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| Original file line number | Diff line number | Diff line change |
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| %global __brp_check_rpaths %{nil} | ||
| %global __requires_exclude ^libmpi | ||
| %global packname BioTIMEr | ||
| %global packver 0.2.3 | ||
| %global rlibdir /usr/local/lib/R/library | ||
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| Name: R-CRAN-%{packname} | ||
| Version: 0.2.3 | ||
| Release: 1%{?dist}%{?buildtag} | ||
| Summary: Tools to Use and Explore the 'BioTIME' Database | ||
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| License: MIT + file LICENSE | ||
| URL: https://cran.r-project.org/package=%{packname} | ||
| Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz | ||
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| BuildRequires: R-devel >= 3.5.0 | ||
| Requires: R-core >= 3.5.0 | ||
| BuildArch: noarch | ||
| BuildRequires: R-CRAN-dggridR >= 3.1.0 | ||
| BuildRequires: R-CRAN-dplyr | ||
| BuildRequires: R-CRAN-tidyr | ||
| BuildRequires: R-CRAN-ggplot2 | ||
| BuildRequires: R-CRAN-vegan | ||
| BuildRequires: R-CRAN-checkmate | ||
| Requires: R-CRAN-dggridR >= 3.1.0 | ||
| Requires: R-CRAN-dplyr | ||
| Requires: R-CRAN-tidyr | ||
| Requires: R-CRAN-ggplot2 | ||
| Requires: R-CRAN-vegan | ||
| Requires: R-CRAN-checkmate | ||
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| %description | ||
| The 'BioTIME' database was first published in 2018 and inspired ideas, | ||
| questions, project and research article. To make it even more accessible, | ||
| an R package was created. The 'BioTIMEr' package provides tools designed | ||
| to interact with the 'BioTIME' database. The functions provided include | ||
| the 'BioTIME' recommended methods for preparing (gridding and rarefaction) | ||
| time series data, a selection of standard biodiversity metrics (including | ||
| species richness, numerical abundance and exponential Shannon) alongside | ||
| examples on how to display change over time. It also includes a sample | ||
| subset of both the query and meta data, the full versions of which are | ||
| freely available on the 'BioTIME' website | ||
| <https://biotime.st-andrews.ac.uk/home.php>. | ||
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| %prep | ||
| %setup -q -c -n %{packname} | ||
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| # 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' {} \; | ||
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| %build | ||
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| %install | ||
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| 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" {} \; | ||
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| %files | ||
| %{rlibdir}/%{packname} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| %global __brp_check_rpaths %{nil} | ||
| %global __requires_exclude ^libmpi | ||
| %global packname LifemapR | ||
| %global packver 1.1.4 | ||
| %global rlibdir /usr/local/lib/R/library | ||
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| Name: R-CRAN-%{packname} | ||
| Version: 1.1.4 | ||
| Release: 1%{?dist}%{?buildtag} | ||
| Summary: Data Visualisation on 'Lifemap' Tree | ||
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| License: MIT + file LICENSE | ||
| URL: https://cran.r-project.org/package=%{packname} | ||
| Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz | ||
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| BuildRequires: R-devel >= 3.5.0 | ||
| Requires: R-core >= 3.5.0 | ||
| BuildArch: noarch | ||
| BuildRequires: R-CRAN-leaflet | ||
| BuildRequires: R-CRAN-shiny | ||
| BuildRequires: R-CRAN-jsonlite | ||
| BuildRequires: R-CRAN-dplyr | ||
| BuildRequires: R-CRAN-tidyr | ||
| BuildRequires: R-CRAN-leaflet.minicharts | ||
| BuildRequires: R-CRAN-htmltools | ||
| BuildRequires: R-CRAN-rlang | ||
| BuildRequires: R-CRAN-RCurl | ||
| BuildRequires: R-CRAN-fastmatch | ||
| Requires: R-CRAN-leaflet | ||
| Requires: R-CRAN-shiny | ||
| Requires: R-CRAN-jsonlite | ||
| Requires: R-CRAN-dplyr | ||
| Requires: R-CRAN-tidyr | ||
| Requires: R-CRAN-leaflet.minicharts | ||
| Requires: R-CRAN-htmltools | ||
| Requires: R-CRAN-rlang | ||
| Requires: R-CRAN-RCurl | ||
| Requires: R-CRAN-fastmatch | ||
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| %description | ||
| Allow to visualise data on the NCBI phylogenetic tree as presented in | ||
| Lifemap <http://lifemap.univ-lyon1.fr/>. It takes as input a dataframe | ||
| with at least a "taxid" column containing NCBI format TaxIds and allows to | ||
| draw multiple layers with different visualisation tools. | ||
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| %prep | ||
| %setup -q -c -n %{packname} | ||
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| # 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' {} \; | ||
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| %build | ||
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| %install | ||
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| 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} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| %global __brp_check_rpaths %{nil} | ||
| %global __requires_exclude ^libmpi | ||
| %global packname PDXpower | ||
| %global packver 1.0.3 | ||
| %global rlibdir /usr/local/lib/R/library | ||
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| Name: R-CRAN-%{packname} | ||
| Version: 1.0.3 | ||
| Release: 1%{?dist}%{?buildtag} | ||
| Summary: Time to Event Outcome in Experimental Designs of Pre-Clinical Studies | ||
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| License: GPL (>= 2) | ||
| URL: https://cran.r-project.org/package=%{packname} | ||
| Source0: %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz | ||
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| BuildRequires: R-devel >= 3.5.0 | ||
| Requires: R-core >= 3.5.0 | ||
| BuildArch: noarch | ||
| BuildRequires: R-CRAN-survival | ||
| BuildRequires: R-stats | ||
| BuildRequires: R-parallel | ||
| BuildRequires: R-CRAN-nlme | ||
| BuildRequires: R-CRAN-ggplot2 | ||
| BuildRequires: R-CRAN-ggpubr | ||
| BuildRequires: R-CRAN-frailtypack | ||
| Requires: R-CRAN-survival | ||
| Requires: R-stats | ||
| Requires: R-parallel | ||
| Requires: R-CRAN-nlme | ||
| Requires: R-CRAN-ggplot2 | ||
| Requires: R-CRAN-ggpubr | ||
| Requires: R-CRAN-frailtypack | ||
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| %description | ||
| Conduct simulation-based customized power calculation for clustered time | ||
| to event data in a mixed crossed/nested design, where a number of cell | ||
| lines and a number of mice within each cell line are considered to achieve | ||
| a desired statistical power, motivated by Eckel-Passow and colleagues | ||
| (2021) <doi:10.1093/neuonc/noab137> and Li and colleagues (2024) | ||
| <doi:10.48550/arXiv.2404.08927>. This package provides two commonly used | ||
| models for powering a design, linear mixed effects and Cox frailty model. | ||
| Both models account for within-subject (cell line) correlation while | ||
| holding different distributional assumptions about the outcome. | ||
| Alternatively, the counterparts of fixed effects model are also available, | ||
| which produces similar estimates of statistical power. | ||
|
|
||
| %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} |
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