diff --git a/specs/R-CRAN-CLVTools.spec b/specs/R-CRAN-CLVTools.spec index 3091c573f..48421cc6c 100644 --- a/specs/R-CRAN-CLVTools.spec +++ b/specs/R-CRAN-CLVTools.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname CLVTools -%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: Tools for Customer Lifetime Value Estimation diff --git a/specs/R-CRAN-Certara.VPCResults.spec b/specs/R-CRAN-Certara.VPCResults.spec index 285009be7..727b24a0a 100644 --- a/specs/R-CRAN-Certara.VPCResults.spec +++ b/specs/R-CRAN-Certara.VPCResults.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname Certara.VPCResults -%global packver 3.0.1 +%global packver 3.0.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.0.1 +Version: 3.0.2 Release: 1%{?dist}%{?buildtag} Summary: Generate Visual Predictive Checks (VPC) Using 'shiny' diff --git a/specs/R-CRAN-Cyclops.spec b/specs/R-CRAN-Cyclops.spec index de05d30a5..ae55435a4 100644 --- a/specs/R-CRAN-Cyclops.spec +++ b/specs/R-CRAN-Cyclops.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname Cyclops -%global packver 3.4.1 +%global packver 3.5.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 3.4.1 +Version: 3.5.0 Release: 1%{?dist}%{?buildtag} Summary: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis diff --git a/specs/R-CRAN-GET.spec b/specs/R-CRAN-GET.spec index fe409522b..a1384c299 100644 --- a/specs/R-CRAN-GET.spec +++ b/specs/R-CRAN-GET.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname GET -%global packver 1.0-3 +%global packver 1.0-4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.3 +Version: 1.0.4 Release: 1%{?dist}%{?buildtag} Summary: Global Envelopes @@ -50,8 +50,8 @@ test of correspondence of distribution functions), for central regions of functional or multivariate data (e.g. outlier detection, functional boxplot) and for global confidence and prediction bands (e.g. confidence band in polynomial regression, Bayesian posterior prediction). See -Myllymäki and Mrkvička (2023) , Myllymäki -et al. (2017) , Mrkvička and Myllymäki (2023) +Myllymäki and Mrkvička (2024) , Myllymäki et +al. (2017) , Mrkvička and Myllymäki (2023) , Mrkvička et al. (2016) , Mrkvička et al. (2017) , Mrkvička et al. (2020) @@ -61,7 +61,7 @@ et al. (2017) , Mrkvička and Myllymäki (2023) , Dai et al. (2022) , Dvořák and Mrkvička (2022) , Mrkvička et al. (2023) , and Konstantinou et al. (2024) -. +. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-HDTSA.spec b/specs/R-CRAN-HDTSA.spec index 71c7027fb..55874e291 100644 --- a/specs/R-CRAN-HDTSA.spec +++ b/specs/R-CRAN-HDTSA.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname HDTSA -%global packver 1.0.4 +%global packver 1.0.5 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.4 +Version: 1.0.5 Release: 1%{?dist}%{?buildtag} Summary: High Dimensional Time Series Analysis Tools @@ -24,6 +24,8 @@ BuildRequires: R-methods BuildRequires: R-CRAN-MASS BuildRequires: R-CRAN-geigen BuildRequires: R-CRAN-jointDiag +BuildRequires: R-CRAN-vars +BuildRequires: R-CRAN-forecast BuildRequires: R-CRAN-RcppEigen Requires: R-stats Requires: R-CRAN-Rcpp @@ -33,22 +35,24 @@ Requires: R-methods Requires: R-CRAN-MASS Requires: R-CRAN-geigen Requires: R-CRAN-jointDiag +Requires: R-CRAN-vars +Requires: R-CRAN-forecast %description -Procedures for high-dimensional time series analysis including factor -analysis proposed by Lam and Yao (2012) and Chang, -Guo and Yao (2015) ,martingale -difference test proposed by Chang, Jiang and Shao (2022) - in press,principal component analysis -proposed by Chang, Guo and Yao (2018) , -identifying cointegration proposed by Zhang, Robinson and Yao (2019) -, unit root test proposed by Chang, -Cheng and Yao (2021) , white noise test -proposed by Chang, Yao and Zhou (2017) , -CP-decomposition for high-dimensional matrix time series proposed by -Chang, He, Yang and Yao(2023) and Chang, Du, -Huang and Yao (2024+), and Statistical inference for high-dimensional -spectral density matrix porposed by Chang, Jiang, McElroy and Shao (2023) +An implementation for high-dimensional time series analysis methods, +including factor model for vector time series proposed by Lam and Yao +(2012) and Chang, Guo and Yao (2015) +, martingale difference test proposed +by Chang, Jiang and Shao (2023) , +principal component analysis for vector time series proposed by Chang, Guo +and Yao (2018) , cointegration analysis proposed +by Zhang, Robinson and Yao (2019) , +unit root test proposed by Chang, Cheng and Yao (2022) +, white noise test proposed by Chang, Yao and +Zhou (2017) , CP-decomposition for matrix time +series proposed by Chang et al. (2023) and +Chang et al. (2024) , and statistical +inference for spectral density matrix proposed by Chang et al. (2022) . %prep diff --git a/specs/R-CRAN-Hmisc.spec b/specs/R-CRAN-Hmisc.spec index d59632dc9..a3e0e2a1f 100644 --- a/specs/R-CRAN-Hmisc.spec +++ b/specs/R-CRAN-Hmisc.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname Hmisc -%global packver 5.2-0 +%global packver 5.2-1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 5.2.0 +Version: 5.2.1 Release: 1%{?dist}%{?buildtag} Summary: Harrell Miscellaneous diff --git a/specs/R-CRAN-multiDoE.spec b/specs/R-CRAN-ILRCM.spec similarity index 64% rename from specs/R-CRAN-multiDoE.spec rename to specs/R-CRAN-ILRCM.spec index d85c398fe..92b08ae8f 100644 --- a/specs/R-CRAN-multiDoE.spec +++ b/specs/R-CRAN-ILRCM.spec @@ -1,15 +1,15 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi -%global packname multiDoE -%global packver 0.9.2 +%global packname ILRCM +%global packver 0.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.9.2 +Version: 0.1.0 Release: 1%{?dist}%{?buildtag} -Summary: Multi-Criteria Design of Experiments for Optimal Design +Summary: Convert Irregular Longitudinal Data to Regular Intervals and Perform Clustering -License: CC BY 4.0 +License: GPL-3 URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz @@ -18,21 +18,16 @@ BuildRequires: R-devel >= 3.5.0 Requires: R-core >= 3.5.0 BuildArch: noarch BuildRequires: R-CRAN-ggplot2 -BuildRequires: R-CRAN-magrittr -BuildRequires: R-CRAN-plotly -BuildRequires: R-CRAN-pracma +BuildRequires: R-CRAN-scales Requires: R-CRAN-ggplot2 -Requires: R-CRAN-magrittr -Requires: R-CRAN-plotly -Requires: R-CRAN-pracma +Requires: R-CRAN-scales %description -Multi-criteria design of experiments algorithm that simultaneously -optimizes up to six different criteria ('I', 'Id', 'D', 'Ds', 'A' and -'As'). The algorithm finds the optimal Pareto front and, if requested, -selects a possible symmetrical design on it. The symmetrical design is -selected based on two techniques: minimum distance with the Utopia point -or the 'TOPSIS' approach. +Convert irregularly spaced longitudinal data into regular intervals for +further analysis, and perform clustering using advanced machine learning +techniques. The package is designed for handling complex longitudinal +datasets, optimizing them for research in healthcare, demography, and +other fields requiring temporal data modeling. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-MAP.spec b/specs/R-CRAN-MAP.spec index fbe319fd4..5c932cb79 100644 --- a/specs/R-CRAN-MAP.spec +++ b/specs/R-CRAN-MAP.spec @@ -1,14 +1,15 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname MAP -%global packver 0.1.3 +%global packver 1.0.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.3 -Release: 3%{?dist}%{?buildtag} +Version: 1.0.0 +Release: 1%{?dist}%{?buildtag} Summary: Multimodal Automated Phenotyping -License: GPL-2 +License: GPL-3 URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz @@ -17,9 +18,11 @@ BuildRequires: R-devel >= 3.4.0 Requires: R-core >= 3.4.0 BuildArch: noarch BuildRequires: R-CRAN-flexmix >= 2.3.14 -BuildRequires: R-Matrix >= 1.2.10 +BuildRequires: R-CRAN-Matrix >= 1.2.10 +BuildRequires: R-CRAN-magrittr Requires: R-CRAN-flexmix >= 2.3.14 -Requires: R-Matrix >= 1.2.10 +Requires: R-CRAN-Matrix >= 1.2.10 +Requires: R-CRAN-magrittr %description Electronic health records (EHR) linked with biorepositories are a powerful @@ -33,11 +36,20 @@ algorithm), fits an ensemble of latent mixture models on aggregated ICD and NLP counts along with healthcare utilization. The MAP algorithm yields a predicted probability of phenotype for each patient and a threshold for classifying subjects with phenotype yes/no (See Katherine P. Liao, et al. -(2019) .). +(2019) .). %prep %setup -q -c -n %{packname} +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; %build @@ -47,6 +59,8 @@ mkdir -p %{buildroot}%{rlibdir} %{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; %files %{rlibdir}/%{packname} diff --git a/specs/R-CRAN-MEDesigns.spec b/specs/R-CRAN-MEDesigns.spec new file mode 100644 index 000000000..d005d45f5 --- /dev/null +++ b/specs/R-CRAN-MEDesigns.spec @@ -0,0 +1,57 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname MEDesigns +%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: Mating Environmental Designs + +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 +BuildArch: noarch + +%description +In breeding experiments, mating environmental (ME) designs are very +popular as mating designs are directly implemented in the field +environment using block or row-column designs. Here, three functions are +given related to three new methods which will generate mating diallel +cross designs (Hinkelmann and Kempthorne, 1963) or +mating environmental (ME) designs along with design parameters, C matrix, +eigenvalues (EVs), degree of fractionations (DF) and canonical efficiency +factor (CEF). Another one function is added to check the properties of a +given ME diallel cross design. + +%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-NNS.spec b/specs/R-CRAN-NNS.spec index af0034a80..3dd133fed 100644 --- a/specs/R-CRAN-NNS.spec +++ b/specs/R-CRAN-NNS.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname NNS -%global packver 10.9.3 +%global packver 10.9.4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 10.9.3 +Version: 10.9.4 Release: 1%{?dist}%{?buildtag} Summary: Nonlinear Nonparametric Statistics diff --git a/specs/R-CRAN-OpenRepGrid.spec b/specs/R-CRAN-OpenRepGrid.spec index cf24a7f82..6c87f687d 100644 --- a/specs/R-CRAN-OpenRepGrid.spec +++ b/specs/R-CRAN-OpenRepGrid.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname OpenRepGrid -%global packver 0.1.15 +%global packver 0.1.16 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.15 +Version: 0.1.16 Release: 1%{?dist}%{?buildtag} Summary: Tools to Analyze Repertory Grid Data diff --git a/specs/R-CRAN-PaRe.spec b/specs/R-CRAN-PaRe.spec index 2bb6a8c5f..e10f591bd 100644 --- a/specs/R-CRAN-PaRe.spec +++ b/specs/R-CRAN-PaRe.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname PaRe -%global packver 0.1.14 +%global packver 0.1.15 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.14 +Version: 0.1.15 Release: 1%{?dist}%{?buildtag} Summary: A Way to Perform Code Review or QA on Other Packages diff --git a/specs/R-CRAN-PerRegMod.spec b/specs/R-CRAN-PerRegMod.spec index 1f49f4bf9..f6f4cac18 100644 --- a/specs/R-CRAN-PerRegMod.spec +++ b/specs/R-CRAN-PerRegMod.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname PerRegMod -%global packver 4.4.2 +%global packver 4.4.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 4.4.2 +Version: 4.4.3 Release: 1%{?dist}%{?buildtag} Summary: Fitting Periodic Coefficients Linear Regression Models diff --git a/specs/R-CRAN-RCMsize.spec b/specs/R-CRAN-RCMsize.spec new file mode 100644 index 000000000..7f66bcf2c --- /dev/null +++ b/specs/R-CRAN-RCMsize.spec @@ -0,0 +1,56 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname RCMsize +%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: Sample Size Calculation in Reversible Catalytic 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-binom +BuildRequires: R-stats +Requires: R-CRAN-binom +Requires: R-stats + +%description +Sample size and confidence interval calculations in reversible catalytic +models, with applications in malaria research. Further details can be +found in the paper by Sepúlveda and Drakeley (2015, +). + +%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-REDCapCAST.spec b/specs/R-CRAN-REDCapCAST.spec index eba798d32..15b9a17c9 100644 --- a/specs/R-CRAN-REDCapCAST.spec +++ b/specs/R-CRAN-REDCapCAST.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname REDCapCAST -%global packver 24.11.2 +%global packver 24.12.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 24.11.2 +Version: 24.12.1 Release: 1%{?dist}%{?buildtag} Summary: REDCap Metadata Casting and Castellated Data Handling @@ -37,6 +37,7 @@ BuildRequires: R-CRAN-gt BuildRequires: R-CRAN-bslib BuildRequires: R-CRAN-here BuildRequires: R-CRAN-glue +BuildRequires: R-CRAN-gtsummary Requires: R-CRAN-dplyr Requires: R-CRAN-REDCapR Requires: R-CRAN-tidyr @@ -57,6 +58,7 @@ Requires: R-CRAN-gt Requires: R-CRAN-bslib Requires: R-CRAN-here Requires: R-CRAN-glue +Requires: R-CRAN-gtsummary %description Casting metadata for REDCap database creation and handling of castellated diff --git a/specs/R-CRAN-ReIns.spec b/specs/R-CRAN-ReIns.spec index ba2da0f5c..c23b5e98e 100644 --- a/specs/R-CRAN-ReIns.spec +++ b/specs/R-CRAN-ReIns.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ReIns -%global packver 1.0.14 +%global packver 1.0.15 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.14 +Version: 1.0.15 Release: 1%{?dist}%{?buildtag} Summary: Functions from "Reinsurance: Actuarial and Statistical Aspects" diff --git a/specs/R-CRAN-ReportSubtotal.spec b/specs/R-CRAN-ReportSubtotal.spec index 746dd93c4..cc2e1d820 100644 --- a/specs/R-CRAN-ReportSubtotal.spec +++ b/specs/R-CRAN-ReportSubtotal.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname ReportSubtotal -%global packver 0.1 +%global packver 0.1.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1 +Version: 0.1.2 Release: 1%{?dist}%{?buildtag} Summary: Adds Subtotals to Data Reports @@ -27,7 +27,7 @@ Requires: R-utils Requires: R-CRAN-magrittr %description -Adds subtotal rows / sections (a la the SAS "Proc Tabulate" "All" option) +Adds subtotal rows / sections (a la the 'SAS' 'Proc Tabulate' All option) to a Group By output by running a series of Group By functions with partial sets of the same variables and combining the results with the original. Can be used to add comprehensive information to a data report or diff --git a/specs/R-CRAN-SAKERNAS.spec b/specs/R-CRAN-SAKERNAS.spec new file mode 100644 index 000000000..1282eeed1 --- /dev/null +++ b/specs/R-CRAN-SAKERNAS.spec @@ -0,0 +1,53 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname SAKERNAS +%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: A National Labor Force Survey of Indonesia + +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-readxl +Requires: R-CRAN-readxl + +%description +Surveys to collect employment data so as to obtain data estimates on the +number of employed people, the number of unemployed, and other employment +indicators. + +%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-STICr.spec b/specs/R-CRAN-STICr.spec index 05a398a9c..a1039d95b 100644 --- a/specs/R-CRAN-STICr.spec +++ b/specs/R-CRAN-STICr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname STICr -%global packver 1.0 +%global packver 1.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0 +Version: 1.1 Release: 1%{?dist}%{?buildtag} Summary: Process Stream Temperature, Intermittency, and Conductivity (STIC) Sensor Data diff --git a/specs/R-CRAN-affiner.spec b/specs/R-CRAN-affiner.spec index 3290e56eb..065d754d8 100644 --- a/specs/R-CRAN-affiner.spec +++ b/specs/R-CRAN-affiner.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname affiner -%global packver 0.1.1 +%global packver 0.1.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.1 +Version: 0.1.3 Release: 1%{?dist}%{?buildtag} Summary: A Finer Way to Render 3D Illustrated Objects in 'grid' Using Affine Transformations diff --git a/specs/R-CRAN-antaresViz.spec b/specs/R-CRAN-antaresViz.spec new file mode 100644 index 000000000..de496f35c --- /dev/null +++ b/specs/R-CRAN-antaresViz.spec @@ -0,0 +1,102 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname antaresViz +%global packver 0.18.3 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.18.3 +Release: 1%{?dist}%{?buildtag} +Summary: Antares Visualizations + +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-plotly >= 4.5.6 +BuildRequires: R-CRAN-antaresRead >= 2.2.9 +BuildRequires: R-CRAN-sp >= 2.0.0 +BuildRequires: R-CRAN-dygraphs >= 1.1.1.6 +BuildRequires: R-CRAN-leaflet >= 1.1.0 +BuildRequires: R-CRAN-htmlwidgets >= 0.7.0 +BuildRequires: R-CRAN-leaflet.minicharts >= 0.5.3 +BuildRequires: R-CRAN-spMaps >= 0.5.0 +BuildRequires: R-CRAN-antaresProcessing >= 0.13.0 +BuildRequires: R-CRAN-shiny >= 0.13.0 +BuildRequires: R-CRAN-manipulateWidget >= 0.10.0 +BuildRequires: R-CRAN-htmltools +BuildRequires: R-CRAN-sf +BuildRequires: R-CRAN-webshot +BuildRequires: R-CRAN-data.table +BuildRequires: R-methods +BuildRequires: R-CRAN-lubridate +BuildRequires: R-CRAN-geojsonio +BuildRequires: R-graphics +BuildRequires: R-stats +BuildRequires: R-CRAN-assertthat +BuildRequires: R-CRAN-rAmCharts +BuildRequires: R-utils +BuildRequires: R-CRAN-lifecycle +Requires: R-CRAN-plotly >= 4.5.6 +Requires: R-CRAN-antaresRead >= 2.2.9 +Requires: R-CRAN-sp >= 2.0.0 +Requires: R-CRAN-dygraphs >= 1.1.1.6 +Requires: R-CRAN-leaflet >= 1.1.0 +Requires: R-CRAN-htmlwidgets >= 0.7.0 +Requires: R-CRAN-leaflet.minicharts >= 0.5.3 +Requires: R-CRAN-spMaps >= 0.5.0 +Requires: R-CRAN-antaresProcessing >= 0.13.0 +Requires: R-CRAN-shiny >= 0.13.0 +Requires: R-CRAN-manipulateWidget >= 0.10.0 +Requires: R-CRAN-htmltools +Requires: R-CRAN-sf +Requires: R-CRAN-webshot +Requires: R-CRAN-data.table +Requires: R-methods +Requires: R-CRAN-lubridate +Requires: R-CRAN-geojsonio +Requires: R-graphics +Requires: R-stats +Requires: R-CRAN-assertthat +Requires: R-CRAN-rAmCharts +Requires: R-utils +Requires: R-CRAN-lifecycle + +%description +Visualize results generated by Antares, a powerful open source software +developed by RTE to simulate and study electric power systems (more +information about 'Antares' here: +). This package +provides functions that create interactive charts to help 'Antares' users +visually explore the results of their simulations. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%install + +mkdir -p %{buildroot}%{rlibdir} +%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} +test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) +rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; + +%files +%{rlibdir}/%{packname} diff --git a/specs/R-CRAN-anytime.spec b/specs/R-CRAN-anytime.spec index 5fa1a7b80..55bf54bd1 100644 --- a/specs/R-CRAN-anytime.spec +++ b/specs/R-CRAN-anytime.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname anytime -%global packver 0.3.9 +%global packver 0.3.10 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.3.9 +Version: 0.3.10 Release: 1%{?dist}%{?buildtag} Summary: Anything to 'POSIXct' or 'Date' Converter @@ -28,9 +29,15 @@ parsing. %prep %setup -q -c -n %{packname} +# fix end of executable files find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping [ -d %{packname}/src ] && find %{packname}/src -type f -exec \ sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; %build @@ -40,6 +47,7 @@ mkdir -p %{buildroot}%{rlibdir} %{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; %files diff --git a/specs/R-CRAN-apache.sedona.spec b/specs/R-CRAN-apache.sedona.spec index 045d4496b..5a253c64e 100644 --- a/specs/R-CRAN-apache.sedona.spec +++ b/specs/R-CRAN-apache.sedona.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname apache.sedona -%global packver 1.6.1 +%global packver 1.7.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.6.1 +Version: 1.7.0 Release: 1%{?dist}%{?buildtag} Summary: R Interface for Apache Sedona diff --git a/specs/R-CRAN-atime.spec b/specs/R-CRAN-atime.spec index 8c3370992..42a7fdd28 100644 --- a/specs/R-CRAN-atime.spec +++ b/specs/R-CRAN-atime.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname atime -%global packver 2024.11.19 +%global packver 2024.11.29 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2024.11.19 +Version: 2024.11.29 Release: 1%{?dist}%{?buildtag} Summary: Asymptotic Timing diff --git a/specs/R-CRAN-bbk.spec b/specs/R-CRAN-bbk.spec index bc8f40997..fba63940f 100644 --- a/specs/R-CRAN-bbk.spec +++ b/specs/R-CRAN-bbk.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname bbk -%global packver 0.4.0 +%global packver 0.5.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4.0 +Version: 0.5.0 Release: 1%{?dist}%{?buildtag} Summary: Client for the Deutsche Bundesbank and European Central Bank APIs @@ -17,11 +17,13 @@ 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-httr2 +BuildRequires: R-CRAN-httr2 >= 1.0.0 +BuildRequires: R-CRAN-curl BuildRequires: R-stats BuildRequires: R-utils BuildRequires: R-CRAN-xml2 -Requires: R-CRAN-httr2 +Requires: R-CRAN-httr2 >= 1.0.0 +Requires: R-CRAN-curl Requires: R-stats Requires: R-utils Requires: R-CRAN-xml2 diff --git a/specs/R-CRAN-bplsr.spec b/specs/R-CRAN-bplsr.spec index 6a85479c7..e8957ace8 100644 --- a/specs/R-CRAN-bplsr.spec +++ b/specs/R-CRAN-bplsr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname bplsr -%global packver 1.0.0 +%global packver 1.0.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.0.1 Release: 1%{?dist}%{?buildtag} Summary: Bayesian partial least squares regression diff --git a/specs/R-CRAN-clinicalsignificance.spec b/specs/R-CRAN-clinicalsignificance.spec index 6fadc9926..52de2f1f1 100644 --- a/specs/R-CRAN-clinicalsignificance.spec +++ b/specs/R-CRAN-clinicalsignificance.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname clinicalsignificance -%global packver 2.0.0 +%global packver 2.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.0.0 +Version: 2.1.0 Release: 1%{?dist}%{?buildtag} Summary: A Toolbox for Clinical Significance Analyses in Intervention Studies @@ -44,7 +44,8 @@ Requires: R-CRAN-tidyr A clinical significance analysis can be used to determine if an intervention has a meaningful or practical effect for patients. You provide a tidy data set plus a few more metrics and this package will take -care of it to make your results publication ready. +care of it to make your results publication ready. Accompanying package to +Claus et al. . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-container.spec b/specs/R-CRAN-container.spec index 91d4cd834..ac1536d29 100644 --- a/specs/R-CRAN-container.spec +++ b/specs/R-CRAN-container.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname container -%global packver 1.0.4 +%global packver 1.0.5 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.4 +Version: 1.0.5 Release: 1%{?dist}%{?buildtag} Summary: Extending Base 'R' Lists diff --git a/specs/R-CRAN-cptcity.spec b/specs/R-CRAN-cptcity.spec index 0a9e60ee7..5685c5f2d 100644 --- a/specs/R-CRAN-cptcity.spec +++ b/specs/R-CRAN-cptcity.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname cptcity -%global packver 1.0.6 +%global packver 1.1.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.6 +Version: 1.1.1 Release: 1%{?dist}%{?buildtag} Summary: 'cpt-city' Colour Gradients @@ -13,22 +14,28 @@ 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 +BuildRequires: R-devel >= 3.5.0 +Requires: R-core >= 3.5.0 BuildArch: noarch BuildRequires: R-grDevices Requires: R-grDevices %description Incorporates colour gradients from the 'cpt-city' web archive available at -. +. %prep %setup -q -c -n %{packname} +# fix end of executable files find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping [ -d %{packname}/src ] && find %{packname}/src -type f -exec \ sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; %build @@ -38,6 +45,7 @@ mkdir -p %{buildroot}%{rlibdir} %{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; %files diff --git a/specs/R-CRAN-crimedatasets.spec b/specs/R-CRAN-crimedatasets.spec new file mode 100644 index 000000000..c47cde4a4 --- /dev/null +++ b/specs/R-CRAN-crimedatasets.spec @@ -0,0 +1,54 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname crimedatasets +%global packver 0.1.0 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.0 +Release: 1%{?dist}%{?buildtag} +Summary: A Comprehensive Collection of Crime-Related Datasets + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.5.0 +Requires: R-core >= 3.5.0 +BuildArch: noarch + +%description +A comprehensive collection of datasets exclusively focused on crimes, +criminal activities, and related topics. This package serves as a valuable +resource for researchers, analysts, and students interested in crime +analysis, criminology, social and economic studies related to criminal +behavior. Datasets span global and local contexts, with a mix of tabular +and spatial data. + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$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-crumble.spec b/specs/R-CRAN-crumble.spec index fa397681e..c356ce538 100644 --- a/specs/R-CRAN-crumble.spec +++ b/specs/R-CRAN-crumble.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname crumble -%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: Flexible and General Mediation Analysis Using Riesz Representers diff --git a/specs/R-CRAN-deepregression.spec b/specs/R-CRAN-deepregression.spec index d6d93d4a8..ff8d8f978 100644 --- a/specs/R-CRAN-deepregression.spec +++ b/specs/R-CRAN-deepregression.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname deepregression -%global packver 1.0.0 +%global packver 2.2.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 2.2.0 Release: 1%{?dist}%{?buildtag} Summary: Fitting Deep Distributional Regression @@ -20,6 +20,9 @@ BuildArch: noarch BuildRequires: R-CRAN-tensorflow >= 2.2.0 BuildRequires: R-CRAN-keras >= 2.2.0 BuildRequires: R-CRAN-reticulate >= 1.14 +BuildRequires: R-CRAN-coro >= 1.0.3 +BuildRequires: R-CRAN-torchvision >= 0.5.1 +BuildRequires: R-CRAN-luz >= 0.4.0 BuildRequires: R-CRAN-tfprobability BuildRequires: R-CRAN-mgcv BuildRequires: R-CRAN-dplyr @@ -28,9 +31,13 @@ BuildRequires: R-CRAN-Matrix BuildRequires: R-CRAN-magrittr BuildRequires: R-CRAN-tfruns BuildRequires: R-methods +BuildRequires: R-CRAN-torch Requires: R-CRAN-tensorflow >= 2.2.0 Requires: R-CRAN-keras >= 2.2.0 Requires: R-CRAN-reticulate >= 1.14 +Requires: R-CRAN-coro >= 1.0.3 +Requires: R-CRAN-torchvision >= 0.5.1 +Requires: R-CRAN-luz >= 0.4.0 Requires: R-CRAN-tfprobability Requires: R-CRAN-mgcv Requires: R-CRAN-dplyr @@ -39,6 +46,7 @@ Requires: R-CRAN-Matrix Requires: R-CRAN-magrittr Requires: R-CRAN-tfruns Requires: R-methods +Requires: R-CRAN-torch %description Allows for the specification of semi-structured deep distributional diff --git a/specs/R-CRAN-diemr.spec b/specs/R-CRAN-diemr.spec index b0c7ec4ee..17fd7731a 100644 --- a/specs/R-CRAN-diemr.spec +++ b/specs/R-CRAN-diemr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname diemr -%global packver 1.4.1 +%global packver 1.4.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.4.1 +Version: 1.4.2 Release: 1%{?dist}%{?buildtag} Summary: Diagnostic Index Expectation Maximisation in R diff --git a/specs/R-CRAN-douconca.spec b/specs/R-CRAN-douconca.spec index f0776ec34..4e15d28d2 100644 --- a/specs/R-CRAN-douconca.spec +++ b/specs/R-CRAN-douconca.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname douconca -%global packver 1.2.1 +%global packver 1.2.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.2.1 +Version: 1.2.2 Release: 1%{?dist}%{?buildtag} Summary: Double Constrained Correspondence Analysis for Trait-Environment Analysis in Ecology diff --git a/specs/R-CRAN-dtreg.spec b/specs/R-CRAN-dtreg.spec index 75ed98c41..08214bcd3 100644 --- a/specs/R-CRAN-dtreg.spec +++ b/specs/R-CRAN-dtreg.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname dtreg -%global packver 1.0.0 +%global packver 1.1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.0 +Version: 1.1.0 Release: 1%{?dist}%{?buildtag} Summary: Interact with Data Type Registries and Create Machine-Readable Data diff --git a/specs/R-CRAN-fastplyr.spec b/specs/R-CRAN-fastplyr.spec index 09238ab93..fdf934f45 100644 --- a/specs/R-CRAN-fastplyr.spec +++ b/specs/R-CRAN-fastplyr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname fastplyr -%global packver 0.4.0 +%global packver 0.5.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4.0 +Version: 0.5.0 Release: 1%{?dist}%{?buildtag} Summary: Fast Alternatives to 'tidyverse' Functions @@ -18,7 +18,7 @@ BuildRequires: R-devel >= 3.6.1 Requires: R-core >= 3.6.1 BuildRequires: R-CRAN-collapse >= 2.0.0 BuildRequires: R-CRAN-dplyr >= 1.1.0 -BuildRequires: R-CRAN-cheapr >= 0.9.9 +BuildRequires: R-CRAN-cheapr >= 0.9.91 BuildRequires: R-CRAN-vctrs >= 0.6.0 BuildRequires: R-CRAN-lifecycle BuildRequires: R-CRAN-magrittr @@ -28,7 +28,7 @@ BuildRequires: R-CRAN-tidyselect BuildRequires: R-CRAN-cpp11 Requires: R-CRAN-collapse >= 2.0.0 Requires: R-CRAN-dplyr >= 1.1.0 -Requires: R-CRAN-cheapr >= 0.9.9 +Requires: R-CRAN-cheapr >= 0.9.91 Requires: R-CRAN-vctrs >= 0.6.0 Requires: R-CRAN-lifecycle Requires: R-CRAN-magrittr diff --git a/specs/R-CRAN-gbmt.spec b/specs/R-CRAN-gbmt.spec index 866bd74f9..7cbfb514a 100644 --- a/specs/R-CRAN-gbmt.spec +++ b/specs/R-CRAN-gbmt.spec @@ -1,10 +1,11 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname gbmt -%global packver 0.1.3 +%global packver 0.1.4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.3 +Version: 0.1.4 Release: 1%{?dist}%{?buildtag} Summary: Group-Based Multivariate Trajectory Modeling diff --git a/specs/R-CRAN-gdm.spec b/specs/R-CRAN-gdm.spec index ff7f694da..fd17f6dbd 100644 --- a/specs/R-CRAN-gdm.spec +++ b/specs/R-CRAN-gdm.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname gdm -%global packver 1.6.0-3 +%global packver 1.6.0-4 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.6.0.3 +Version: 1.6.0.4 Release: 1%{?dist}%{?buildtag} Summary: Generalized Dissimilarity Modeling diff --git a/specs/R-CRAN-genridge.spec b/specs/R-CRAN-genridge.spec index 486f42c73..f03b436b1 100644 --- a/specs/R-CRAN-genridge.spec +++ b/specs/R-CRAN-genridge.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname genridge -%global packver 0.7.1 +%global packver 0.8.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.7.1 +Version: 0.8.0 Release: 1%{?dist}%{?buildtag} Summary: Generalized Ridge Trace Plots for Ridge Regression @@ -14,8 +14,8 @@ URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz -BuildRequires: R-devel >= 2.11.1 -Requires: R-core >= 2.11.1 +BuildRequires: R-devel >= 3.5.0 +Requires: R-core >= 3.5.0 BuildArch: noarch BuildRequires: R-CRAN-car BuildRequires: R-CRAN-rgl diff --git a/specs/R-CRAN-gfoRmulaICE.spec b/specs/R-CRAN-gfoRmulaICE.spec new file mode 100644 index 000000000..47066b7f0 --- /dev/null +++ b/specs/R-CRAN-gfoRmulaICE.spec @@ -0,0 +1,88 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname gfoRmulaICE +%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: Parametric Iterative Conditional Expectation G-Formula + +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-data.table +BuildRequires: R-CRAN-ggplot2 +BuildRequires: R-CRAN-nnet +BuildRequires: R-CRAN-doParallel +BuildRequires: R-parallel +BuildRequires: R-CRAN-foreach +BuildRequires: R-CRAN-stringr +BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-rlang +BuildRequires: R-CRAN-reshape2 +BuildRequires: R-CRAN-speedglm +BuildRequires: R-methods +BuildRequires: R-CRAN-Hmisc +BuildRequires: R-splines +Requires: R-CRAN-data.table +Requires: R-CRAN-ggplot2 +Requires: R-CRAN-nnet +Requires: R-CRAN-doParallel +Requires: R-parallel +Requires: R-CRAN-foreach +Requires: R-CRAN-stringr +Requires: R-CRAN-magrittr +Requires: R-CRAN-dplyr +Requires: R-CRAN-rlang +Requires: R-CRAN-reshape2 +Requires: R-CRAN-speedglm +Requires: R-methods +Requires: R-CRAN-Hmisc +Requires: R-splines + +%description +Implements iterative conditional expectation (ICE) estimators of the +plug-in g-formula (Wen, Young, Robins, and Hernán (2020) ). Both singly robust and doubly robust ICE estimators +based on parametric models are available. The package can be used to +estimate survival curves under sustained treatment strategies +(interventions) using longitudinal data with time-varying treatments, +time-varying confounders, censoring, and competing events. The +interventions can be static or dynamic, and deterministic or stochastic +(including threshold interventions). Both prespecified and user-defined +interventions are available. + +%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-gtfs2emis.spec b/specs/R-CRAN-gtfs2emis.spec new file mode 100644 index 000000000..1f3106e7f --- /dev/null +++ b/specs/R-CRAN-gtfs2emis.spec @@ -0,0 +1,81 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname gtfs2emis +%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: Estimating Public Transport Emissions from General Transit Feed Specification (GTFS) Data + +License: MIT + file LICENSE +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 3.6 +Requires: R-core >= 3.6 +BuildArch: noarch +BuildRequires: R-CRAN-sf >= 0.9.0 +BuildRequires: R-CRAN-checkmate +BuildRequires: R-CRAN-data.table +BuildRequires: R-CRAN-furrr +BuildRequires: R-CRAN-future +BuildRequires: R-CRAN-gtfs2gps +BuildRequires: R-methods +BuildRequires: R-CRAN-sfheaders +BuildRequires: R-CRAN-terra +BuildRequires: R-CRAN-units +Requires: R-CRAN-sf >= 0.9.0 +Requires: R-CRAN-checkmate +Requires: R-CRAN-data.table +Requires: R-CRAN-furrr +Requires: R-CRAN-future +Requires: R-CRAN-gtfs2gps +Requires: R-methods +Requires: R-CRAN-sfheaders +Requires: R-CRAN-terra +Requires: R-CRAN-units + +%description +A bottom up model to estimate the emission levels of public transport +systems based on General Transit Feed Specification (GTFS) data. The +package requires two main inputs: i) Public transport data in the GTFS +standard format; and ii) Some basic information on fleet characteristics +such as fleet age, technology, fuel and Euro stage. As it stands, the +package estimates several pollutants at high spatial and temporal +resolutions. Pollution levels can be calculated for specific transport +routes, trips, time of the day or for the transport system as a whole. The +output with emission estimates can be extracted in different formats, +supporting analysis on how emission levels vary across space, time and by +fleet characteristics. A full description of the methods used in the +'gtfs2emis' model is presented in Vieira, J. P. B.; Pereira, R. H. M.; +Andrade, P. R. (2022) . + +%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-kimisc.spec b/specs/R-CRAN-kimisc.spec index 758d67ebe..44c977c43 100644 --- a/specs/R-CRAN-kimisc.spec +++ b/specs/R-CRAN-kimisc.spec @@ -1,14 +1,15 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname kimisc -%global packver 0.4 +%global packver 1.0.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4 -Release: 3%{?dist}%{?buildtag} +Version: 1.0.0 +Release: 1%{?dist}%{?buildtag} Summary: Kirill's Miscellaneous Functions -License: GPL-3 +License: MIT + file LICENSE URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz @@ -31,6 +32,15 @@ containment in an interval, and an alternative interface to assign(). %prep %setup -q -c -n %{packname} +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; %build @@ -40,6 +50,8 @@ mkdir -p %{buildroot}%{rlibdir} %{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname} test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so) rm -f %{buildroot}%{rlibdir}/R.css +# remove buildroot from installed files +find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \; %files %{rlibdir}/%{packname} diff --git a/specs/R-CRAN-laminr.spec b/specs/R-CRAN-laminr.spec index c25cb6398..60a24986f 100644 --- a/specs/R-CRAN-laminr.spec +++ b/specs/R-CRAN-laminr.spec @@ -1,13 +1,13 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname laminr -%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: Interface for 'LaminDB' +Summary: Client for 'LaminDB' License: Apache License (>= 2) URL: https://cran.r-project.org/package=%{packname} @@ -21,6 +21,7 @@ BuildRequires: R-CRAN-cli BuildRequires: R-CRAN-httr BuildRequires: R-CRAN-jsonlite BuildRequires: R-CRAN-purrr +BuildRequires: R-CRAN-R.utils BuildRequires: R-CRAN-R6 BuildRequires: R-CRAN-rlang BuildRequires: R-CRAN-tibble @@ -28,6 +29,7 @@ Requires: R-CRAN-cli Requires: R-CRAN-httr Requires: R-CRAN-jsonlite Requires: R-CRAN-purrr +Requires: R-CRAN-R.utils Requires: R-CRAN-R6 Requires: R-CRAN-rlang Requires: R-CRAN-tibble diff --git a/specs/R-CRAN-ldmppr.spec b/specs/R-CRAN-ldmppr.spec new file mode 100644 index 000000000..db6a8daca --- /dev/null +++ b/specs/R-CRAN-ldmppr.spec @@ -0,0 +1,106 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname ldmppr +%global packver 1.0.3 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0.3 +Release: 1%{?dist}%{?buildtag} +Summary: Estimate and Simulate from Location Dependent Marked Point Processes + +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 >= 1.0.12 +BuildRequires: R-CRAN-terra +BuildRequires: R-CRAN-doParallel +BuildRequires: R-CRAN-xgboost +BuildRequires: R-CRAN-ranger +BuildRequires: R-CRAN-parsnip +BuildRequires: R-CRAN-dials +BuildRequires: R-CRAN-bundle +BuildRequires: R-CRAN-recipes +BuildRequires: R-CRAN-rsample +BuildRequires: R-CRAN-tune +BuildRequires: R-CRAN-workflows +BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-hardhat +BuildRequires: R-CRAN-ggplot2 +BuildRequires: R-CRAN-spatstat.geom +BuildRequires: R-CRAN-spatstat.explore +BuildRequires: R-CRAN-nloptr +BuildRequires: R-CRAN-GET +BuildRequires: R-CRAN-progress +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-future +BuildRequires: R-CRAN-furrr +BuildRequires: R-CRAN-yardstick +BuildRequires: R-CRAN-RcppArmadillo +Requires: R-CRAN-Rcpp >= 1.0.12 +Requires: R-CRAN-terra +Requires: R-CRAN-doParallel +Requires: R-CRAN-xgboost +Requires: R-CRAN-ranger +Requires: R-CRAN-parsnip +Requires: R-CRAN-dials +Requires: R-CRAN-bundle +Requires: R-CRAN-recipes +Requires: R-CRAN-rsample +Requires: R-CRAN-tune +Requires: R-CRAN-workflows +Requires: R-CRAN-magrittr +Requires: R-CRAN-hardhat +Requires: R-CRAN-ggplot2 +Requires: R-CRAN-spatstat.geom +Requires: R-CRAN-spatstat.explore +Requires: R-CRAN-nloptr +Requires: R-CRAN-GET +Requires: R-CRAN-progress +Requires: R-CRAN-dplyr +Requires: R-CRAN-future +Requires: R-CRAN-furrr +Requires: R-CRAN-yardstick + +%description +A suite of tools for estimating, assessing model fit, simulating from, and +visualizing location dependent marked point processes characterized by +regularity in the pattern. You provide a reference marked point process, a +set of raster images containing location specific covariates, and select +the estimation algorithm and type of mark model. 'ldmppr' estimates the +process and mark models and allows you to check the appropriateness of the +model using a variety of diagnostic tools. Once a satisfactory model fit +is obtained, you can simulate from the model and visualize the results. +Documentation for the package 'ldmppr' is available in the form of a +vignette. + +%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-migraph.spec b/specs/R-CRAN-migraph.spec index 4d9ae15a4..5a86fd47b 100644 --- a/specs/R-CRAN-migraph.spec +++ b/specs/R-CRAN-migraph.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname migraph -%global packver 1.4.3 +%global packver 1.4.5 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.4.3 +Version: 1.4.5 Release: 1%{?dist}%{?buildtag} Summary: Univariate and Multivariate Tests for Multimodal and Other Networks diff --git a/specs/R-CRAN-mixgb.spec b/specs/R-CRAN-mixgb.spec index 365a581b1..2795efbf8 100644 --- a/specs/R-CRAN-mixgb.spec +++ b/specs/R-CRAN-mixgb.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname mixgb -%global packver 1.0.2 +%global packver 1.5.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.0.2 +Version: 1.5.2 Release: 1%{?dist}%{?buildtag} Summary: Multiple Imputation Through 'XGBoost' @@ -14,43 +14,35 @@ 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-devel >= 3.6.0 +Requires: R-core >= 3.6.0 +BuildRequires: R-CRAN-xgboost >= 1.7.5.1 BuildRequires: R-CRAN-data.table -BuildRequires: R-CRAN-ggplot2 BuildRequires: R-CRAN-Matrix BuildRequires: R-CRAN-mice +BuildRequires: R-CRAN-Rcpp BuildRequires: R-CRAN-Rfast -BuildRequires: R-CRAN-rlang -BuildRequires: R-CRAN-scales BuildRequires: R-stats -BuildRequires: R-CRAN-tidyr BuildRequires: R-utils -BuildRequires: R-CRAN-xgboost +BuildRequires: R-CRAN-magrittr +BuildRequires: R-CRAN-RcppArmadillo +Requires: R-CRAN-xgboost >= 1.7.5.1 Requires: R-CRAN-data.table -Requires: R-CRAN-ggplot2 Requires: R-CRAN-Matrix Requires: R-CRAN-mice +Requires: R-CRAN-Rcpp Requires: R-CRAN-Rfast -Requires: R-CRAN-rlang -Requires: R-CRAN-scales Requires: R-stats -Requires: R-CRAN-tidyr Requires: R-utils -Requires: R-CRAN-xgboost +Requires: R-CRAN-magrittr %description Multiple imputation using 'XGBoost', subsampling, and predictive mean -matching as described in Deng and Lumley (2023) . Our -method utilizes the capabilities of XGBoost, a highly efficient -implementation of gradient boosted trees, to capture interactions and -non-linear relations automatically. Moreover, we have integrated -subsampling and predictive mean matching to minimize bias and reflect -appropriate imputation variability. This package supports various types of -variables and offers flexible settings for subsampling and predictive mean -matching. Additionally, it includes diagnostic tools for evaluating the -quality of the imputed values. +matching as described in Deng and Lumley (2023) +. The package supports various types +of variables, offers flexible settings, and enables saving an imputation +model to impute new data. Data processing and memory usage have been +optimised to speed up the imputation process. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-mlr3benchmark.spec b/specs/R-CRAN-mlr3benchmark.spec index ac1b24f02..cd3bcfe24 100644 --- a/specs/R-CRAN-mlr3benchmark.spec +++ b/specs/R-CRAN-mlr3benchmark.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname mlr3benchmark -%global packver 0.1.6 +%global packver 0.1.7 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.6 +Version: 0.1.7 Release: 1%{?dist}%{?buildtag} Summary: Analysis and Visualisation of Benchmark Experiments diff --git a/specs/R-CRAN-multibias.spec b/specs/R-CRAN-multibias.spec index 0900beb9d..4e2d9bd42 100644 --- a/specs/R-CRAN-multibias.spec +++ b/specs/R-CRAN-multibias.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname multibias -%global packver 1.6 +%global packver 1.6.1 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.6 +Version: 1.6.1 Release: 1%{?dist}%{?buildtag} Summary: Simultaneous Multi-Bias Adjustment diff --git a/specs/R-CRAN-nanonext.spec b/specs/R-CRAN-nanonext.spec index 30395c5d3..bffa208f3 100644 --- a/specs/R-CRAN-nanonext.spec +++ b/specs/R-CRAN-nanonext.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname nanonext -%global packver 1.3.2 +%global packver 1.4.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.3.2 +Version: 1.4.0 Release: 1%{?dist}%{?buildtag} Summary: NNG (Nanomsg Next Gen) Lightweight Messaging Library diff --git a/specs/R-CRAN-nipals.spec b/specs/R-CRAN-nipals.spec index 068ded987..42cbb789f 100644 --- a/specs/R-CRAN-nipals.spec +++ b/specs/R-CRAN-nipals.spec @@ -1,14 +1,15 @@ %global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi %global packname nipals -%global packver 0.8 +%global packver 1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.8 +Version: 1.0 Release: 1%{?dist}%{?buildtag} Summary: Principal Components Analysis using NIPALS or Weighted EMPCA, with Gram-Schmidt Orthogonalization -License: GPL-3 +License: MIT + file LICENSE URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz diff --git a/specs/R-CRAN-orthGS.spec b/specs/R-CRAN-orthGS.spec new file mode 100644 index 000000000..bb9522379 --- /dev/null +++ b/specs/R-CRAN-orthGS.spec @@ -0,0 +1,66 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname orthGS +%global packver 0.1.6 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.1.6 +Release: 1%{?dist}%{?buildtag} +Summary: Orthology vs Paralogy Relationships among Glutamine Synthetase from Plants + +License: GPL (>= 2) +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-ape +BuildRequires: R-CRAN-bio3d +BuildRequires: R-CRAN-castor +BuildRequires: R-CRAN-igraph +BuildRequires: R-CRAN-phangorn +BuildRequires: R-CRAN-phytools +BuildRequires: R-CRAN-seqinr +BuildRequires: R-CRAN-TreeTools +Requires: R-CRAN-ape +Requires: R-CRAN-bio3d +Requires: R-CRAN-castor +Requires: R-CRAN-igraph +Requires: R-CRAN-phangorn +Requires: R-CRAN-phytools +Requires: R-CRAN-seqinr +Requires: R-CRAN-TreeTools + +%description +Tools to analyze and infer orthology and paralogy relationships between +glutamine synthetase proteins in seed plants. + +%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-partykit.spec b/specs/R-CRAN-partykit.spec index ae373413c..f2b9bb680 100644 --- a/specs/R-CRAN-partykit.spec +++ b/specs/R-CRAN-partykit.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname partykit -%global packver 1.2-22 +%global packver 1.2-23 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.2.22 +Version: 1.2.23 Release: 1%{?dist}%{?buildtag} Summary: A Toolkit for Recursive Partytioning diff --git a/specs/R-CRAN-pctax.spec b/specs/R-CRAN-pctax.spec index b4d31c905..884fb64ca 100644 --- a/specs/R-CRAN-pctax.spec +++ b/specs/R-CRAN-pctax.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname pctax -%global packver 0.1.1 +%global packver 0.1.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.1 +Version: 0.1.3 Release: 1%{?dist}%{?buildtag} Summary: Professional Comprehensive Omics Data Analysis @@ -14,8 +14,8 @@ URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz -BuildRequires: R-devel >= 4.1.0 -Requires: R-core >= 4.1.0 +BuildRequires: R-devel >= 4.2.0 +Requires: R-core >= 4.2.0 BuildArch: noarch BuildRequires: R-CRAN-ggplot2 >= 3.2.0 BuildRequires: R-CRAN-pcutils >= 0.2.5 diff --git a/specs/R-CRAN-pikchr.spec b/specs/R-CRAN-pikchr.spec index 1d51dfd42..7305c5a97 100644 --- a/specs/R-CRAN-pikchr.spec +++ b/specs/R-CRAN-pikchr.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname pikchr -%global packver 0.97 +%global packver 1.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.97 +Version: 1.0 Release: 1%{?dist}%{?buildtag} Summary: R Wrapper for 'pikchr' (PIC) Diagram Language @@ -14,8 +14,9 @@ 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 >= 4.0 +Requires: R-core >= 4.0 +BuildRequires: R-CRAN-dplyr BuildRequires: R-CRAN-knitr BuildRequires: R-CRAN-brio BuildRequires: R-CRAN-htmltools @@ -23,6 +24,7 @@ BuildRequires: R-CRAN-rlang BuildRequires: R-CRAN-purrr BuildRequires: R-CRAN-stringr BuildRequires: R-CRAN-rsvg +Requires: R-CRAN-dplyr Requires: R-CRAN-knitr Requires: R-CRAN-brio Requires: R-CRAN-htmltools diff --git a/specs/R-CRAN-pipeflow.spec b/specs/R-CRAN-pipeflow.spec new file mode 100644 index 000000000..3b34630c0 --- /dev/null +++ b/specs/R-CRAN-pipeflow.spec @@ -0,0 +1,68 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname pipeflow +%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: Implement Data Analysis Workflows with Pipelines + +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-data.table +BuildRequires: R-CRAN-jsonlite +BuildRequires: R-CRAN-lgr +BuildRequires: R-methods +BuildRequires: R-CRAN-R6 +BuildRequires: R-stats +BuildRequires: R-utils +Requires: R-CRAN-data.table +Requires: R-CRAN-jsonlite +Requires: R-CRAN-lgr +Requires: R-methods +Requires: R-CRAN-R6 +Requires: R-stats +Requires: R-utils + +%description +A lightweight yet powerful framework for creating data analysis pipelines. +You build your pipelines simply by defining a sequence of R functions and +'pipeflow' takes care of tracking dependencies among steps and managing +all the analysis parameters. The framework is easy to get started with for +the typical R user, but also provides advanced features to enable complex +workflows. + +%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-qs2.spec b/specs/R-CRAN-qs2.spec index 546665ee1..e7cd22626 100644 --- a/specs/R-CRAN-qs2.spec +++ b/specs/R-CRAN-qs2.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname qs2 -%global packver 0.1.2 +%global packver 0.1.3 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.1.2 +Version: 0.1.3 Release: 1%{?dist}%{?buildtag} Summary: Efficient Serialization of R Objects diff --git a/specs/R-CRAN-quickcode.spec b/specs/R-CRAN-quickcode.spec index 811ca83e6..d6b6c15e8 100644 --- a/specs/R-CRAN-quickcode.spec +++ b/specs/R-CRAN-quickcode.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname quickcode -%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: Quick and Essential 'R' Tricks for Better Scripts diff --git a/specs/R-CRAN-rSPDE.spec b/specs/R-CRAN-rSPDE.spec index d4c4abde8..deda4882b 100644 --- a/specs/R-CRAN-rSPDE.spec +++ b/specs/R-CRAN-rSPDE.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname rSPDE -%global packver 2.3.3 +%global packver 2.4.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 2.3.3 +Version: 2.4.0 Release: 1%{?dist}%{?buildtag} Summary: Rational Approximations of Fractional Stochastic Partial Differential Equations @@ -17,16 +17,16 @@ 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-fmesher >= 0.2.0 BuildRequires: R-CRAN-Matrix BuildRequires: R-stats BuildRequires: R-methods -BuildRequires: R-CRAN-fmesher BuildRequires: R-CRAN-lifecycle BuildRequires: R-CRAN-broom +Requires: R-CRAN-fmesher >= 0.2.0 Requires: R-CRAN-Matrix Requires: R-stats Requires: R-methods -Requires: R-CRAN-fmesher Requires: R-CRAN-lifecycle Requires: R-CRAN-broom diff --git a/specs/R-CRAN-rospca.spec b/specs/R-CRAN-rospca.spec index 8775dd1ab..7b9dd81e7 100644 --- a/specs/R-CRAN-rospca.spec +++ b/specs/R-CRAN-rospca.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname rospca -%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: Robust Sparse PCA using the ROSPCA Algorithm diff --git a/specs/R-CRAN-samplezoo.spec b/specs/R-CRAN-samplezoo.spec index dd5933f24..c48725ebe 100644 --- a/specs/R-CRAN-samplezoo.spec +++ b/specs/R-CRAN-samplezoo.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname samplezoo -%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: Generate Samples with a Variety of Probability Distributions @@ -19,15 +19,11 @@ Requires: R-core BuildArch: noarch %description -The 'samplezoo' package streamlines the process of generating samples from -various probability distributions, enabling users to quickly create data -frames for demonstrations, troubleshooting, or teaching. By prioritizing -simplicity and efficiency,'samplezoo' reduces the need for repetitive -code, making it particularly useful for beginners or anyone seeking to -save time. The package implements standard methods for generating random -samples from probability distributions commonly available in base R, with -no specific external references. For more details, visit the package -documentation. +Simplifies the process of generating samples from a variety of probability +distributions, allowing users to quickly create data frames for +demonstrations, troubleshooting, or teaching purposes. Data is available +in multiple sizes—small, medium, and large. For more information, refer to +the package documentation. %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-scR.spec b/specs/R-CRAN-scR.spec new file mode 100644 index 000000000..015fb5c8b --- /dev/null +++ b/specs/R-CRAN-scR.spec @@ -0,0 +1,70 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname scR +%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: Estimate Vapnik-Chervonenkis Dimension and Sample Complexity + +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-parallel +BuildRequires: R-CRAN-pbapply +BuildRequires: R-CRAN-caret +BuildRequires: R-CRAN-dplyr +BuildRequires: R-CRAN-tidyr +BuildRequires: R-CRAN-ggplot2 +BuildRequires: R-CRAN-plotly +Requires: R-parallel +Requires: R-CRAN-pbapply +Requires: R-CRAN-caret +Requires: R-CRAN-dplyr +Requires: R-CRAN-tidyr +Requires: R-CRAN-ggplot2 +Requires: R-CRAN-plotly + +%description +We provide a suite of tools for estimating the sample complexity of a +chosen model through theoretical bounds and simulation. The package +incorporates methods for estimating the Vapnik-Chervonenkis dimension +(VCD) of a chosen algorithm, which can be used to estimate its sample +complexity. Alternatively, we provide simulation methods to estimate +sample complexity directly. For more details, see Carter, P & Choi, D +(2024). "Learning from Noise: Applying Sample Complexity for Political +Science Research" . + +%prep +%setup -q -c -n %{packname} + +# fix end of executable files +find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \; +# prevent binary stripping +[ -d %{packname}/src ] && find %{packname}/src -type f -exec \ + sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true +[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \ + sed -i 's@-g0@@g' {} \; || true +# don't allow local prefix in executable scripts +find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \; + +%build + +%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-smurf.spec b/specs/R-CRAN-smurf.spec index aac870abe..0cf7306f8 100644 --- a/specs/R-CRAN-smurf.spec +++ b/specs/R-CRAN-smurf.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname smurf -%global packver 1.1.5 +%global packver 1.1.6 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.1.5 +Version: 1.1.6 Release: 1%{?dist}%{?buildtag} Summary: Sparse Multi-Type Regularized Feature Modeling diff --git a/specs/R-CRAN-spatialreg.spec b/specs/R-CRAN-spatialreg.spec index e7c2c1c31..c10a7c5f9 100644 --- a/specs/R-CRAN-spatialreg.spec +++ b/specs/R-CRAN-spatialreg.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname spatialreg -%global packver 1.3-5 +%global packver 1.3-6 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.3.5 +Version: 1.3.6 Release: 1%{?dist}%{?buildtag} Summary: Spatial Regression Analysis @@ -64,7 +64,9 @@ provided by 'Bivand', 'Millo' and 'Piras' (2021) . 'spatialreg' >= 1.1-* corresponded to 'spdep' >= 1.1-1, in which the model fitting functions were deprecated and passed through to 'spatialreg', but masked those in 'spatialreg'. From versions -1.2-*, the functions have been made defunct in 'spdep'. +1.2-*, the functions have been made defunct in 'spdep'. From version +1.3-6, add Anselin-Kelejian (1997) test to `stsls` for residual spatial +autocorrelation . %prep %setup -q -c -n %{packname} diff --git a/specs/R-CRAN-spdep.spec b/specs/R-CRAN-spdep.spec index 6a7c4bc29..ddaf0b329 100644 --- a/specs/R-CRAN-spdep.spec +++ b/specs/R-CRAN-spdep.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname spdep -%global packver 1.3-7 +%global packver 1.3-8 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.3.7 +Version: 1.3.8 Release: 1%{?dist}%{?buildtag} Summary: Spatial Dependence: Weighting Schemes, Statistics @@ -70,7 +70,10 @@ these measures is described in 'Bivand' and 'Wong' (2018) dependence in linear models are provided ('Anselin et al'. 1996) , as are 'Rao' score tests for hypothesised spatial 'Durbin' models based on linear models ('Koley' and -'Bera' 2023) . From 'spdep' and +'Bera' 2023) . A local indicators for +categorical data (LICD) implementation based on 'Carrer et al.' (2021) + and 'Bivand et al.' (2017) + was added in 1.3-7. From 'spdep' and 'spatialreg' versions >= 1.2-1, the model fitting functions previously present in this package are defunct in 'spdep' and may be found in 'spatialreg'. diff --git a/specs/R-CRAN-statsExpressions.spec b/specs/R-CRAN-statsExpressions.spec index cd60868e6..1f238c46e 100644 --- a/specs/R-CRAN-statsExpressions.spec +++ b/specs/R-CRAN-statsExpressions.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname statsExpressions -%global packver 1.6.1 +%global packver 1.6.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.6.1 +Version: 1.6.2 Release: 1%{?dist}%{?buildtag} Summary: Tidy Dataframes and Expressions with Statistical Details @@ -14,11 +14,11 @@ URL: https://cran.r-project.org/package=%{packname} Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz -BuildRequires: R-devel >= 4.1.0 -Requires: R-core >= 4.1.0 +BuildRequires: R-devel >= 4.3.0 +Requires: R-core >= 4.3.0 BuildArch: noarch -BuildRequires: R-CRAN-tibble >= 3.2.1 BuildRequires: R-CRAN-withr >= 3.0.2 +BuildRequires: R-CRAN-rstantools >= 2.4.0 BuildRequires: R-CRAN-magrittr >= 2.0.3 BuildRequires: R-CRAN-PMCMRplus >= 1.9.12 BuildRequires: R-CRAN-glue >= 1.8.0 @@ -28,18 +28,18 @@ BuildRequires: R-CRAN-WRS2 >= 1.1.6 BuildRequires: R-CRAN-dplyr >= 1.1.4 BuildRequires: R-CRAN-rlang >= 1.1.4 BuildRequires: R-CRAN-purrr >= 1.0.2 +BuildRequires: R-CRAN-insight >= 1.0.0 BuildRequires: R-CRAN-BayesFactor >= 0.9.12.4.7 BuildRequires: R-CRAN-effectsize >= 0.8.9 BuildRequires: R-CRAN-correlation >= 0.8.6 -BuildRequires: R-CRAN-parameters >= 0.23.0 -BuildRequires: R-CRAN-insight >= 0.20.5 +BuildRequires: R-CRAN-parameters >= 0.24.0 BuildRequires: R-CRAN-bayestestR >= 0.15.0 BuildRequires: R-CRAN-datawizard >= 0.13.0 BuildRequires: R-CRAN-performance >= 0.12.4 BuildRequires: R-CRAN-zeallot >= 0.1.0 BuildRequires: R-stats -Requires: R-CRAN-tibble >= 3.2.1 Requires: R-CRAN-withr >= 3.0.2 +Requires: R-CRAN-rstantools >= 2.4.0 Requires: R-CRAN-magrittr >= 2.0.3 Requires: R-CRAN-PMCMRplus >= 1.9.12 Requires: R-CRAN-glue >= 1.8.0 @@ -49,11 +49,11 @@ Requires: R-CRAN-WRS2 >= 1.1.6 Requires: R-CRAN-dplyr >= 1.1.4 Requires: R-CRAN-rlang >= 1.1.4 Requires: R-CRAN-purrr >= 1.0.2 +Requires: R-CRAN-insight >= 1.0.0 Requires: R-CRAN-BayesFactor >= 0.9.12.4.7 Requires: R-CRAN-effectsize >= 0.8.9 Requires: R-CRAN-correlation >= 0.8.6 -Requires: R-CRAN-parameters >= 0.23.0 -Requires: R-CRAN-insight >= 0.20.5 +Requires: R-CRAN-parameters >= 0.24.0 Requires: R-CRAN-bayestestR >= 0.15.0 Requires: R-CRAN-datawizard >= 0.13.0 Requires: R-CRAN-performance >= 0.12.4 diff --git a/specs/R-CRAN-survPen.spec b/specs/R-CRAN-survPen.spec index dd380216b..724bb00e5 100644 --- a/specs/R-CRAN-survPen.spec +++ b/specs/R-CRAN-survPen.spec @@ -1,13 +1,13 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname survPen -%global packver 1.6.0 +%global packver 2.0.0 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 1.6.0 +Version: 2.0.0 Release: 1%{?dist}%{?buildtag} -Summary: Multidimensional Penalized Splines for Survival and Net Survival Models +Summary: Multidimensional Penalized Splines for (Excess) Hazard Models, Relative Mortality Ratio Models and Marginal Intensity Models License: GPL-3 | file LICENSE URL: https://cran.r-project.org/package=%{packname} @@ -25,27 +25,32 @@ Requires: R-CRAN-statmod Requires: R-stats %description -Fits hazard and excess hazard models with multidimensional penalized -splines allowing for time-dependent effects, non-linear effects and -interactions between several continuous covariates. In survival and net -survival analysis, in addition to modelling the effect of time (via the -baseline hazard), one has often to deal with several continuous covariates -and model their functional forms, their time-dependent effects, and their -interactions. Model specification becomes therefore a complex problem and -penalized regression splines represent an appealing solution to that -problem as splines offer the required flexibility while penalization -limits overfitting issues. Current implementations of penalized survival -models can be slow or unstable and sometimes lack some key features like -taking into account expected mortality to provide net survival and excess -hazard estimates. In contrast, survPen provides an automated, fast, and -stable implementation (thanks to explicit calculation of the derivatives -of the likelihood) and offers a unified framework for multidimensional -penalized hazard and excess hazard models. survPen may be of interest to -those who 1) analyse any kind of time-to-event data: mortality, disease -relapse, machinery breakdown, unemployment, etc 2) wish to describe the -associated hazard and to understand which predictors impact its dynamics. -See Fauvernier et al. (2019a) for an overview of -the package and Fauvernier et al. (2019b) for the +Fits (excess) hazard, relative mortality ratio or marginal intensity +models with multidimensional penalized splines allowing for time-dependent +effects, non-linear effects and interactions between several continuous +covariates. In survival and net survival analysis, in addition to +modelling the effect of time (via the baseline hazard), one has often to +deal with several continuous covariates and model their functional forms, +their time-dependent effects, and their interactions. Model specification +becomes therefore a complex problem and penalized regression splines +represent an appealing solution to that problem as splines offer the +required flexibility while penalization limits overfitting issues. Current +implementations of penalized survival models can be slow or unstable and +sometimes lack some key features like taking into account expected +mortality to provide net survival and excess hazard estimates. In +contrast, survPen provides an automated, fast, and stable implementation +(thanks to explicit calculation of the derivatives of the likelihood) and +offers a unified framework for multidimensional penalized hazard and +excess hazard models. Later versions (>2.0.0) include penalized models for +relative mortality ratio, and marginal intensity in recurrent event +setting. survPen may be of interest to those who 1) analyse any kind of +time-to-event data: mortality, disease relapse, machinery breakdown, +unemployment, etc 2) wish to describe the associated hazard and to +understand which predictors impact its dynamics, 3) wish to model the +relative mortality ratio between a cohort and a reference population, 4) +wish to describe the marginal intensity for recurrent event data. See +Fauvernier et al. (2019a) for an overview of the +package and Fauvernier et al. (2019b) for the method. %prep diff --git a/specs/R-CRAN-tidyfinance.spec b/specs/R-CRAN-tidyfinance.spec index 491b92b0f..007515872 100644 --- a/specs/R-CRAN-tidyfinance.spec +++ b/specs/R-CRAN-tidyfinance.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname tidyfinance -%global packver 0.4.1 +%global packver 0.4.2 %global rlibdir /usr/local/lib/R/library Name: R-CRAN-%{packname} -Version: 0.4.1 +Version: 0.4.2 Release: 1%{?dist}%{?buildtag} Summary: Tidy Finance Helper Functions diff --git a/specs/R-CRAN-twc.spec b/specs/R-CRAN-twc.spec new file mode 100644 index 000000000..4f082fd7b --- /dev/null +++ b/specs/R-CRAN-twc.spec @@ -0,0 +1,75 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname twc +%global packver 0.0.1 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 0.0.1 +Release: 1%{?dist}%{?buildtag} +Summary: Terrestrial Water Cycle + +License: GPL-3 +URL: https://cran.r-project.org/package=%{packname} +Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz + + +BuildRequires: R-devel >= 4.0.0 +Requires: R-core >= 4.0.0 +BuildArch: noarch +BuildRequires: R-CRAN-data.table +BuildRequires: R-CRAN-doParallel +BuildRequires: R-CRAN-foreach +BuildRequires: R-CRAN-lubridate +BuildRequires: R-CRAN-magrittr +BuildRequires: R-methods +BuildRequires: R-CRAN-ncdf4 +BuildRequires: R-parallel +BuildRequires: R-CRAN-raster +BuildRequires: R-CRAN-sf +BuildRequires: R-CRAN-sp +BuildRequires: R-utils +Requires: R-CRAN-data.table +Requires: R-CRAN-doParallel +Requires: R-CRAN-foreach +Requires: R-CRAN-lubridate +Requires: R-CRAN-magrittr +Requires: R-methods +Requires: R-CRAN-ncdf4 +Requires: R-parallel +Requires: R-CRAN-raster +Requires: R-CRAN-sf +Requires: R-CRAN-sp +Requires: R-utils + +%description +An open-access tool/framework that constitutes the core functions to +analyze terrestrial water cycle data across various spatio-temporal +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-wdiEF.spec b/specs/R-CRAN-wdiEF.spec new file mode 100644 index 000000000..107f21ab5 --- /dev/null +++ b/specs/R-CRAN-wdiEF.spec @@ -0,0 +1,58 @@ +%global __brp_check_rpaths %{nil} +%global __requires_exclude ^libmpi +%global packname wdiEF +%global packver 1.0.2 +%global rlibdir /usr/local/lib/R/library + +Name: R-CRAN-%{packname} +Version: 1.0.2 +Release: 1%{?dist}%{?buildtag} +Summary: Calculation of the Water Deficit Index (WDI) and the Evaporative Fraction (EF) on Rasters + +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-dplyr +BuildRequires: R-stats +BuildRequires: R-CRAN-terra +Requires: R-CRAN-dplyr +Requires: R-stats +Requires: R-CRAN-terra + +%description +Calculates the Water Deficit Index (WDI) and the Evaporative Fraction (EF) +using geospatial data, such as fractional vegetation cover (FVC) and +surface-air temperature difference (TS-TA). Terms like "raster", "CRS" are +part of standard geospatial terminology. + +%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-webdav.spec b/specs/R-CRAN-webdav.spec index 6065b0631..4cd9b5d9f 100644 --- a/specs/R-CRAN-webdav.spec +++ b/specs/R-CRAN-webdav.spec @@ -1,11 +1,11 @@ %global __brp_check_rpaths %{nil} %global __requires_exclude ^libmpi %global packname webdav -%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: A Simple Interface for Interacting with 'WebDAV' Servers