea632ebd..260be6e8e 100644 --- a/specs/R-CRAN-rapiclient.spec +++ b/specs/R-CRAN-rapiclient.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname rapiclient -%global packver 0.1.6 +%global packver 0.1.8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.6 +Version: 0.1.8 Release: 1%{?dist}%{?buildtag} Summary: Dynamic OpenAPI/Swagger Client diff --git a/specs/R-CRAN-rcontroll.spec b/specs/R-CRAN-rcontroll.spec index ff8dafa3c..b81370dd1 100644 --- a/specs/R-CRAN-rcontroll.spec +++ b/specs/R-CRAN-rcontroll.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname rcontroll -%global packver 0.1.1 +%global packver 0.1.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.1 +Version: 0.1.2 Release: 1%{?dist}%{?buildtag} Summary: Individual-Based Forest Growth Simulator 'TROLL' diff --git a/specs/R-CRAN-ready4.spec b/specs/R-CRAN-ready4.spec new file mode 100644 index 000000000..4476570bc --- /dev/null +++ b/specs/R-CRAN-ready4.spec @@ -0,0 +1,98 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname ready4 +%global packver 0.1.18 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.18 +Release: 1%{?dist}%{?buildtag} +Summary: Develop and Use Modular Health Economic Models + +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-curl +BuildRequires: R-CRAN-dataverse +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-gh +BuildRequires: R-CRAN-kableExtra +BuildRequires: R-CRAN-lifecycle +BuildRequires: R-CRAN-magrittr +BuildRequires: R-methods +BuildRequires: R-CRAN-piggyback +BuildRequires: R-CRAN-purrr +BuildRequires: R-CRAN-rlang +BuildRequires: R-CRAN-rvest +BuildRequires: R-stats +BuildRequires: R-CRAN-stringi +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-tibble +BuildRequires: R-CRAN-tidyRSS +BuildRequires: R-CRAN-tidyselect +BuildRequires: R-tools +BuildRequires: R-utils +Requires: R-CRAN-curl +Requires: R-CRAN-dataverse +Requires: R-CRAN-dplyr +Requires: R-CRAN-gh +Requires: R-CRAN-kableExtra +Requires: R-CRAN-lifecycle +Requires: R-CRAN-magrittr +Requires: R-methods +Requires: R-CRAN-piggyback +Requires: R-CRAN-purrr +Requires: R-CRAN-rlang +Requires: R-CRAN-rvest +Requires: R-stats +Requires: R-CRAN-stringi +Requires: R-CRAN-stringr +Requires: R-CRAN-tibble +Requires: R-CRAN-tidyRSS +Requires: R-CRAN-tidyselect +Requires: R-tools +Requires: R-utils + +%description +A template model module, tools to help find model modules derived from +this template and a programming syntax to use these modules in health +economic analyses. These elements are the foundation for a prototype +software framework for developing living and transferable models and using +those models in reproducible health economic analyses. The software +framework is extended by other R libraries. For detailed documentation +about the framework and how to use it visit . +For a background to the methodological issues that the framework is +attempting to help solve, see Hamilton et al. (2024) +. + +%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-restatapi.spec b/specs/R-CRAN-restatapi.spec index 2282463b2..0dc685b66 100644 --- a/specs/R-CRAN-restatapi.spec +++ b/specs/R-CRAN-restatapi.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname restatapi -%global packver 0.23.1 +%global packver 0.23.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.23.1 +Version: 0.23.2 Release: 1%{?dist}%{?buildtag} Summary: Search and Retrieve Data from Eurostat Database diff --git a/specs/R-CRAN-sdsfun.spec b/specs/R-CRAN-sdsfun.spec index 4b00ab947..a9bd4ad6e 100644 --- a/specs/R-CRAN-sdsfun.spec +++ b/specs/R-CRAN-sdsfun.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname sdsfun -%global packver 0.2.1 +%global packver 0.3.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.1 +Version: 0.3.0 Release: 1%{?dist}%{?buildtag} Summary: Spatial Data Science Complementary Features @@ -16,17 +16,19 @@ Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz BuildRequires: R-devel >= 4.1.0 Requires: R-core >= 4.1.0 -BuildArch: noarch BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-geosphere BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-purrr BuildRequires: R-CRAN-sf BuildRequires: R-CRAN-spdep BuildRequires: R-stats BuildRequires: R-CRAN-tibble +BuildRequires: R-CRAN-Rcpp Requires: R-CRAN-dplyr Requires: R-CRAN-geosphere Requires: R-CRAN-magrittr +Requires: R-CRAN-purrr Requires: R-CRAN-sf Requires: R-CRAN-spdep Requires: R-stats diff --git a/specs/R-CRAN-seq2R.spec b/specs/R-CRAN-seq2R.spec new file mode 100644 index 000000000..685d34527 --- /dev/null +++ b/specs/R-CRAN-seq2R.spec @@ -0,0 +1,58 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname seq2R +%global packver 2.0.1 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 2.0.1 +Release: 1%{?dist}%{?buildtag} +Summary: Simple Method to Detect Compositional Changes in Genomic Sequences + +License: GPL +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 2.15.1 +Requires: R-core >= 2.15.1 +BuildRequires: R-CRAN-seqinr +Requires: R-CRAN-seqinr + +%description +This software is useful for loading '.fasta' or '.gbk' files, and for +retrieving sequences from 'GenBank' dataset +. This package allows to detect +differences or asymmetries based on nucleotide composition by using local +linear kernel smoothers. Also, it is possible to draw inference about +critical points (i. e. maximum or minimum points) related with the +derivative curves. Additionally, bootstrap methods have been used for +estimating confidence intervals and speed computational techniques +(binning techniques) have been implemented in 'seq2R'. + +%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-simaerep.spec b/specs/R-CRAN-simaerep.spec index 22ab814bf..4d473be55 100644 --- a/specs/R-CRAN-simaerep.spec +++ b/specs/R-CRAN-simaerep.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname simaerep -%global packver 0.5.0 +%global packver 0.6.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.5.0 +Version: 0.6.0 Release: 1%{?dist}%{?buildtag} Summary: Find Clinical Trial Sites Under-Reporting Adverse Events @@ -31,6 +31,7 @@ BuildRequires: R-CRAN-RColorBrewer BuildRequires: R-CRAN-progressr BuildRequires: R-CRAN-knitr BuildRequires: R-CRAN-tibble +BuildRequires: R-CRAN-dbplyr Requires: R-CRAN-tidyr >= 1.1.0 Requires: R-CRAN-dplyr >= 1.0.0 Requires: R-CRAN-furrr >= 0.2.1 @@ -45,6 +46,7 @@ Requires: R-CRAN-RColorBrewer Requires: R-CRAN-progressr Requires: R-CRAN-knitr Requires: R-CRAN-tibble +Requires: R-CRAN-dbplyr %description Monitoring of Adverse Event (AE) reporting in clinical trials is important diff --git a/specs/R-CRAN-snotelr.spec b/specs/R-CRAN-snotelr.spec index 036abe4be..331e2cb12 100644 --- a/specs/R-CRAN-snotelr.spec +++ b/specs/R-CRAN-snotelr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname snotelr -%global packver 1.4 +%global packver 1.5 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.4 +Version: 1.5 Release: 1%{?dist}%{?buildtag} Summary: Calculate and Visualize 'SNOTEL' Snow Data and Seasonality diff --git a/specs/R-CRAN-swdpwr.spec b/specs/R-CRAN-swdpwr.spec index b84a48c93..2b5c900e5 100644 --- a/specs/R-CRAN-swdpwr.spec +++ b/specs/R-CRAN-swdpwr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname swdpwr -%global packver 1.9 +%global packver 1.10 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.9 +Version: 1.10 Release: 1%{?dist}%{?buildtag} Summary: Power Calculation for Stepped Wedge Cluster Randomized Trials @@ -25,14 +25,15 @@ cluster randomized trials, we developed this software. Different parameters can be specified by users for different scenarios, including: cross-sectional and cohort designs, binary and continuous outcomes, marginal (GEE) and conditional models (mixed effects model), three link -functions (identity, log, logit links), with and without time effects -under exchangeable, nested exchangeable and block exchangeable correlation -structures. Unequal numbers of clusters per sequence are also allowed. The -methods included in this package: Zhou et al. (2020) -, Li et al. (2018) -. Supplementary documents can be found at: -. The Shiny app for -swdpwr can be accessed at: +functions (identity, log, logit links), with and without time effects (the +default specification assumes no-time-effect) under exchangeable, nested +exchangeable and block exchangeable correlation structures. Unequal +numbers of clusters per sequence are also allowed. The methods included in +this package: Zhou et al. (2020) , Li et +al. (2018) . Supplementary documents can be found +at: +. +The Shiny app for swdpwr can be accessed at: . The package also includes functions that perform calculations for the intra-cluster correlation coefficients based on the random effects variances as input diff --git a/specs/R-CRAN-tsxtreme.spec b/specs/R-CRAN-tsxtreme.spec index 483c67073..1343aba56 100644 --- a/specs/R-CRAN-tsxtreme.spec +++ b/specs/R-CRAN-tsxtreme.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname tsxtreme -%global packver 0.3.3 +%global packver 0.3.4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.3.3 +Version: 0.3.4 Release: 1%{?dist}%{?buildtag} Summary: Bayesian Modelling of Extremal Dependence in Time Series @@ -47,6 +48,8 @@ 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-usaidplot.spec b/specs/R-CRAN-usaidplot.spec new file mode 100644 index 000000000..4c5ec637a --- /dev/null +++ b/specs/R-CRAN-usaidplot.spec @@ -0,0 +1,57 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname usaidplot +%global packver 2.0.2 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 2.0.2 +Release: 1%{?dist}%{?buildtag} +Summary: Make Graphs with US Agency for International Development Colors + +License: MIT + file LICENSE +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-extrafont +BuildRequires: R-CRAN-extrafontdb +BuildRequires: R-CRAN-ggplot2 +Requires: R-CRAN-extrafont +Requires: R-CRAN-extrafontdb +Requires: R-CRAN-ggplot2 + +%description +Automatically apply the United States Agency for International +Development's color palette and fonts for either discrete or continuous +variables. + +%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-vectorsurvR.spec b/specs/R-CRAN-vectorsurvR.spec index 99541ac41..df4d40ac8 100644 --- a/specs/R-CRAN-vectorsurvR.spec +++ b/specs/R-CRAN-vectorsurvR.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname vectorsurvR -%global packver 0.2.0 +%global packver 1.2.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.2.0 +Version: 1.2.1 Release: 1%{?dist}%{?buildtag} Summary: Data Access and Analytical Tools for 'VectorSurv' Users