pkgdb.csv

name,build,run,revised,comment
a5R,,,FALSE,"Cargo (Rust's package manager), rustc"
abba,,,FALSE,"kubectl (optional, for Kubernetes backend), SLURM(optional, sbatch/scontrol/sacct/squeue for SLURM backend),Posit Workbench (optional, for Workbench backend)"
abn,cmake gsl libjpeg gdal geos proj udunits openssl curl jags,,TRUE,"pkg-config, cmake, gsl, jpeg, gdal, geos, proj,udunits-2, openssl, libcurl, jags"
accessr,,,TRUE,"OfficeToPDF -https://github.com/cognidox/OfficeToPDF, pandoc -https://pandoc.org"
acro,,,TRUE,Python
adaR,,,FALSE,GCC(or Clang withequivalent  support)
adbcpostgresql,postgresql,,FALSE,libpq
adbcsqlite,sqlite,,FALSE,SQLite3
adimpro,,imagemagick-bin dcraw,TRUE,"Image Magick (for reading non PPM format), dcraw(for reading RAW images)."
adlaplace,,,FALSE,OpenMP
admetshiny,,,FALSE,Java; only required for the optionalCDK-based descriptor calculation (rcdk) module.
admisc,,,FALSE,POSIX threads
AdmixPoly,,,FALSE,A system with a C++ compiler supporting OpenMP
admixr,,,TRUE,ADMIXTOOLS suite of command-line utilities forpopulation genetics. See<https://github.com/dreichlab/admixtools> for the most recentinstallation instructions and further information.
AFR,,,TRUE,
agenticr,,,FALSE,"ripgrep (optional, for fast file search; installwith 'winget install BurntSushi.ripgrep.MSVC' on Windows or seehttps://github.com/BurntSushi/ripgrep)"
AgePopDenom,,,TRUE,TMB
agregR,,,TRUE,CmdStan(https://mc-stan.org/users/interfaces/cmdstan)
ahocorasick,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
aifeducation,,,TRUE,"PyTorch (see vignette ""Get started"")"
alfr,,,TRUE,Alfresco Content Repository (Community orEnterprise)
AlphaSDM,,,FALSE,Python with the 'earthengine-api' module;'reticulate' installs it automatically when needed.
altair,,,TRUE,"Python, (Python) Altair,vega_datasets. To use image functions for MacOS: X11"
altmeta,,,TRUE,JAGSx.y (http://mcmc-jags.sourceforge.net)
AMAPVox,,java-bin,TRUE,
animation,,tex-latex ffmpeg-bin,TRUE,ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org) or LyX(http://www.lyx.org) for saveGIF(); (PDF)LaTeX for saveLatex();SWF Tools (http://swftools.org) for saveSWF(); FFmpeg(http://ffmpeg.org) or avconv (https://libav.org/avconv.html)for saveVideo()
animl,,,FALSE,"Python, animl-py"
anotherSAS7bdat,,,FALSE,"POSIX threads, iconv"
anticlust,,,TRUE,Rendering the vignette requires pandoc(<https://pandoc.org/>).
apache.sedona,,,TRUE,'Apache Spark'x
apathe,,,TRUE,"Rendering the document template requires pandoc; https://pandoc.org) and for PDFs a TeX distribution, suchas TinyTeX; https://yihui.org/tinytex/)"
apcf,geos,,TRUE,GEOS
APRScenario,,,TRUE,LAPACK
arcgis,,,TRUE,"Cargo (Rust's package manager), rustc"
arcgisgeocode,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
arcgisplaces,cargo openssl,,TRUE,"Cargo (Rust's package manager), rustc, OpenSSL"
arcgisutils,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
archive,libarchive,,TRUE,"libarchive: libarchive-dev (deb), libarchive-devel(rpm), libarchive (homebrew), libarchive_dev (csw)"
arcpbf,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
arcpy,,,TRUE,"Conda, ArcGIS Pro"
ardea,,,FALSE,"OpenCL,"
argparse,,python3,TRUE,python
arity,,,FALSE,"Cargo (Rust's package manager), rustc"
arrangements,gmp,,TRUE,gmp
arrow,arrow curl openssl,,FALSE,"for AWS S3 support on Linux, libcurl andopenssl, and libxml2 for Azure (optional); cmake(build-time only, and only for full source build)"
artma,jags,,TRUE,
arulesCBA,,java-bin,TRUE,Java
arulesNBMiner,,java-bin,TRUE,Java
asbio,xvfb,bwidget,TRUE,BWidget
asleep,,,FALSE,"Python, 'asleep' Python module"
asremlPlus,,,TRUE,asreml
ast2ast,,,FALSE,Rtools on Windows
astgrepr,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
AsyPeer,,,FALSE,"Requires the OpenMP library for parallel computing.If the OpenMP library is not available, the code is executedsequentially, and a warning is printed."
atime,,,FALSE,git command line program for bisect
autoharp,,,TRUE,pandoc - http://pandoc.org
automerge,cargo,,FALSE,"'automerge-c', or Cargo (Rust's package manager)and rustcto build from package sources."
autonewsmd,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
autotab,,,FALSE,"Python; TensorFlow, <;Keras; TensorFlow Addons"
av,ffmpeg,,TRUE,"FFmpeg; with at least libx264 and lame(mp3) drivers. MacOS Homebrew: ffmpeg. Debian/Ubuntu:libavfilter-dev. Fedora/RHEL: either ffmpeg-devel fromhttps://rpmfusion.org (preferred), or libavfilter-free-develwhich is a more limited version available on Fedora/EPEL9."
AV1R,ffmpeg vulkan,,FALSE,"FFmpeg with 'libsvtav1', libvulkan-dev andglslc (optional, for GPU encoding on Linux), Vulkan SDK(optional, for GPU encoding on Windows)"
awdb,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
AWR,,,TRUE,AWS Java SDK (see README.md for more details)
b32,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
b64,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
babelwhale,,docker singularity,TRUE,Docker and/or Singularity
babette,,,TRUE,BEAST2 (https://www.beast2.org/)
bacenR,,,TRUE,qpdf
bacistool,,,TRUE,JAGS
BaHZING,,,TRUE,
baker,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
bamdit,,,TRUE,JAGS (seehttp://mcmc-jags.sourceforge.net)
bamm,,,TRUE,"GDAL: gdal-bin (deb), libgdal-dev (deb)or gdal-devel (rmp), GEOS, PROJ:libproj-dev (deb), sqlite3, ImageMagick++: imagemagick (deb),libmagic-dev (deb), libmagick++-dev (deb) orImageMagick-c++-devel (rpm) ImageMagick(http://imagemagick.org) or GraphicsMagick(http://www.graphicsmagick.org) or LyX (http://www.lyx.org) forsaveGIF(); (PDF)LaTeX for saveLatex(); SWF Tools(http://swftools.org) for saveSWF(); FFmpeg (http://ffmpeg.org)or avconv (https://libav.org/avconv.html) for saveVideo()"
bartMachine,,,FALSE,"Java, TornadoVM (if you want GPUoptimization)"
bartMachineJARs,,,TRUE,Java
basifoR,,,FALSE,Microsoft Access driver on Windows for Accessbackends; mdbtools on Unix-like systems
BayesCACE,,,TRUE,JAGSx.y (http://mcmc-jags.sourceforge.net)
bayescount,,,TRUE,JAGS (https://mcmc-jags.sourceforge.net)
BayesForge,,,FALSE,"Python, 'bayesforge' python library."
BayesGWQS,,,TRUE,JAGS
BayesianDEB,,,FALSE,CmdStan(https://mc-stan.org/users/interfaces/cmdstan)
BayesianInference,,,TRUE,"Python, 'BayesInference' python library."
bayesplot,,pandoc,FALSE,pandoc
BayesPostEst,,,TRUE,JAGS (http://mcmc-jags.sourceforge.io)
bayesQRsurvey,,,TRUE,"BLAS, LAPACK"
BayesTools,,,TRUE,JAGS(https://mcmc-jags.sourceforge.io/)
BayesVarSel,gsl,,TRUE,GNU Scientific Library
BayLum,,,TRUE,JAGS(https://mcmc-jags.sourceforge.io/)
bayprior,,,FALSE,"Quarto CLI, https://quarto.org)"
bbl,gsl,,TRUE,
BCFM,,,TRUE,pandoc for building vignettes
BCHM,,,TRUE,JAGS
BCodifSIS,,,FALSE,C99
bcputility,,,TRUE,bcp Utility
bdpar,,python3,TRUE,Pythonor
beastier,,,TRUE,BEAST2 (https://www.beast2.org/)
BeastJar,,,TRUE,Java
bedr,,,TRUE,"Preferred genomic operations engine: 'BEDTools','BEDOPS' and 'Tabix'."
BeQut,,,TRUE,JAGSx.y
bertopicr,,,TRUE,"Python; BERTopic and Python packages:sentence-transformers, umap-learn, hdbscan, scikit-learn"
bfw,,java-bin,TRUE,"JAGS<https://mcmc-jags.sourceforge.io>,Java JDK<https://www.java.com/en/download/manual.jsp>"
bgns,,,FALSE,optional OpenMP
bhmbasket,,,TRUE,JAGSx.y (http://mcmc-jags.sourceforge.net)
biblio,,pandoc,TRUE,pandoc - http://pandoc.org
BIDistances,,,FALSE,"OpenCL library (optional, for GPUacceleration), pandoc, needed for vignettes)"
bigGP,openmpi,openmpi-bin,TRUE,OpenMPI or MPICH2
bigMICE,,,TRUE,"Spark:x, orx"
bigPLSR,,,TRUE,Optional CBLAS (detected at compile time)
bigrquerystorage,protobuf,,TRUE,grpc/protobuf headers and compilers. For examplelibprotobuf-dev libgrpc++-dev protobuf-compiler-grpc (Debian)or protobuf-devel grpc-devel grpc-plugins (Fedora/RHEL)
bigsimr,,,TRUE,"Julia, Bigsimr.jl, Distributions.jl"
bigsnpr,,,TRUE,A few functions from package 'bigsnpr' wrapexisting software such as 'PLINK'<www.cog-genomics.org/plink2>. Functions are provided todownload these software. Note that these external softwaremight not work for some operating systems (e.g. 'PLINK' mightnot work on Solaris).
bioacoustics,cmake fftw,,TRUE,"fftw3,"
biocohort,,,FALSE,"CrossMap (optional, for the CrossMap liftoverbackend)"
bioimagetools,libtiff fftw curl openssl,,TRUE,tiff fftw libcurl openssl
biplotbootGUI,xvfb,bwidget,TRUE,Tcl/Tk package BWidget.
BiplotGUI,,,TRUE,windows
birp,,,FALSE,cmake
bittermelon,,,TRUE,'monobit' for reading/writing additional bitmapfont formats.
blandr,,,TRUE,pandoc
blastula,,,TRUE,pandoc - http://pandoc.org
blindreview,,,TRUE,
blogdown,,hugo,TRUE,Hugo (<https://gohugo.io>) and Pandoc(<https://pandoc.org>)
blosc,blosc,,TRUE,blosc: blosc-devel (rpm) or libblosc-dev (deb)
bnlearn,,,TRUE,USE_C17
BNSP,gsl,,TRUE,
bookdown,,,TRUE,Pandoc
bootStateSpace,,,TRUE,GNU GSL
botor,,,TRUE,Python and boto3(https://aws.amazon.com/sdk-for-python)
breathtestcore,,pandoc,TRUE,pandoc
breathteststan,,pandoc,TRUE,
brinton,,,TRUE,"Pandoc, web browser"
brms,,,TRUE,pngquant
bsam,,,TRUE,
bspm,,,TRUE,"systemd, dbus-python, PyGObject,python-(dnf|apt|alpm)"
bssm,,,TRUE,"pandoc, needed for vignettes)"
bsub,,,TRUE,"Platform LSF, bsub"
BTSPAS,,,TRUE,JAGS
BuildSys,,gdb,TRUE,"'Microsoft Visual Code', 'Rtools' on 'Windows','gdb' or 'lldb' depending on which OS"
buzzMed,,,FALSE,JAGS
cagedr,,,FALSE,libarchive (via the 'archive' package)
Cairo,cairo,,TRUE,cairohttp://www.cairographics.org/)
callme,,,TRUE,"Rtools (suitable for the installed R) for Windows,Xcode for Mac"
camtrapR,,exiftool,TRUE,ExifTool (https://exiftool.org/)
caracas,,,TRUE,Python
cartogramR,fftw,,TRUE,"FFTW; possible package: fftw-devel (rpm),libfftw3-dev (deb) or fftw (brew)."
cartography,gdal geos proj sqlite,,TRUE,
catmodeling,,,FALSE,xz
caugi,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
causact,,,TRUE,Python and numpyro are needed for Bayesianinference computations; python with header files andshared library; numpyrov0.12.1;https://https://num.pyro.ai/en/latest/index.html); arvizv0.15.1; https://https://python.arviz.org/en/stable/)
caviarpd,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
CBSr,,,TRUE,Java
cdtmbnma,,,FALSE,A working Stan backend through cmdstanr/CmdStan orrstan.
cgvR,,,FALSE,"C17,   pkg-config, libvulkan-dev(Linux) or LunarG 'Vulkan' 'SDK' (Windows, macOS), libglfw3-dev(Linux) or glfw via Homebrew (macOS), ffmpeg (optional, forcgv_record_*). Optional configure flags: --with-vulkan /--without-vulkan, --with-simd for SSE4.1 + PCLMUL fpng."
charr,,,FALSE,ICU4Cor(optional;bundled otherwise)
chicane,,,TRUE,bedtools
chopin,,,TRUE,netcdf
ChoR,,,TRUE,
chromote,,,TRUE,Google Chrome or other Chromium-based browser.chromium: chromium (rpm) or chromium-browser (deb)
churon,,,FALSE,"Cargo, rustc; ONNX Runtime(>=, optional at runtime)"
cidian,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
ciflyr,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
CirceR,,,TRUE,Java
circuitscaper,,,FALSE,"Julia, Circuitscape.jl, Omniscape.jl"
cit,gsl,,TRUE,gsl (with development libraries libgsl-dev)
citestR,,,FALSE,Python with the 'midasverse-citest-api'package
clarabel,cargo,,TRUE,"Cargo (Rust's package manager), rustc,and"
cld3,protobuf,,TRUE,libprotobuf and protobuf-compiler
cleanNLP,,,TRUE,Python
clim4health,,,FALSE,"CDO (Climate Data Operators,https://code.mpimet.mpg.de/projects/cdo), NCO (NetCDFOperators, https://nco.sourceforge.net/)"
clinDataReview,,,TRUE,pandoc (to create a clinical data review report)
clinUtils,,,TRUE,pandoc (for export clin DT to a file - inclusion oflist of interactive plots/objects with knitr)
clipr,,xclip,TRUE,"xclip (https://github.com/astrand/xclip) or xsel(http://www.vergenet.net/~conrad/software/xsel/) for accessingthe X11 clipboard, or wl-clipboard(https://github.com/bugaevc/wl-clipboard) for systems usingWayland."
cloudml,,,TRUE,Python
clustermq,zeromq,,TRUE,ZeroMQ (libzmq)(optional; otherwisebundled)
ClusterR,,,TRUE,
CLVTools,gsl,,TRUE,GNU GSL
cmaRs,,,TRUE,MOSEK (http://www.mosek.com) and MOSEK License foruse of Rmosek
CMCMC,,,FALSE,Optional CUDA toolkit and NVIDIA GPU for the CUDAbackend; OpenMP for parallel CPU execution.
cmtkr,,,TRUE,zlib
cncaGUI,xvfb,bwidget,TRUE,Tcl/Tk package BWidget.
codacore,,,TRUE,TensorFlow (https://www.tensorflow.org/)
CodeCarbonR,,,FALSE,"Python; codecarbon Python package, installed via setup_carbon_tracker()"
codriver,,,FALSE,"RStudio,https://posit.co/download/rstudio-desktop/)"
coga,gsl,,TRUE,GNU GSL
cogmapr,,,TRUE,libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb).
CohortContrast,,,FALSE,Python
CohortIncidence,,,FALSE,Java
CohortMethod,,,FALSE,Java
coinclp,,,FALSE,"COIN-OR Clp with development headers, anda  compiler. Debian/Ubuntu: coinor-libclp-dev, Fedora:coin-or-Clp-devel, macOS: brew install clp, Windows: suppliedby Rtoolsor later). CLP_CFLAGS and CLP_LIBS point thebuild at an installation elsewhere."
colorizer,,,TRUE,ImageMagick++: ImageMagick-c++-devel (rpm) orlibmagick++-dev (deb)
Colossus,,,TRUE,"make,"
COMBO,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
CommonJavaJars,,java-bin,TRUE,Java
compdb,,,TRUE,Clang
compost,,,FALSE,ffmpeg
concaveman,,,TRUE,"GDAL, GEOS, PROJ.4"
condor,,,TRUE,htcondor
conflibertR,,,FALSE,"Python; the Python modules 'torch','transformers', 'accelerate', 'peft', 'scikit-learn'and 'numpy', installable via conflibert_install()"
CoNI,,python3,TRUE,python3
conquestr,,,TRUE,ACER ConQuest
convertxlsform,,,FALSE,"'LibreOffice' (optional, for PDF output)"
CoordinateCleaner,,,TRUE,GDAL
CopernicusDEM,,awscli,TRUE,"awscli: apt install -y awscli (deb), aws-configure:aws configure (deb)"
CopernicusMarine,,,TRUE,Requires GDALwith BLOSC support See<https://pepijn-devries.github.io/CopernicusMarine/articles/blosc.html>
copernicusR,,,TRUE,"Python, copernicusmarine Python library"
copula,,,TRUE,pdfcrop (part of TexLive) is required to rebuildthe vignettes.
cordillera,,,TRUE,
corehunter,,,TRUE,Java
coreNLP,,,TRUE,Java; Stanford CoreNLP<http://nlp.stanford.edu/ software/corenlp.shtml>
corteza,,,FALSE,"On Windows, Rtools45 (Rx) or Rtools44 (R4.4.x) is recommended so the 'bash' shell tool is available;minimal installs fall back to a 'cmd' tool. 'git' is requiredfor the git_status, git_diff, and git_log tools (install Gitfor Windows, or 'pacman -Sy git' from an Rtools shell)."
coveffectsplot,,pandoc,TRUE,pandoc with https support
COveR,gsl,,TRUE,Gnu Scientific Library version
cpp11bigwig,,,FALSE,"libcurl (optional, for remote file access):libcurl-devel (rpm) or libcurl4-openssl-dev (deb)"
cpp11qpdf,libjpeg,,TRUE,
cppcheckR,,cppcheck,TRUE,cppcheck
cppSim,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
craftgrn,,,FALSE,"Optional Shiny app support on Linux may requirelibuv headers, for example libuv1-dev, or cmake for bundledlibuv builds in transitive dependencies."
crandep,,,TRUE,pandoc - http://pandoc.org
crc32c,cmake,,TRUE,cmake
credentials,,git,TRUE,git (optional)
cronR,,cronie,TRUE,cron
Crossover,,,TRUE,Java
CSDownscale,,,TRUE,cdo
cTMed,gsl,,TRUE,GNU GSL
ctrdata,,,TRUE,
ctsmTMB,,,TRUE,
CTxCC,,,TRUE,Intel MKL (optional for optimized BLAS/LAPACKperformance)
cubature,,,TRUE,and USE_C17
cuda.ml,,,FALSE,Native operations require Linux x86_64 with glibc2.28 or newer. GPU-backed operations require a supported NVIDIAGPU and driveror newer.
cudaverse,,,FALSE,"For GPU execution on Windows or Linux: NVIDIACUDA-capable GPU, NVIDIA driver with CUDA Driver API, NVIDIAcuBLAS, and NVIDIA cuSOLVER"
curl,curl,,TRUE,libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb)
cusna,,,FALSE,optionally a CUDAx toolkit (nvcc) forthe GPU path
CytOpT,,,TRUE,Python
DALY,xvfb,,TRUE,"Tcl/Tk, Tktable"
dasklyr,,,FALSE,"Python with the dask (dataframe, distributed),pandas, and pyarrow packages"
data.table,,,TRUE,
DatabaseConnector,,,TRUE,Java
DatabionicSwarm,,,TRUE,"pandoc, needed for vignettes)"
datacaged,,,FALSE,"7-Zip (optional, required for PPMd-compressed filesfrom CAGED antigo and CAGED Ajustes)"
DataExplorer,,,TRUE,pandoc - http://pandoc.org
dataMaid,,,TRUE,"pandoc; https://pandoc.org), git, whoami"
DataPackageR,,,TRUE,pandoc - https://pandoc.org
dataprep,,,FALSE,optional OpenMP
dataReporter,,,TRUE,"pandoc; https://pandoc.org), git, whoami"
datasusr,,,FALSE,C99
datefixR,cargo,,FALSE,"Cargo (Rust's package manager), rustc, xz"
datr,,,TRUE,dat
dawnn,,,FALSE,"Python with TensorFlow, typicallyinstalled in a conda environment and selected via the'tf_conda_env' argument of run_dawnn(). See the packagedocumentation for setup instructions."
dbcturbo,,,FALSE,C99 compiler
dbmss,,pandoc,TRUE,"pandoc,"
dclone,,,TRUE,"none, one or more of JAGS, WinBUGS, OpenBUGS, Stan"
dcmle,,,TRUE,JAGS
deadwood,,,TRUE,OpenMP
deckglgeoarrow,,,FALSE,Quarto command line tool(<https://github.com/quarto-dev/quarto-cli>).
Deducer,,,TRUE,"Java, JRI"
deepspat,,,TRUE,"TensorFlow (https://www.tensorflow.org/),"
deforestable,,,TRUE,"GDAL, GEOS, PROJ,sqlite3"
Delaporte,,,TRUE,A version of Fortran supporting the LOG_GAMMAIntrinsic and the ieee_arithmetic module.
delta.sharing,,,FALSE,"Cargo (Rust's package manager), rustc"
denguedatahub,,,TRUE,"Java: openjdk-11-jdk (deb),java-11-openjdk.x86_64 (rpm), openjdk@11 (brew)"
devEMF,,,FALSE,fontconfig or zlib (only needed for platforms otherthan modern macOS and Windows)
devianLM,,,TRUE,"OpenMP (optional, for parallel execution)"
dialr,,,TRUE,java
dialrjars,,,TRUE,java
didintrjl,,,FALSE,"Julia, DiDInt.jl"
diffeqr,,,TRUE,"Julia, DifferentialEquations.jl,ModelingToolkit.jl"
DiNAMIC.Duo,,,TRUE,"Python, NumPy Python library"
dismo,,java-bin,TRUE,Java
divent,,,TRUE,pandoc
diversitree,fftw gsl,,TRUE,"fftw3, gsl"
DIZutils,,,TRUE,libpq: libpq-dev (deb) or postgresql-devel(rpm)
DLCA,,,FALSE,OpenMP
DNNSIM,,,TRUE,Python; PyTorch (https://pytorch.org/);NumPy (https://numpy.org/); SciPy (https://scipy.org/); sklearn(https://scikit-learn.org/stable/);
docknitr,,docker,TRUE,"Docker, RStudio>=1.2"
doclingr,,,FALSE,"Python, docling; tested with2.107.0)"
doconv,,libreoffice,FALSE,"LibreOffice, Microsoft Word, Microsoft PowerPoint,Microsoft Excel"
docxtractr,,libreoffice,TRUE,LibreOffice (<https://www.libreoffice.org/>)required to extract data fromdoc files or performpptxconversion.
domino,,,TRUE,domino (~>1.7.1)
doubletrs,,,FALSE,"Cargo (Rust's package manager), rustc"
DownBallotR,,,FALSE,"Python, pip"
DQAstats,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
dragonfarm,,,FALSE,'Python'. The 'uv' tool is installedautomatically by 'reticulate' to build the 'Python'environment.
dress.graph,,,TRUE,
drhur,,,FALSE,Quarto command-line tool (https://quarto.org)
DRIP,gsl,,TRUE,
drogonR,,,FALSE,"OpenSSL (optional, for HTTPS)"
drugsens,,,TRUE,QuPath™or higher
dti,gsl,,TRUE,gsl
duckdb,,,TRUE,
duet,,ffmpeg-bin,TRUE,FFmpeg (https://ffmpeg.org/)
dwg2geo,,,FALSE,"Cargo (Rust's package manager), rustc"
DynareR,,,TRUE,"Dynare, Octave"
dynaSpec,,ffmpeg-bin,TRUE,ffmpeg
dynBiplotGUI,xvfb,,TRUE,gmake
dynr,gsl,,TRUE,
eaf,gsl,,TRUE,Gnu Scientific Library
easyNCDF,,,TRUE,netcdf development libraries
EBASE,,,TRUE,JAGSx.y (https://mcmc-jags.sourceforge.net)
ebvcube,,,FALSE,GDAL binaries
EcoDiet,,,TRUE,JAGS
econetwork,,,TRUE,
ecotourism,,,TRUE,Quarto
edgemodelr,,,TRUE,or equivalent for building
eDMA,,,TRUE,"Requires the OpenMP library for parallel computing.If the OpenMP library is not available, the code is executedsequentially and a warning is printed."
effectcheck,,,TRUE,
EHRmuse,gsl,,TRUE,GNU Scientific Library version
EIAapi,,,TRUE,The package required the jq command line library.Please check https://stedolan.github.io/jq/download/ fordownload instructions.
elexr,,python3,TRUE,Pythonor and elex package
elliptic,,pari,TRUE,pari/gp
emayili,,,TRUE,The function render() requires Pandoc(http://pandoc.org). To use PGP/GnuPG encryption requires gpg.
EmpiricalDynamics,,,TRUE,Julia
enderecobr,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
EnTraineR,,,TRUE,Pandoc (for DOCX/HTML conversion when usingrmarkdown)
entropart,,pandoc,TRUE,pandoc
EpiSignalDetection,,,TRUE,pandoc
eplusr,,,FALSE,"EnergyPlus (optional) (<https://energyplus.net>);udunits2 (optional, for units support)"
eqty.sdk.r,,,FALSE,Python
ergm,,,TRUE,
eseis,,,TRUE,gipptools dataselect
esviz,,,TRUE,"GDAL, GEOS, PROJ"
eulerr,,,FALSE,"Cargo (Rust's package manager), rustc"
evapoRe,,,TRUE,"PROJ, https://proj.org/download.html), GDAL(>=, https://gdal.org/download.html), NetCDF,https://www.unidata.ucar.edu/software/netcdf/)."
EvidenceSynthesis,,,TRUE,Java
EviewsR,,,TRUE,EViews
EWOC.Comb,,,TRUE,"JAGS. For installation instructions, seehttp://mcmc-jags.sourceforge.net/"
exactextractr,geos,,TRUE,GEOS
exams,,,TRUE,pandoc
excerptr,,,TRUE,Python
excursions,gsl,,TRUE,Gnu Scientific Library version
exdqlm,,,TRUE,OpenMP (optional)
exifr,exiftool,exiftool,TRUE,Perl
exiftoolr,exiftool,exiftool,TRUE,Perl
exmort,,,FALSE,pandoc for report rendering; a LaTeXinstallation (for example TinyTeX) is required only for PDFreports.
extraDistr,,,TRUE,
ezknitr,,,TRUE,pandoc with https support
factset.protobuf.stach.v2,,,TRUE,"ProtoBuf libraries and compiler versionorlater; On Debian/Ubuntu these can be installed aslibprotoc-dev, libprotobuf-dev and protobuf-compiler, while onFedora/CentOS protobuf-devel and protobuf-compiler are needed."
fairGATE,,,TRUE,Optional 'LibTorch' backend; install viatorch::install_torch().
fairGNN,,,TRUE,Optional 'LibTorch' backend; install viatorch::install_torch().
fangs,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
fasterRaster,,,TRUE,GRASS
fastgeojson,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
fastGLCM,,,TRUE,"apt-get-pip: apt-get install -y python3-pip (deb),python3-pip: python3 -m pip install -U pip (deb), numpy: pip3install -U numpy (deb), cv2: pip3 install -U opencv-python(deb), matplotlib: pip3 install -U matplotlib (deb), skimage:pip3 install -U scikit-image (deb), libarmadillo: apt-getinstall -y libarmadillo-dev (deb), libblas: apt-get install -ylibblas-dev (deb), liblapack: apt-get install -y liblapack-dev(deb), libarpack++2: apt-get install -y libarpack++2-dev (deb),: apt-get install -y  (deb)"
FastHamming,,,TRUE,"C compiler (C99), OpenMP"
FastKRR,,,TRUE,OpenMP (optional)
fastLISA,,,FALSE,"C99, optional OpenMP"
fastPLS,,,FALSE,"Optional OpenBLAS development libraries for fasterCPU matrix operations; optional NVIDIA CUDA Toolkit with CUDARuntime, cuBLAS, cuSOLVER and cuRAND plus a compatibleseparately managed NVIDIA driver; optional Apple Metalframework on macOS. CPU-only builds do not require GPUsoftware."
fastrda,,,FALSE,OpenMP
fastText,,,TRUE,
fcl,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
FCPS,,pandoc,TRUE,Pandoc
fdars,cargo,,TRUE,
feather,,,TRUE,
fect,,,TRUE,
FedData,,,TRUE,GDAL
FeNEU,,,FALSE,"pandoc and a LaTeX distribution (e.g.TinyTeX, see ?tinytex::install_tinytex) with the booktabs,longtable, siunitx, and makecell LaTeX packages are requiredfor the *_pdf() output functions."
fereg,,,FALSE,"Cargo (Rust's package manager), rustc"
FFD,xvfb,bwidget,TRUE,BWidget
fftw,fftw,,TRUE,fftw3
fftwtools,fftw,,TRUE,"fftw3 (libfftw3-dev (deb), or fftw-devel (rpm))"
fgitR,,git,TRUE,Git
fibr,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
fieldopt,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
findInFiles,,grep,TRUE,grep
findInGit,,grep git,TRUE,"grep, git"
fio,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
fitbitViz,,,TRUE,
flan,gsl,,TRUE,
flexsiteboard,,,TRUE,pandoc - http://pandoc.org
flint,flint mpfr gmp,,TRUE,"flint, mpfr, gmp"
Fluidigm,,,TRUE,"perl, plink"
fluidsynth,fluidsynth,,TRUE,fluidsynth: fluidsynth-devel (rpm) orlibfluidsynth-dev (deb). On Linux you also need a soundfontprovided by 'fluid-soundfont-gm' (Fedora) or 'sf3-soundfont-gm'(Debian/Ubuntu)
FMAT,,,TRUE,Python
fmriAR,,,TRUE,OpenMP (optional)
footBayes,,pandoc,TRUE,"CmdStan(https://mc-stan.org/users/interfaces/cmdstan), pandoc, pandoc-citeproc"
forensim,,,TRUE,Tcl/Tk package TkTable
foresightr,,,FALSE,"Cargo (Rust's package manager), rustc"
forestsearch,,,FALSE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli)
forsearch,,,TRUE,
fozziejoin,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
fpROC,,,TRUE,"OpenMP, TBB"
freestiler,,,FALSE,"Cargo (Rust's package manager), rustc"
freesurfer,,,FALSE,FreeSurfer (https://freesurfer.net/)
frequency,,,TRUE,pandoc - http://pandoc.org
fRLR,gsl,,TRUE,GNU Scientific Library (GSL). Note: users shouldhave GSL installed.
fru,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
fs,libuv,,TRUE,libuv: libuv-devel (rpm) or libuv1-dev (deb).Alternatively to build the vendored libuv 'cmake' is required..
fsdaR,,,TRUE,"(license-free) MATLAB Runtime (MCR) V, Java(>=8)"
fslr,,,TRUE,FSL
fst,,,TRUE,little-endian platform
fstcore,,,TRUE,little-endian platform
ftExtra,,,TRUE,pandoc - http://pandoc.org
FTSgof,,,TRUE,XQuartz (https://www.xquartz.org/)
fuzzywuzzyR,,,TRUE,"Python, difflib, fuzzywuzzy,python-Levenshtein. Detailed installationinstructions can be found in the README file."
fvfmR,,,FALSE,"Python, fvfmPy"
fz,,,FALSE,"Python, funz-fz Python package"
gadjid,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
ganDataModel,,,TRUE,TensorFlow (https://www.tensorflow.org)
ganGenerativeData,,,TRUE,TensorFlow (https://www.tensorflow.org)
gcbd,,,TRUE,"Debian or Ubuntu system with access to Goto Blas,Intel MKL, Atlas development build as well as a Nvidia GPU withCUDA support"
GCPM,,,TRUE,"Windows, Linux, OS X"
gdalcubes,gdal proj netcdf sqlite,,TRUE,
gdalraster,gdal,,TRUE,"GDAL, built against GEOS)"
gdata,,perl,TRUE,
gdtools,cairo freetype,,TRUE,"cairo, freetype2, fontconfig"
gdxtools,,,FALSE,GAMS is only required if you callgams()
GeneralizedUmatrix,,,TRUE,"pandoc, needed for vignettes)"
GeneralizedUmatrixGPU,,,TRUE,"pandoc, needed forvignettes), OpenCL shared library (provided by an SDK such asAMD/NVIDIA)"
GeneralizedWendland,gsl,,TRUE,gsl
genie,,,TRUE,
genieclust,,,TRUE,OpenMP
genlogis,,,TRUE,RStudio -https://posit.co/products/open-source/rstudio/
geno2proteo,,perl,TRUE,Perl
geoarrowWidget,,,TRUE,Quarto command line tool(<https://github.com/quarto-dev/quarto-cli>).
GeoFIS,gmp mpfr,,TRUE,"gmp, mpfr"
geojsonR,,,TRUE,libarmadillo: apt-get install -y libarmadillo-dev(deb)
GeoModels,,,FALSE,OpenMP (optional)
GeoMongo,,,TRUE,"MongoDB, Python. Installationinstructions and links can be found in the README file."
geopytorch,,,FALSE,Python
GerminaR,,,TRUE,pandoc
gert,libgit2,,TRUE,libgit2: libgit2-devel (rpm) orlibgit2-dev (deb)
geslaR,,,TRUE,arrow
GetoptLong,,perl-getopt-long,TRUE,"Perl, Getopt::Long"
GGally,,,TRUE,openssl
ggcolonviz,,,FALSE,"GDAL, GEOS, PROJ,sqlite3"
ggdemetra,,,TRUE,Java
ggExtra,,pandoc,TRUE,pandoc with https support
ggiraph,libpng,,TRUE,libpng
gglinedensity,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
ggmlR,vulkan glslc,,TRUE,"libvulkan-dev, glslc (optional,for GPU on Linux), 'Vulkan' 'SDK' (optional, for GPU onWindows)"
ggquickeda,,pandoc,TRUE,pandoc with https support
ggseg,,,TRUE,
ggsql,,,FALSE,"Cargo (Rust's package manager), rustc,ODBC driver manager (unixODBC on Linux, iODBC or unixODBC onmacOS; built into Windows)"
ggtrace,,pandoc,TRUE,pandoc
gibasa,mecab,,FALSE,"MeCab (libmecab-dev (deb), mecab-devel(rpm))"
gifski,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
git2r,libgit2 openssl libssh2,,TRUE,libgit2 and its dependencies libssh2 andopenssl header and libraries.
gitcreds,,git,TRUE,git
gittargets,,git,TRUE,Git
glioblastomaEHRsData,,,TRUE,"pandoc - http://pandoc.org, tcltk(optional)"
glmbayes,,,FALSE,"Optional OpenCL support. If available, GPUacceleration will be used; otherwise, computation runs on CPU."
glmbayesCore,,,FALSE,"Optional OpenCL support. If available, GPUacceleration will be used; otherwise, computation runs on CPU."
glmulti,,,TRUE,Java
glpkAPI,glpk gmp,,TRUE,
glpsol,,,FALSE,"GLPK: libglpk-dev (deb), glpk-devel (rpm),glpk (brew)"
gm,,musescore,TRUE,MuseScore - https://musescore.org/
gMCP,,,TRUE,Java
gmp,gmp,,TRUE,gmp
gmt,,gmt,TRUE,gmt
gnn,,,TRUE,TensorFlow (https://www.tensorflow.org/)
govdown,,,TRUE,pandoc - http://pandoc.org
goxygen,,,TRUE,"pandoc, pandoc-citeproc"
GPBayes,gsl,,TRUE,GNU Scientific Library version
gputools,,,FALSE,NVIDIA CUDA toolkit; an NVIDIA GPU to runthe GPU functions
GreedyExperimentalDesign,,,FALSE,"Java; wgpu-native(optional,for GPU acceleration, seehttps://github.com/gfx-rs/wgpu-native)"
GreedyExperimentalDesignJARs,,,TRUE,Java
greta,,,FALSE,Python with header files and sharedlibrary; TensorFlowv2.0.0; https://www.tensorflow.org/);TensorFlow Probability (v0.8.0;https://www.tensorflow.org/probability/)
greta.dynamics,,,FALSE,Python with header files and sharedlibrary; TensorFlowv2.0.0; https://www.tensorflow.org/);TensorFlow Probability (v0.8.0;https://www.tensorflow.org/probability/)
greta.gp,,,FALSE,Python with header files and sharedlibrary; TensorFlowv2.0.0; https://www.tensorflow.org/);TensorFlow Probability (v0.8.0;https://www.tensorflow.org/probability/)
gretlR,,gretl,TRUE,gretl
gridDebug,,,TRUE,graphviz
gridGraphviz,,graphviz,TRUE,graphviz
gridmicrotex,,,FALSE,"FreeType, pkg-config, FriBidi(optional)"
grImport,,ghostscript,TRUE,ghostscript
GroupSeq,xvfb,,TRUE,
grwat,,,TRUE,pandoc
gsl,gsl,,TRUE,Gnu Scientific Library version
gslnls,gsl,,TRUE,GSL
gsynth,,,TRUE,
gtfsrealtime,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
guildai,,,TRUE,Python
gWidgets2tcltk,xvfb,,TRUE,
GWnnegPCA,,,TRUE,"GDAL, GEOS, PROJ"
GWpcor,,,TRUE,"GDAL, GEOS, PROJ"
h2o,,java-bin,TRUE,"Java, <="
h2o4gpu,,,TRUE,Python with header files and sharedlibrary; H2O4GPU (https://github.com/h2oai/h2o4gpu)
h2oplyr,,,FALSE,"Java, a running H2O cluster matching the h2oR package version"
h3jsr,,,TRUE,"V8 engine version+ is needed for modern JS andWASM support. On Debian / Ubuntu install either libv8-dev orlibnode-dev, on Fedora use v8-devel."
h3o,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
happign,,,TRUE,
haven,,,TRUE,"zlib: zlib1g-dev (deb), zlib-devel (rpm)"
hdbayes,,,TRUE,CmdStan(https://mc-stan.org/users/interfaces/cmdstan)
hdf5r,hdf5,,TRUE,HDF5
hdfqlr,,,TRUE,HDFql
HDNRA,,,FALSE,OpenMP
hdtg,,,TRUE,CPU with AVX/SSE4.2 (optional for betterperformance)
heck,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
helloJavaWorld,,,TRUE,Java
hellorust,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
heritable,,,TRUE,asreml
hexify,,,TRUE,C99
hgwrr,gsl,,TRUE,
HiClimR,netcdf,,TRUE,NetCDF
hicream,,,TRUE,Python
HighFive,,,TRUE,hdf5
highs,cmake,,TRUE,"Bash, PkgConfig, CMAKE,"
hive,,,TRUE,"Apache Hadoop(https://hadoop.apache.org/releases.html#Download); Obsolete:Hadoop coreand <=or CDH3(https://www.cloudera.com); standard unix tools (e.g., chmod)"
hobbs,,,FALSE,"Cargo (Rust's package manager), rustc, C compiler"
HOIF,,,FALSE,"For the default Python backend: Pythonwith the 'u-stats', 'numpy' and 'torch' packages (provisionedautomatically on first use via 'reticulate', or viaustats::setup_ustats()). Not needed when pure_R_codeTRUE."
hoopR,,pandoc,TRUE,"pandoc, pandoc-citeproc"
hpsreg,,,FALSE,OpenMP (optional)
HRTnomaly,,,FALSE,C11 compiler
hSDM,gsl,,TRUE,GNU GSL
httpuv,,,TRUE,zlib
huito,,,TRUE,pandoc
huxtable,,tex-adjustbox tex-array tex-calc tex-caption tex-colortbl tex-fontspec tex-graphicx tex-hhline tex-hyperref tex-multirow tex-siunitx tex-tabularx tex-threeparttable tex-ulem tex-wrapfig,FALSE,"LaTeX packages: adjustbox, array, calc, caption,colortbl, fontspec, graphicx, hhline, hyperref, longtable,multirow, siunitx, tabularx, threeparttable, threeparttablex,ulem, wrapfig"
hypergeo2,gmp mpfr,,TRUE,"gmp, mpfr"
iai,,,TRUE,Julia and Interpretable AI System Image(>=
icebergr,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
IceSat2R,,,TRUE,
ICESat2VegR,,,FALSE,- GDAL - PROJ - HDF5
idiogramFISH,,pandoc,TRUE,pandoc
idm,,,TRUE,ImageMagick (http://imagemagick.org) orGraphicsMagick (http://www.graphicsmagick.org)
ieeeround,,,TRUE,A C library with the fesetround/fegetroundfunctions.
igate,,,TRUE,
igraph,libxml2 glpk,,TRUE,"libxml2 (optional), glpk, optional)"
ijtiff,fftw libtiff libjpeg libwebp,,TRUE,"fftw3, libtiff, libbz2, libdeflate, libjpeg,liblzma, libwebp, libzstd, X11, zlib"
image.CannyEdges,libpng fftw,,TRUE,"libpng, fftw3"
imager,fftw libtiff,,TRUE,"fftw3, libtiff, X11"
impectR,,,FALSE,"ffmpeg (optional, only required forgetVideoClips())"
implyr,,,TRUE,Impala driver to support a 'DBI'-compatible Rinterface
ImprintCapASM,,,FALSE,samtools
iMRMC,,java-bin,TRUE,
informativeSCI,,,TRUE,Java
inlpubs,,,TRUE,"Complete functionality necessitates Amazon Corretto(win), and default-jre, pandoc, libxml2-dev,libpoppler-cpp-dev, libmagick++-dev, optipng, libtesseract-dev,libleptonica-dev, tesseract-ocr-eng (deb)"
inpdfr,,xpdf,TRUE,XPDF (http://www.foolabs.com/xpdf/download.html)
InsectLabelR,,,FALSE,pdflatex
InSilicoVA,,,TRUE,Java
IntegMultiReg,,,FALSE,GSL
inTextSummaryTable,,pandoc,TRUE,pandoc (to export an interactive summary table to afile)
inti,,,TRUE,pandoc
IP,libidn,,FALSE,libidn: libidn11-dev (deb)
ip2location,,,TRUE,IP2Location Python library<https://www.ip2location.com/development-libraries/ip2location/python>
ip2locationio,,,TRUE,IP2Location.io Python library<https://github.com/ip2location/ip2location-io-python>
ip2proxy,,,TRUE,IP2Proxy Python library<https://www.ip2location.com/development-libraries/ip2proxy/python>
ip2whois,,,TRUE,IP2WHOIS Python library<https://github.com/ip2whois/ip2whois-python>
ipf,,,FALSE,"Cargo (Rust's package manager), rustc"
iplots,xvfb,,TRUE,
IRISSeismic,,,FALSE,Java JREor later
IRkernel,,,TRUE,"jupyter, jupyter_kernel_test (Python package fortesting)"
ISEtools,,,TRUE,OpenBUGS or JAGS
isodistrreg,,,FALSE,"Cargo (Rust's package manager), rustc"
jagstargets,,,TRUE,JAGSx.y (https://mcmc-jags.sourceforge.net)
jagsUI,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
janssonr,,,FALSE,"jansson is linked when present:libjansson-dev (deb), jansson-devel (rpm), jansson (brew). Whenit is absent, and always on Windows, the bundled Janssonis compiled into the package."
jarbes,,,TRUE,JAGS (seehttp://mcmc-jags.sourceforge.net)
JavaGD,,,TRUE,and Java JDKor higher
jekylldown,,,FALSE,"Ruby, jekyll, bundler"
JFE,xvfb,,TRUE,
JGR,,,TRUE,Java
jiebaRS,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
jlmerclusterperm,,,TRUE,Julia
jlview,,,FALSE,"Julia, https://julialang.org/downloads/)"
JMbayes,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
jmotif,,,TRUE,
jmvconnect,,,TRUE,jamovi
JointAI,,,TRUE,JAGS (https://mcmc-jags.sourceforge.io/)
jpeg,libjpeg,,TRUE,libjpeg
jqr,jq,,TRUE,libjq: jq-devel (rpm) or libjq-dev (deb)
jSDM,gsl,,TRUE,GNU GSL
jsslintr,,,FALSE,"Cargo (Rust's package manager), rustc"
juicr,,,TRUE,
JuliaCall,,julia,TRUE,"Julia, RCall.jl"
JuliaConnectoR,,julia,TRUE,Julia
kantorovich,,,TRUE,
KernelKnn,,,TRUE,"libarmadillo: apt-get install -y libarmadillo-dev(deb), libblas: apt-get install -y libblas-dev (deb),liblapack: apt-get install -y liblapack-dev (deb),libarpack++2: apt-get install -y libarpack++2-dev (deb),: apt-get install -y  (deb)"
KeyNubLicDongle,,,FALSE,"the KeyNub License Dongle native library(keynub_licdongle) for the platform, seehttps://github.com/AB-KeyNub/KeyNub-SDK/blob/master/NATIVES.md"
keyring,libsecret,,TRUE,"Optional: libsecret on Linux (libsecret-1-dev onDebian/Ubuntu, libsecret-devel on Fedora/CentOS)"
klaR,,,TRUE,SVMlight
klic,,,TRUE,
knitr,,pandoc rst2pdf,TRUE,Package vignettes based on R Markdown v2 orreStructuredText require Pandoc (http://pandoc.org). Thefunction rst2pdf() requires rst2pdf(https://github.com/rst2pdf/rst2pdf).
knitroff,,,FALSE,GNU groff for render_roff(); pdfinfo(poppler) for figures in PDF output
koopman.dmd,,,FALSE,"Cargo (Rust's package manager), rustc"
KSgeneral,fftw,,TRUE,fftw3
kuenm2,,,FALSE,"GDAL, GEOS, PROJ"
kza,fftw,,TRUE,fftw
landsepi,gsl,,TRUE,gsl
languageserversetup,,procps,TRUE,"procps (linux), ps (macos), wmic (windows)"
latdiag,,graphviz,TRUE,dot from graphviz
latexdiffr,,latexdiff,TRUE,latexdiff
latte,,latte 4ti2,TRUE,"LattE <https://www.math.ucdavis.edu/~latte/>,ti2<http://www.4ti2.de/>"
lava,,,FALSE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
LCMCR,gsl,,TRUE,Gnu Scientific Library version
lcra,,,TRUE,JAGSx.y or WinBUGS
LDATS,,,TRUE,gsl
leaf,,,FALSE,"Conda, Python"
LeafArea,,imagej,TRUE,"ImageJ, ij.jar (seehttp://imagej.nih.gov/ij/), Java"
learnr,,,TRUE,pandoc - http://pandoc.org
learnr2,,,FALSE,Quarto command line tool(https://github.com/quarto-dev/quarto-cli).
ledger,,ledger hledger,FALSE,"ledger, hledger, beanquery orrustledger"
leidenAlg,libxml2 glpk,,TRUE,"(optional), libxml2 (optional), glpk, optional)"
libdeflate,cmake,,TRUE,CMake
libimath,cmake,,TRUE,cmake
libipldr,,,FALSE,"Cargo (Rust's package manager), rustc"
libopenexr,,,FALSE,"CMake,"
Libra,gsl,,TRUE,GNU Scientific Library (GSL)
libstable4u,gsl,,TRUE,GNU GSL
liftr,,docker,TRUE,Docker (see <https://docs.docker.com/install/>)
lightsout,,pandoc,TRUE,pandoc with https support
lincom,,,TRUE,"MOSEK, MOSEK License"
lira,,,TRUE,
liteformats,,,FALSE,"Chromium, Google Chrome, or Microsoft Edge (for PDFoutput)"
littler,,,TRUE,libR
livelink,,,FALSE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
LLMing,,,TRUE,"Python with packages: torch,transformers, pandas, numpy"
llmjson,,,FALSE,"Cargo (Rust's package manager), rustc"
lnmixsurv,,,FALSE,"GNU,  GSL"
localLLM,curl,,TRUE,"libcurl (optional, for model downloading)"
localsolver,,,TRUE,
locfit,,,TRUE,USE_C17
LOMAR,gmp fftw,,TRUE,"gmp, fftw3"
loo,,pandoc,TRUE,"pandoc, pandoc-citeproc"
loon,xvfb,,TRUE,
loon.ggplot,xvfb,,TRUE,
loon.shiny,xvfb,,TRUE,
loon.tourr,xvfb,,TRUE,
lpmec,,,TRUE,"Python with jax, numpy, numpyro(optional; for NumPyro backend via reticulate)"
LSAMBA,,,TRUE,'Monolix'(<https://monolixsuite.slp-software.com/monolix/2024R1/>)
lstar,,,FALSE,"zlib,  libzstd (optional, forreading Zstd-compressed Zarr v3 stores)"
lubridate,,,TRUE,A system with zoneinfo data (e.g./usr/share/zoneinfo). On Windows the zoneinfo included with Ris used.
lumbermark,,,FALSE,OpenMP
lwgeom,geos proj sqlite,,TRUE,"GEOS, PROJ, sqlite3"
m2r,,,TRUE,Macaulay2 <https://www.macaulay2.com>
magick,imagemagick,,TRUE,ImageMagick++: ImageMagick-c++-devel (rpm) orlibmagick++-dev (deb)
magickGUI,,,TRUE,ImageMagick
maGUI,,,TRUE,Tktable
mailR,,,TRUE,Java
mallet,,,TRUE,java
manipulate,,,TRUE,RStudio - http://www.rstudio.com/products/rstudio/
manureshed,,,FALSE,"GDAL, GEOS, PROJ"
MaOEA,,,TRUE,"Pythonx with following modules: PyGMO, NumPy,and cloudpickle"
mapme.biodiversity,,,TRUE,"GDAL, PROJ"
marcxmlr,,,FALSE,"libxml2, Expat (optional, for recordfiltering)"
marked,,,TRUE,ADMB version<http://admb-project.org/> foruse.admb=TRUE; see readme.txt
markovchain,,,FALSE,Quarto
matchingMarkets,,,TRUE,Java
MatchingPursuit,,,FALSE,"external tool (installed via empi_install()function). The package uses the implementation of the MatchingPursuit algorithm (Enhanced Matching Pursuit Implementation;EMPI) by Piotr T. Różański, available athttps://github.com/develancer/empi."
matlabr,,,TRUE,MATLAB
mauricer,,,TRUE,BEAST2 (https://www.beast2.org/)
MaxentVariableSelection,,java-bin,TRUE,
MBNMAdose,,,TRUE,JAGS(https://mcmc-jags.sourceforge.net/)
MBNMAtime,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
mBvs,gsl,,TRUE,
mcbette,,,TRUE,BEAST2 (https://www.beast2.org/)
mdbr,,mdbtools,TRUE,
MDCcure,,,TRUE,TBB
mdendro,,,TRUE,
MDSGUI,,bwidget,TRUE,"windows, 'BWidget', 'Tktable'"
meltt,,,TRUE,Python
memoiR,,,TRUE,pandoc
metagear,,,TRUE,Tcl/Tk toolkit (X11 Quarts for Mac)
metajam,,,FALSE,"Mac OSX: redland ; Linux: librdf0, librdf0-dev"
metapost,,mpost,TRUE,mpost
MetaSKAT,,,TRUE,Little Endian
MethComp,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
MethScope,,,FALSE,zlib
MFPCA,fftw,,TRUE,libfftw3
MFSIS,,,TRUE,Python
mgwrsar,,,FALSE,(OpenMP optional; enable withMGWRSAR_OPENMP=1)
microbenchmark,,,TRUE,"On a Unix-alike, one of the C functionsmach_absolute_time (macOS), clock_gettime or gethrtime. If noneof these is found, the obsolescent POSIX function gettimeofdaywill be tried."
MicrobiomeStat,,,TRUE,"NLopt library (optional, for high-performance BMDDmode)"
MigConnectivity,,,TRUE,JAGS (https://mcmc-jags.sourceforge.net)
MIMSunit,,,FALSE,"memoryGB) Ubuntu: build-essential,libxml2-dev, libssl-dev, libcurl4-openssl-dev Windows: Rtools(>="
mindr,,,TRUE,pandoc - http://pandoc.org
MineSDG,,,FALSE,"Quarto CLI (optional, for reportrendering)"
minidown,,,TRUE,pandoc - http://pandoc.org
minimaxALT,gsl,,TRUE,"GNU Scientific Library (GSL), OpenMP"
minired,,,TRUE,
minirocketR,,,FALSE,OpenMP
misha,,,FALSE,"samtools; optional, required only for BAMinput), bedGraphToBigWig or wigToBigWig from UCSC (optional,required only for bigWig export; available as the biocondapackage ucsc-bedgraphtobigwig)"
mixcat,gsl,,TRUE,
mixgb,,,TRUE,macOS: Accelerate framework
MixSIAR,,,TRUE,JAGS
mixture,,,TRUE,GNU GSL
ml,,,FALSE,"Cargo ('Rust' package manager), rustc,optional)"
ML2Pvae,,,TRUE,"TensorFlow (https://www.tensorflow.org), Keras(https://keras.io), TensorFlow Probability(https://www.tensorflow.org/probability)"
mlexperiments,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
mllrnrs,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
mlpack,,,TRUE,
mlr,,,TRUE,"gdal (optional), geos (optional), proj (optional),udunits (optional), gsl (optional), gmp (optional), glu(optional), jags (optional), mpfr (optional), openmpi(optional)"
mlsurvlrnrs,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
MoBPS,,,TRUE,MiXBLUP (optional; used for multi-trait genomicevaluations); blupf90-family (optional; used for multi-traitgenomic evaluations)
mod09nrt,,,TRUE,MRTSwath
mongolite,openssl sasl,,TRUE,"OpenSSL, Cyrus SASL (aka libsasl2)"
monoreg,gsl,,TRUE,GNU GSL
morse,,,TRUE,JAGS (seehttps://mcmc-jags.sourceforge.io)
morseDR,,,FALSE,JAGS
motifr,,numpy pandas,TRUE,"Python, numpy, pandas"
MPCR,,,FALSE,"CMake, BLAS, LAPACK (includingsingle-precision complex routines), optional CUDA"
MplusTrees,,,TRUE,'Mplus' (<http://www.statmodel.com>)
MRIreduce,,,FALSE,"FSL (FMRIB Software Library, available athttps://fsl.fmrib.ox.ac.uk/fsl/docs/#/install/index)"
mRpostman,,,TRUE,libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb)
mscstexta4r,,,TRUE,"A valid account MUST be registered with Microsoft'sCognitive Services website<https://www.microsoft.com/cognitive-services/> in order toobtain a (free) API key. Without an API key, this package willnot work properly."
mscsweblm4r,,,TRUE,"A valid account MUST be registered with Microsoft'sCognitive Services website<https://www.microsoft.com/cognitive-services/> in order toobtain a (free) API key. Without an API key, this package willnot work properly."
multibiplotGUI,xvfb,bwidget,TRUE,Tcl/Tk package BWidget.
multibridge,gmp mpfr,,TRUE,"mpfr, gmp_1)"
multichainr,,,FALSE,MultiChain<https://www.multichain.com/download-install/>
multinet,,,TRUE,
mutossGUI,,,TRUE,Java
mvalpha,,,FALSE,OpenMP
mvst,gsl,,TRUE,GNU Scientific Library
mwa,,,TRUE,Java
mwcsr,,java-bin,FALSE,Java
mx.crypto,,,FALSE,"Cargo (Rust's package manager), rustc"
NACHO,,,FALSE,pandoc
nanoarrow,,,FALSE,"libzstd (optional), liblz4 (optional)"
nanonext,cmake,,FALSE,"'libnng'and 'libmbedtls'(optional,bundled sources compiled otherwise)"
nativeORT,,,FALSE,libonnxruntime
nbconvertR,,pandoc nbconvert,TRUE,
ncdf4,netcdf,,TRUE,netcdf library versionor later
ndjson,,,TRUE,"zlib,"
neo2R,,,FALSE,neo4j <https://neo4j.com/>
neo4jshell,,,TRUE,"neo4j - http://www.neo4j.com, cypher-shell -https://github.com/neo4j/cypher-shell/releases"
neojags,,,TRUE,JAGS(https://mcmc-jags.sourceforge.io/)
neptune,,,TRUE,"Python, Neptune (https://neptune.ai/)"
nethist,,,FALSE,Fortran compiler (for linking LAPACK/BLAS via'RcppArmadillo')
netmhc2pan,,,TRUE,NetMHC2pan(https://services.healthtech.dtu.dk/service.php?NetMHCIIpan-3.2)
NetRep,,,TRUE,
NeuralEstimators,,,TRUE,Julia
neuralGAM,,,TRUE,"python, keras, tensorflow"
ngboostForecast,,,TRUE,Python
NGCHM,,,TRUE,Java Git
nhdR,,p7zip,TRUE,7-zip command line toolz)
nirs4alldatasets,,,TRUE,
nloptr,cmake,,TRUE,cmake which is used only on Linux ormacOS systems when no system build of nlopt can befound.
nlrx,,java-bin pandoc,TRUE,"NetLogo, Java, pandoc, OpenSSL,udunits-2, PROJ.4, GEOS, GDAL, libxml2"
NMADTA,,,TRUE,JAGSx.y (http://mcmc-jags.sourceforge.net)
nmathopencl,,,FALSE,"Optional 'OpenCL' support. If available, GPUacceleration will be used; otherwise, computation runs on CPU."
nmslibR,,,TRUE,"python3-dev: apt-get install -y python3-dev (deb),python3-pip: apt-get install -y python3-pip (deb), numpy: pip3install numpy (deb), scipy: pip3 install scipy (deb), nmslib:pip3 install --no-binary :all: nmslib (deb)"
NobBS,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net/) foranalysis of Bayesian hierarchical models
nomnoml,,,TRUE,"A chromium based browser, required by ""webshot2""<https://rstudio.github.io/webshot2/>"
npRmpi,,,FALSE,MPI
nQuack,,,FALSE,samtools
nucim,,,TRUE,tiff fftw libcurl openssl
occumb,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
oceanmap,,imagemagick-bin,TRUE,ImageMagick
odbc,odbc,,TRUE,An ODBC3 driver manager and drivers.
oddsapiR,,pandoc,TRUE,"pandoc, pandoc-citeproc"
odiffr,,,TRUE,odiff -https://github.com/dmtrKovalenko/odiff
officedown,,,TRUE,pandoc - http://pandoc.org
OncoBayes2,,pandoc,TRUE,"pandoc, pngquant,"
Open.Visualization.Academy,,,TRUE,quarto
OpenCL,pocl,,TRUE,"OpenCL library,"
opencltools,,,FALSE,"Optional 'OpenCL' support. If available, GPUacceleration will be used; otherwise, computation runs on CPU."
opencpu,,,TRUE,"pandoc, apparmor (optional)"
opencv,opencv,,TRUE,"OpenCVor newer: libopencv-dev (Debian, Ubuntu)or opencv-devel (Fedora). The QR code detector requires atleast libopencv"
openfhe.R,,,FALSE,"cmake,"
OpenImageR,,,TRUE,"libarmadillo: apt-get install -y libarmadillo-dev(deb), libblas: apt-get install -y libblas-dev (deb),liblapack: apt-get install -y liblapack-dev (deb),libarpack++2: apt-get install -y libarpack++2-dev (deb),: apt-get install -y  (deb), libjpeg-dev:apt-get install -y libjpeg-dev (deb), libpng-dev: apt-getinstall -y libpng-dev (deb), libfftw3-dev: apt-get install -ylibfftw3-dev (deb), libtiff5-dev: apt-get install -ylibtiff5-dev (deb)"
openNLP,,,TRUE,Java
openNLPdata,,,TRUE,Java
openssl,openssl,,TRUE,OpenSSL
OpenStreetMap,,,TRUE,"Java, JRI"
opentimsr,,,FALSE,libzstd
optbdmaeAT,xvfb,,TRUE,
optimalThreshold,,,TRUE,JAGSx.y
optrcdmaeAT,xvfb,,TRUE,
orbweaver,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
Orcs,,p7zip dos2unix,TRUE,"zip, unix2dos"
orderanalyzer,,,TRUE,"Tesseract, libtesseract-dev (deb),tesseract-devel (rpm), libleptonica-dev (deb), leptonica-devel(rpm), tesseract-ocr-eng (deb), libpoppler-cpp-dev (deb),poppler-cpp-devel (rpm), poppler-data (rpm/deb), libxml2-dev(deb), libxml2-devel (rpm)"
orderly,,git,TRUE,
ordinalbayes,,,TRUE,JAGS
ORscraper,,,TRUE,poppler-cpp
osmnxr,,,FALSE,"Cargo (Rust's package manager), rustc"
osrm.backend,,,FALSE,OSRM backend binariesv5.27.0); packagedownloads binaries automatically from<https://github.com/e-kotov/osrm-binaries> by default; upstreamOSRM binaries from<https://github.com/Project-OSRM/osrm-backend> are available asan optional provider
osrmr,,,TRUE,"To use the Localhost of OSRM, you need to buildOSRM<https://github.com/Project-OSRM/osrm-backend/wiki/Building-OSRM>locally"
otelsdk,cmake protobuf curl,,TRUE,"cmake, protobuf-compiler, libprotobuf, libcurl,zlib,"
pagedown,,,TRUE,Pandoc
pairwiseLLM,,,FALSE,CmdStan and a  toolchain (optional; neededonly for Bayesian and adaptive modeling)
pak,curl,,TRUE,
pander,,pandoc,TRUE,pandoc (https://johnmacfarlane.net/pandoc) forexporting markdown files to other formats.
pandocfilters,,pandoc,TRUE,pandoc
papaja,,,TRUE,"Rendering the document template requires pandoc; https://pandoc.org) and for PDFs a TeX distribution, suchas TinyTeX; https://yihui.org/tinytex/)"
paramlink,,,TRUE,"For multipoint linkage analysis, 'MERLIN'(http://csg.sph.umich.edu/abecasis/merlin/index.html)."
paramlink2,,,TRUE,MERLIN (https://csg.sph.umich.edu/abecasis/merlin/)for multipoint linkage analysis.
parseLatex,,,TRUE,"gettext, bison"
patchDVI,,,TRUE,The 'Japanese.Rnw' vignette requires uplatex anddvipdfmx.
pathfindR,,java-bin,TRUE,
pathling,,,TRUE,Spark:x
patientProfilesVis,,tex-latex,TRUE,"latex, cairo (for report creation)"
paws.common,,pandoc,TRUE,
pbdMPI,openmpi,openmpi-bin,TRUE,"OpenMPI on Linux, Mac, and FreeBSD.MS-MPI (Microsoft MPI v7.1 (SDK) and Microsoft HPC PackR2MS-MPI Redistributable Package) on Windows."
pbdSLAP,openmpi,openmpi-bin,TRUE,"'OpenMPI' on Solaris, Linux, Mac, andFreeBSD. 'MS-MPI' (Microsoft HPC PackR2 MS-MPIRedistributable Package) on Windows."
pbdZMQ,zeromq,,TRUE,"Linux, Mac OSX, and Windows, or 'ZeroMQ' librarySolarisneeds 'ZeroMQ' libraryand 'OpenCSW'."
PBSmodelling,xvfb,bwidget,TRUE,BWidget
pcaL1,coin-or-clp,,TRUE,COIN-OR Clp
pcnetmeta,,,TRUE,JAGSx.y (http://mcmc-jags.sourceforge.net)
PDE,,xpdf,TRUE,XPDF(4.02)(https://github.com/erikstricker/PDE/tree/master/inst/examples/bin)
pdfminer,,pandas,TRUE,"Python>=3.6, pdfminer.six>=20200402, pandas"
pdfsigner,,,FALSE,"Cargo (Rust's package manager), rustc"
pdftools,poppler,,TRUE,"Poppler C++ API: libpoppler-cpp-dev (deb) orpoppler-cpp-devel (rpm), and poppler-data (rpm/deb) package."
pedometrics,,pandoc,TRUE,pandoc
pedprobr,,,TRUE,MERLIN (https://csg.sph.umich.edu/abecasis/merlin/)for calculations involving multiple linked markers.
PenCoxFrail,,,TRUE,
pensar,,,FALSE,"pandoc (for vault_export()), git (forvault_commit())"
PEPBVS,gsl,,TRUE,GNU GSL
pexm,jags,,TRUE,
pharmr,,,TRUE,Python
phase1PRMD,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
phonfieldwork,,,TRUE,
piecepackr,,ghostscript,TRUE,
pivmet,,pandoc,TRUE,"pandoc, pandoc-citeproc"
PKbioanalysis,,,TRUE,python
pkgdown,,,TRUE,pandoc
pkgnews,,pandoc,TRUE,pandoc
pkgstats,,,TRUE,"ctags, global"
PKI,openssl,,TRUE,OpenSSL library and headers (openssl-dev orsimilar)
PlanetNICFI,,aria2,TRUE,"aria2: apt-get install -y aria2 (deb), gdal-bin:apt-get install -y gdal-bin (deb), libgdal-dev: apt-get install-y libgdal-dev (deb)"
Plasmidprofiler,,pandoc,TRUE,
plinkQC,,,TRUE,plink
plumberDeploy,,,TRUE,"libssh(the original, not libssh2)"
PMCMRplus,gmp mpfr,,TRUE,"gmp, mpfr | file README.md"
pmparser,,,TRUE,"head, unzip, sqlite"
png,libpng,,TRUE,libpng
poisbinom,fftw,,TRUE,fftw3
PoissonBinomial,fftw,,TRUE,fftw3
PoissonMultinomial,fftw,,TRUE,fftw3(>=3.3)
polyglotSQL,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
pomp,,,TRUE,"For Windows users, Rtools (seehttps://cran.r-project.org/bin/windows/Rtools/)."
PONG2,,,FALSE,"PLINK2, minimac4, optional)"
popbayes,,,TRUE,JAGS
porter,,,FALSE,CastXML
potools,,gettext,TRUE,gettext
pRecipe,,,TRUE,"PROJ, https://proj.org/download.html), GDAL(>=, https://gdal.org/en/latest/download.html), NetCDF(>=,https://www.unidata.ucar.edu/software/netcdf/)."
precommit,,git,TRUE,git
PreKnitPostHTMLRender,,,TRUE,pandoc -http://johnmacfarlane.net/pandoc
prettydoc,,,TRUE,pandoc
prevalence,,,TRUE,JAGS (seehttps://mcmc-jags.sourceforge.io/)
PRIMME,,,TRUE,
proccalibrad,,,TRUE,MRTSwath
ProcData,,,TRUE,"Python, Keras, TensorFlow"
proffer,,graphviz pprof,TRUE,pprof (https://github.com/google/pprof)
PROJ,proj,,TRUE,PROJ
proj4,proj sqlite,,TRUE,projor higher (https://proj.org/)
prolific.api,,,TRUE,curl (https://curl.se/)
protolite,protobuf,,TRUE,libprotobuf and protobuf-compiler
protr,,,TRUE,ncbi-blast+ (see<https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html>)
provolleyballr,,,TRUE,Google Chrome browser
prqlr,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
psbcGroup,gsl,,TRUE,
psborrow2,,,TRUE,cmdstan
psychds,,,FALSE,Node.js
PTXQC,,,TRUE,pandoc (http://pandoc.org) for building Vignettesand output reports as HTML
publishTC,,,FALSE,Java
punycoder,,,FALSE,"GNU libidn2 (optional, for native punycode backend)"
pureseqtmr,,,TRUE,PureseqTM(https://github.com/PureseqTM/pureseqTM_package)
PVAClone,,,TRUE,JAGS
pylintR,,pylint,TRUE,pylint
pysd2r,,,TRUE,'python3' needs to built for the same architectureR is built fororbit).
PytrendsLongitudinalR,,,TRUE,"Python, pip (for installing Pythonpackages), pytrends, pandas, requests"
QCA,,,FALSE,POSIX threads (optional)
qCBA,,,TRUE,Java
QF,gsl,,TRUE,GNU GSL
qgisprocess,,,TRUE,"'QGIS' latest or long-term release currentlysupported according to the 'QGIS' release schedule(<https://www.qgis.org/en/site/getinvolved/development/roadmap.html>).Older 'QGIS' releases are not officially supported, but maywork since 'QGIS'"
qio,,,FALSE,zlib
qpdf,libjpeg,,TRUE,libjpeg
qqconf,fftw,,TRUE,fftw3
qtkit,,,TRUE,"Chromium-based browser (e.g., Chrome, Chromium, orBrave)"
quaqcr,,,FALSE,quaqc (https://github.com/bjmt/quaqc)
quarto,,,TRUE,Quarto command line tool(<https://github.com/quarto-dev/quarto-cli>).
questionr,,xclip,TRUE,xclip (Linux)
quitefastmst,,,TRUE,OpenMP
r.blip,,java-bin,TRUE,
R2admb,,,TRUE,AD Model Builder <http://admb-project.org>
R2camtrapdp,,,FALSE,Python with the 'frictionless' package(optional; only for validate_frictionless())Config/testthat/edition:
R2jags,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
R2MLwiN,,,TRUE,"MLwiN, (OpenBUGS, WinBUGS optional)"
R2OpenBUGS,,openbugs,TRUE,OpenBUGS
r2pmml,,java-bin,TRUE,Java
R2wd,,,TRUE,Windows
R2WinBUGS,,openbugs,TRUE,OpenBugs for functions bugs() and openbugs() orWinBUGSfor function bugs()
r5r,,,TRUE,Java JDK
ragg,freetype libpng libtiff libjpeg libwebp,,TRUE,"freetype2, libpng, libtiff, libjpeg, libwebp,libwebpmux"
raisr,,,FALSE,libarchive (via the 'archive' package)
randomForestRHF,,,FALSE,OpenMP
randomForestSRC,,,FALSE,OpenMP
rapidraker,,,TRUE,Java
RAppArmor,,,TRUE,"linux, libapparmor-dev"
rapport,,,TRUE,pandoc (https://johnmacfarlane.net/pandoc) forexporting markdown files to other formats.
RAQSAPI,,,TRUE,package manual and Vignettes require pandoc http://pandoc.org)
rasciidoc,,asciidoc source-highlight,TRUE,"python, by default rasciidoc uses a systeminstallation of asciidoc. If a system installation of asciidocis not available, it downloads the sources from(<http://gitlab.com/asciidoc>). GNU source-highlight isrecommended."
RAthena,,,TRUE,Python and boto3(https://aws.amazon.com/sdk-for-python)
ravetools,fftw,,TRUE,"fftw3 (libfftw3-dev (deb), or fftw-devel (rpm)),pkg-config"
rBahadur,,,FALSE,"curl, gzip (providing zcat), awk"
RBaseX,,,TRUE,Needs a running BaseX server instance. The testuserwith credentials ('Test'/'testBasex') should have admin rights.
rbch,,,TRUE,BCHunlimited
rbedrock,cmake,,TRUE,"cmake, zlib,"
RBesT,,pandoc,TRUE,"pandoc, pngquant,"
rbi,,,TRUE,LibBi
rbi.helpers,,,TRUE,libbi
rbiogeme,,,FALSE,"Python, Biogeme"
rblimp,,,TRUE,Blimp software(<https://www.appliedmissingdata.com/blimp>)
Rblpapi,,,TRUE,A valid Bloomberg installation. The API headers anddynamic library are downloaded from<https://github.com/Rblp/blp> during the build step. See<https://bloomberg.github.io/blpapi-docs/cpp/3.24.6> as well as<https://www.bloomberg.com/professional/support/api-library/>for API documentation. Currently supported platforms areWindows and Linux (both for x86-64 processors only) as well asmacOS (for arm64 only).Other os-cpu pairings are notsupported by Bloomberg and can therefore not be fully supportedhere.
rblt,,,TRUE,libhdf5
rbm25,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
Rborist,,,TRUE,
rCBA,,,TRUE,Java
RCBR,,,TRUE,"MOSEK (http://www.mosek.com) and MOSEK License foruse of Rmosek,"
rcdd,gmp,,TRUE,GMP (GNU MP bignum library from<https://gmplib.org/>)
rcdk,,,TRUE,Java
rcdo,,,TRUE,cdo
rchallenge,,,TRUE,pandoc -http://johnmacfarlane.net/pandoc
Rcmdr,xvfb,,TRUE,
RcmdrMisc,xvfb,,TRUE,
RcmdrPlugin.aRnova,xvfb,,TRUE,
RcmdrPlugin.depthTools,xvfb,,TRUE,
RcmdrPlugin.DoE,xvfb,,TRUE,
RcmdrPlugin.EBM,xvfb,,TRUE,
RcmdrPlugin.Export,xvfb,,TRUE,
RcmdrPlugin.EZR,xvfb,,TRUE,
RcmdrPlugin.FactoMineR,xvfb,,TRUE,
RcmdrPlugin.HH,xvfb,,TRUE,
RcmdrPlugin.KMggplot2,xvfb,,TRUE,
RcmdrPlugin.MA,xvfb,,TRUE,
RcmdrPlugin.MPAStats,xvfb,,TRUE,
RcmdrPlugin.NMBU,xvfb,,TRUE,
RcmdrPlugin.orloca,xvfb,,TRUE,
RcmdrPlugin.PcaRobust,xvfb,,TRUE,
RcmdrPlugin.RiskDemo,xvfb,,TRUE,
RcmdrPlugin.RMTCJags,xvfb,,TRUE,jags
RcmdrPlugin.ROC,xvfb,,TRUE,
RcmdrPlugin.sos,xvfb,,TRUE,
RcmdrPlugin.survival,xvfb,,TRUE,
RcmdrPlugin.TeachingDemos,xvfb,,TRUE,
RcmdrPlugin.TeachStat,xvfb,,TRUE,
RcmdrPlugin.temis,xvfb,,TRUE,
RcmdrPlugin.UCA,xvfb,,TRUE,
Rcplex,,,TRUE,IBM ILOG CPLEX libraries and headers
RcppAlgos,gmp,,TRUE,gmp
RcppBigIntAlgos,gmp,,TRUE,gmp
RcppCCTZ,,,TRUE,A-bit POSIX OS such as Linux or OS X with IANAtime zone data in /usr/share/zoneinfo. On Windows the zoneinfoincluded with R is used; and time parsing support is enabledvia a backport of std::get_time from the LLVM libc++ library.
RcppCWB,bison flex glib2 ncurses,,TRUE,"pcre2, GLib. OnWindows, no prior installations are necessary, as pre-built(i.e. cross-compiled) binaries of required libraries aredownloaded from a GitHub repository(<https://github.com/PolMine/libcl>) during installation. OnmacOS, static libraries of Glib are downloaded(<https://github.com/PolMine/libglib>) if Glib is not present."
RcppGetconf,,,TRUE,A POSIX system. Currently Linux and macOS are knownto work.
RcppGSL,gsl,gsl,TRUE,GNU GSL
RcppMeCab,mecab,,FALSE,"MeCabor higher for Japanese and Chinese(libmecab-dev (deb), mecab-devel (rpm)), mecab-jiebaforMandarin Chinese (https://github.com/lindera/mecab-jieba),mecab-ko(https://github.com/Pusnow/mecab-ko-msvc) forKorean"
RcppParallel,tbb,tbb,FALSE,CMake
RcppPlanc,cmake hdf5 hwloc,,TRUE,"cmake, hdf5, git, patch, gnumake,hwloc,"
RcppRedis,hiredis,,TRUE,"An available hiredis library (eg via packagelibhiredis-dev on Debian/Ubuntu, hiredis-devel onFedora/RedHat, or directly from source from<https://github.com/redis/hiredis>) can be used but version1.0.2 is also included and built on demand if needed. Theoptional 'rredis' package can be installed from the 'ghrr''drat' repo for additional illustrations and tests."
RcppSimdJson,,,TRUE,
RcppTOML,,,TRUE,A  compiler
RCurl,curl,,TRUE,libcurl
Rcurvep,,,TRUE,Java
RCzechia,,,TRUE,"GDAL, GEOS, PROJ"
rdataretriever,,,TRUE,"Python, retriever (version mustbe listed to patch to allow parsing)"
rde,,xclip,TRUE,xclip (https://github.com/astrand/xclip) or xsel(http://www.vergenet.net/~conrad/software/xsel/) for accessingthe X11 clipboard
rDEA,glpk,,TRUE,GLPK
RDesk,,,FALSE,"Windowsor later, Microsoft 'WebView2' Runtime(https://developer.microsoft.com/microsoft-edge/webview2/)"
RDieHarder,gsl,,TRUE,GNU GSL for the GSL random-number generators
rdkitpyr,,,TRUE,"Python, NumPy, RDKit (Python)"
rdoxygen,,doxygen,TRUE,doxygen
Rduckhts,cmake curl openssl,,TRUE,"cmake, zlib, libbz2, liblzma, libcurl,openssl (development headers)"
rdwd,,pandoc,TRUE,
readbitmap,libjpeg libpng,,TRUE,"libjpeg, libpng"
readepi,,,TRUE,"odbc, libmariadbclient-dev"
readNSx,,,FALSE,little-endian platform
REBayes,,,TRUE,MOSEK (http://www.mosek.com) and MOSEK license.
redatamx,,,TRUE,"'Redatam' runtime engine (see https://redatam.org),The dynamic binary library is downloaded from<https://redatam-core.s3.us-west-2.amazonaws.com> during thebuild step. Currently supported platforms are Windows, Linuxand macOS."
redcas,,,TRUE,"'REDUCE' <http://www.reduce-algebra.com>. At leastone of the 'CSL' or 'PSL' dialects must be installed in orderto use the package. Tested with 'REDUCE' releasesandfor both 'CSL' and 'PSL' on Linux, andandfor 'CSL'on MacOS"
redist,gmp libxml2,python3,TRUE,python
redland,redland,,TRUE,"Mac OSX: redland ; Linux: librdf0, librdf0-dev"
redux,hiredis,,TRUE,hiredis
RegimeChange,,,TRUE,"Julia for optional high-performancebackend, Python with TensorFlow for deep learningmethods"
relMix,,,TRUE,"tcltk, tk"
remiod,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net/)
REMixed,,,TRUE,'Monolix'(<https://monolixsuite.slp-software.com/>)
remotes,,,TRUE,"Subversion for install_svn, git for install_git"
REPLesentR,,,TRUE,Presentations written in (R)Markdown require Pandoc(http://pandoc.org).
RepoGenerator,,,TRUE,"GitHub, 'RStudio'"
reportfactory,,,TRUE,pandoc - http://pandoc.org
reprex,,,TRUE,pandoc - https://pandoc.org/
reproducible,,unrar,FALSE,'unrar' (Linux/macOS) or '7-Zip' (Windows) to workwith '.rar' files.
reproj,,,TRUE,PROJ
reservoirnet,,,TRUE,Python
restoptr,,,TRUE,
ReSurv,,,TRUE,
reticulate,,python3,TRUE,Python
revert,,,TRUE,
revise,,,TRUE,pandoc - http://pandoc.org
rextendr,,cargo,TRUE,Rust 'cargo'; the crate 'libR-sys' must compilewithout error
rfacts,,,TRUE,"FACTS Linux engines, FLFLL,Mono"
rflsgen,,,TRUE,Java
rfriend,,,TRUE,Pandoc
rfviz,xvfb,,TRUE,
rgeedim,,,TRUE,Python
RGF,,scikit-learn numpy scipy,TRUE,"Python, rgf_python, scikit-learn, scipy, numpy. Detailed installation instructions foreach operating system can be found in the README file."
rgl,libgl libglu libpng freetype,,TRUE,"OpenGL and GLU Library (Required for display in R.See ""Installing OpenGL support"" in README.md. Not needed ifonly browser displays using rglwidget() are wanted.), zlib(optional), libpng, optional), FreeType (optional),pandoc, needed for vignettes), LaTeX needed foroptional latex3d() examples."
Rglpk,glpk,,TRUE,"GLPK library package (e.g., libglpk-dev onDebian/Ubuntu)"
rgnparser,,,TRUE,gnparser (<https://github.com/gnames/gnparser>)
rgph,,,TRUE,Java
rgrass,,grass,TRUE,GRASS
rGroovy,,,TRUE,Java
rgrpc,,,FALSE,"gRPC C++ (testedto and protobuflibraries with development headers, found via 'pkg-configgrpc++ protobuf': 'libgrpc++-dev' and 'libprotobuf-dev'(Debian, Ubuntu); 'grpc-cpp', 'grpc-devel' and 'protobuf-devel'(Fedora); 'grpc', 'protobuf' and 'pkgconf' (Homebrew). Windows:bundled with Rtoolsand later. Without them the packageinstalls as a stub whose functions error; see grpc_available()."
RH2,,,TRUE,java runtime
Rhobots,,,FALSE,Microsoft Visual C++ Redistributable(Windowsonly; required by torch)
Rhpc,,,FALSE,"R built as a shared or static library, 'MPI'library."
ridge,gsl,,TRUE,Gnu Scientific Library version
rim,,maxima,TRUE,
rinet,,,TRUE,
rip.opencv,,,FALSE,OpenCVor newer
rirods,,,TRUE,iRODS C++ HTTP API(<https://github.com/irods/irods_client_http_api>)
rixpress,,,TRUE,Nix
rjags,jags,,TRUE,JAGSx.y
rJava,java,,TRUE,"Java JDKor higher (for JRI/REngine JDKorhigher),"
rjd3bench,,,FALSE,Java
rjd3bridge,,,FALSE,Java
rjd3filters,,,FALSE,Java
rjd3highfreq,,,FALSE,Java
rjd3jars,,,FALSE,Java
rjd3providers,,,TRUE,Java
rjd3toolkit,,,TRUE,Java
rjd3tramoseats,,,TRUE,Java
rjd3workspace,,,FALSE,Java
rjd3x13,,,TRUE,Java
rjd3xjars,,,FALSE,Java
RJDemetra,,,TRUE,Java
rjdmarkdown,,,TRUE,Java
rjdqa,,,TRUE,Java
RJSDMX,,,TRUE,Java
rjsf,,,FALSE,"Python, Quarto command line tool"
rjuliabugs,,,TRUE,"Julia with the following packagesinstalled: 'JuliaBUGS.jl', 'LogDensityProblemsAD.jl','ReverseDiff.jl', 'AdvancedHMC.jl', 'AbstractMCMC.jl','LogDensityProblems.jl', 'MCMCChains.jl', 'RCall.jl','Suppressor.jl'."
rkafkajars,,,TRUE,Java JDKor higher
RKEA,,,TRUE,Java
RKEAjars,,,TRUE,Java
rladybugdb,,,FALSE,CMake
rlas,,,FALSE,"GDAL, GEOS, PROJ, sqlite3,"
Rlibeemd,gsl,,TRUE,GNU GSL
rlibkriging,cmake,,TRUE,"cmake,"
RMariaDB,mysql,,TRUE,"libmariadb-client-lgpl-dev or libmariadb-dev orlibmysqlclient-dev, with libssl-dev (deb),mariadb-connector-c-devel or mariadb-devel (rpm),mariadb-connector-c or mysql-connector-c (brew)"
RMark,,,TRUE,"notepad.exe, mark32.exe or mark64.exe on Windowsand only mark on Linux (see README.txt in packagedirectory)"
rmarkdown,,pandoc,TRUE,pandoc - http://pandoc.org
rmatio,,,TRUE,zlib headers and library.
rmcfs,,,TRUE,Java
rmdcev,,,FALSE,CmdStan
RmdConcord,,,TRUE,"pandocwith 'commonmark_x' processing and'sourcepos' extension, needed for 'rmarkdown' formats)."
rmdfiltr,,,TRUE,pandoc; https://pandoc.org)
RmecabKo,mecab,,TRUE,
rMIDAS,,,TRUE,Python
rMIDAS2,,,FALSE,Python with the 'midasverse-midas-api'package
RMOA,,,TRUE,Java
RMOAjars,,,TRUE,Java
rmoriebricklayer,,,FALSE,"libcurl (deb: libcurl4-openssl-dev, rpm:libcurl-devel, brew: curl), zlib (deb: zlib1g-dev, rpm:zlib-devel)."
Rmosek,,,TRUE,MOSEK and MOSEK License
Rmpfr,gmp mpfr,,TRUE,"gmp, mpfr, pdfcrop (part ofTexLive) is required to rebuild the vignettes."
Rmpi,openmpi,openmpi,TRUE,
RMySQL,mysql,,TRUE,"libmariadb-client-dev | libmariadb-client-lgpl-dev| libmysqlclient-dev (deb), mariadb-devel (rpm), mariadb |mysql-connector-c (brew), mysql56_dev (csw)"
rnetcarto,gsl,,TRUE,GNU GSL
RNetCDF,netcdf udunits,,TRUE,"netcdf, udunits-2"
RNetLogo,,,TRUE,"Java, NetLogo"
RoBMA,jags,,TRUE,JAGS(https://mcmc-jags.sourceforge.io/)
RoBSA,jags,,TRUE,JAGS(https://mcmc-jags.sourceforge.io/)
robscale,,,TRUE,
RODBC,odbc,,TRUE,An ODBC3 driver manager and drivers.
rodeo,,,TRUE,The tools to run 'R CMD SHLIB' on 'Fortran' code.The used 'Fortran' compiler must support pointer initializationwhich is a feature of thestandard.
roger,,,TRUE,roger-base (for interface functions only)
Rogue,,,TRUE,
ROI.plugin.symphony,coin-or-symphony,,TRUE,
rolog,,,TRUE,
Romeb,,,TRUE,JAGS
ropenblas,,,TRUE,GCC Compiler Suite (C and Fortran)
ROpenCVLite,,cmake,TRUE,cmake
ROracle,,,TRUE,curl Oracle Instant Client or Oracle DatabaseClient
roxigraph,cargo libclang snappy,,TRUE,"Cargo (Rust's package manager), rustc,lib-dev (for RocksDB bindings), libsnappy-dev (for RocksDBcompression)"
Rpadrino,,,TRUE,libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb).
rpanel,xvfb bwidget,bwidget,TRUE,
RPesto,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
rpic,,,FALSE,"Cargo (Rust's package manager), rustc"
Rpoppler,poppler,,TRUE,"Poppler Glib interface headers and libraries(<http://poppler.freedesktop.org/>) [Debian/Ubuntu:libpoppler-glib-dev, Fedora: poppler-glib-devel]"
rpostgis,,,TRUE,'PostgreSQL' with 'PostGIS' extension
RPostgres,postgresql,,TRUE,libpq: libpq-dev (deb) or postgresql-devel(rpm)
RPostgreSQL,postgresql,,TRUE,
rPref,,,TRUE,Windows: cmd.exe and cscript.exe
RProtoBuf,protobuf,,TRUE,"ProtoBuf libraries and compiler versionorlater; On Debian/Ubuntu these can be installed aslibprotoc-dev, libprotobuf-dev and protobuf-compiler, while onFedora/CentOS protobuf-devel and protobuf-compiler are needed.A modern compiler is required as well."
RPushbullet,,,TRUE,"A user API key (which one can request from thewebsite at <http://www.pushbullet.com>), and one or moredevices to push messages to which may be any one of an (Androidor iOS) phone, a (Chrome or Firefox, or Opera or Safari)browser or the (Windows or Mac) desktop application providedthe corresponding Pushbullet 'app' has been installed on anyone of these."
RPyGeo,,,TRUE,"Python, ArcGIS"
RQuantLib,quantlib boost,,TRUE,"QuantLib library fromhttps://quantlib.org, Boost library from https://www.boost.org"
rriskDistributions,xvfb,,TRUE,"Tcl/Tk, Tktable"
RSAGA,,saga,TRUE,SAGA GISLTS -
Rsagacmd,,saga,TRUE,SAGA-GIS
rsahmi,,,TRUE,
rsamplr,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
RSclient,openssl,,TRUE,
Rserve,,,TRUE,"libR,"
rshift,cargo,,TRUE,rustc & cargo if building from source
RSiena,xvfb,,TRUE,
Rsmlx,,,TRUE,'Monolix' (<https://monolix.lixoft.com>)
rsparkling,,,TRUE,Java
rSRD,,,TRUE,Rtools for Windows
Rssa,fftw,,TRUE,fftw
RsSimulx,,,TRUE,'Simulx' (<http://simulx.lixoft.com/>)
rstan,,pandoc,TRUE,pandoc
rstanarm,,pandoc,TRUE,"pandoc, pandoc-citeproc"
rstantools,,pandoc,TRUE,pandoc
rstudio.prefs,,,FALSE,RStudio
rsubgroup,,,TRUE,Java
rsvg,librsvg2,,TRUE,librsvg2 (at least version
rswipl,cmake libarchive expat,,FALSE,"CMake, pandoc, libarchive,libregex, libexpat, liblzma, libzstd, liblz4, libz2, libz,libbcrypt, libutf8proc"
Rsymphony,coin-or-symphony,,TRUE,SYMPHONY libraries and headers
rsyncrosim,,,TRUE,SyncroSim
rsyslog,,,TRUE,POSIX.1-2001
RTD,,,TRUE,"embulk, embulk-output-td"
rtdists,,,FALSE,GNU GSL (libgsl-dev/gsl)
rtemis.draw,,,FALSE,Node.js for optional SVG export
rtika,,,TRUE,
rtiktoken,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
rtmpt,gsl,,TRUE,GSL
runjags,jags,,TRUE,JAGS(https://mcmc-jags.sourceforge.io/)
rush,,,FALSE,Redis
rvg,,,TRUE,libpng
rviewgraph,,,TRUE,Java
rvisidata,,,TRUE,visidata
rvMF,gmp mpfr,,TRUE,"gmp, mpfr"
RWeka,,,TRUE,Java
RWekajars,,,TRUE,Java
rwig,,,FALSE,"autoconf, CUDA, only for Linux, optional)"
RWinEdt,,,TRUE,WinEdt
rzig,,,FALSE,"Zigx orx(https://ziglang.org/download/), needed to install packagescreated with rzig"
rzmq,zeromq,,TRUE,ZeroMQ: libzmq3-dev (deb) or zeromq-devel(rpm)
s2,cmake openssl abseil,,TRUE,"cmake, OpenSSL, Abseil"
s2dv,,,TRUE,cdo
sacRebleu,,,TRUE,lib/llvm-config
saeHB,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
saeHB.panel,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
saeHB.panel.beta,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
saeHB.spatial,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
saeHB.Spatial.Beta,,,FALSE,JAGS (http://mcmc-jags.sourceforge.net)
saeHB.twofold,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
saeHB.unit,,,TRUE,JAGS (http://mcmc-jags.sourceforge.net)
salso,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
sapo,,,TRUE,"GDAL, GEOS, PROJ"
saros.base,,,TRUE,None.
sarsop,,,TRUE,"mallinfo, hence Linux, MacOS or Windows"
SASmarkdown,,,TRUE,SAS
sasquatch,,,TRUE,"python, SASPy, java required forIOM access method"
sbert,,,FALSE,ONNX Runtime
sbrl,gmp gsl,,TRUE,"gmp, gsl"
scanr,,,FALSE,"Cargo (Rust's package manager), rustc, Quarto CLI"
sceua,,,FALSE,"Cargo (Rust's package manager), rustc"
scip,,,FALSE,"CMake,"
scModels,,,FALSE,"gmp, mpfr"
scNPM,,,FALSE,OpenMP
sd2R,,,FALSE,curl or wget (for downloading vocabularyfiles during installation)
sdcTable,glpk gmp,,TRUE,"GLPK library, including -dev or -devel part"
SDMtune,,java-bin,TRUE,Java
seewave,,,TRUE,LIBSNDFILE
SemiCompRisks,gsl,,TRUE,
sendigR,,,TRUE,Python(>=3.9.6)
seqinr,,,TRUE,zlib headers and library.
seqminer,,,TRUE,"zlib headers and libraries,  optionallyalso bzip2 and POSIX-compliant regex functions."
sequoia,,,TRUE,Fortran95
serodynamics,,,FALSE,JAGS
seroreconstruct,,,FALSE,TBB
sezgi,,,FALSE,"Cargo (Rust's package manager), rustc"
sf,gdal geos proj sqlite,,TRUE,"GDAL, GEOS, PROJ,sqlite3"
sftpR,,,FALSE,libcurl: libcurl (with libssh2 support)
SGP,,tex-pdfpages,TRUE,(PDF)LaTeX (https://www.latex-project.org/) with'pdfpages' package for studentGrowthPlot option in visualizeSGPto bind together student growth plots into school catalogs
shard,,,FALSE,"POSIX shared memory (optional), memory-mapped files"
sharx,,,TRUE,jags
shinyalert,,pandoc,TRUE,
ShinyBlock,,,FALSE,"Python, ecdsa (Python package)"
shinyelectron,,,FALSE,"Node.js, npm"
shinyInvoice,,,TRUE,pandoc
shinyjs,,pandoc,TRUE,
shinyloadtest,,pandoc,TRUE,pandoc - http://pandoc.org
shinyscholar,,,TRUE,pandoc is required for generating reproduciblereports
shinytest,,,TRUE,PhantomJS (http://phantomjs.org/)
shinyWGD,,,TRUE,"pandoc, pandoc-citeproc"
shortcuts,,,TRUE,RStudio
showtext,libpng freetype,,TRUE,"zlib, libpng, FreeType"
shrinkGPR,,,TRUE,"torch backend, for installation guide seehttps://cran.r-project.org/web/packages/torch/vignettes/installation.html"
shrinkr,,,FALSE,compiler
SIBER,,,TRUE,JAGS
simhelpers,,,TRUE,RStudio
SimInf,gsl,,TRUE,GNU Scientific Library (GSL)
simplace,,,TRUE,Java
simplermarkdown,,pandoc,TRUE,Pandoc (http://pandoc.org) needs to installed andavailable in the search path.
sims,,,TRUE,JAGSx.y
simStateSpace,gsl,,TRUE,GNU GSL
sjtable2df,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
slendr,,,TRUE,'SLiM' is a forward simulation software forpopulation genetics and evolutionary biology. See<https://messerlab.org/slim/> for installation instructions andfurther information. The 'Python' coalescent framework'msprime' and the 'tskit' module can by installed by followingthe instructions at <https://tskit.dev/>.
slowraker,,java-bin,TRUE,Java
slurm,,,TRUE,"Slurm command line programs (sacct, squeue)"
smam,gsl,,TRUE,"GNU GSL,"
smile,,,TRUE,"GDAL, GEOS, PROJ"
smoothbp,,,FALSE,"Cargo (Rust's package manager), rustc"
snSMART,,,TRUE,JAGSx.y
socketR,,,FALSE,Linux operating system with POSIX socket APIs and compiler
socratadata,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
sodium,libsodium,,TRUE,libsodium
SOFIA,,,TRUE,
soilFlux,,,FALSE,"Python, TensorFlow, Keras"
soilhypfit,,,TRUE,"gmp, mpfr"
soilVAE,,,FALSE,Python; TensorFlow; Keras
sommer,,,FALSE,"METIS graph partitioning library (optional; enablesnested-dissection sparse ordering for large relationshipmatrices, auto-detected at configure time, falls back to AMDordering when absent), NVIDIA CUDA toolkit with cuBLAS andcuSOLVER (optional; enables GPU kernels on Linux throughSOMMER_CUDA_HOME; CUDA libraries are loaded dynamically)"
soptdmaeA,xvfb,,TRUE,
sound,,,TRUE,"For playing sounds, a command line system tool forplaying wav-files is required."
sourcoise,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
spacemodR,,,FALSE,"Julia (optional, for dispersal with'Omniscape')"
spaMM,gsl,,TRUE,GNU Scientific Library (GSL)
sparkbq,,,TRUE,Sparkx)
sparklyr,,java-bin,TRUE,"Spark:x, orx, orx"
sparklyr.flint,,,TRUE,Spark:x or above
sparklyr.nested,,,TRUE,Spark:x orx
sparktf,,,TRUE,
sparselu,,,FALSE,"SuiteSparse (UMFPACK, AMD, SuiteSparse_config)"
sparsesurv,,,TRUE,JAGSx)
spate,fftw,,TRUE,fftw3
SpatialDownscaling,,,TRUE,"Python, TensorFlow, Keras"
spatPomp,,,TRUE,"For Windows users, Rtools (seehttps://cran.r-project.org/bin/windows/Rtools/)."
spatsoc,,,TRUE,"GDAL, GEOS, PROJ,sqlite3"
spcosa,,,TRUE,Java
speakeasyR,,,TRUE,arpack (optional)
specklestar,fftw,,TRUE,
specmine,,,FALSE,"Python, Python module 'nmrglue'"
spherepc,,,TRUE,XQuartz (on MacOS)
spongecake,,ffmpeg-bin,TRUE,FFmpeg (http://ffmpeg.org)
spopt,,,FALSE,"Cargo (Rust's package manager), rustc"
sportyR,,,TRUE,"pandoc, pandoc-citeproc"
SQLFormatteR,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
SqlRender,,,TRUE,Java
ssh,libssh,,TRUE,"libssh(the original, not libssh2)"
SSHAARP,,gmt ghostscript,TRUE,"GMTor, Ghostscript"
sstvars,,,TRUE,"BLAS, LAPACK"
ssw,,,TRUE,"Python, ssw-py. Detailedinstallation instructions can be found in the README file."
StanHeaders,,,TRUE,pandoc
stanza,,,TRUE,"R, Python, stanza"
staplr,,,TRUE,Java
startR,,,TRUE,cdo ecFlow
starvz,,,TRUE,"arrow package with gzip codec, StarPU"
Statamarkdown,,,TRUE,Stata
statgenGxE,,pdflatex,TRUE,pdflatex
statgenSTA,,pdflatex,TRUE,pdflatex
stddiff.spark,,,TRUE,Apache Spark (tested with
stevedore,,docker,TRUE,docker
sTiles,,,FALSE,"the 'sTiles' solver library (libstiles.so on Linux,libstiles.dylib on macOS, libstiles.dll on Windows), obtainedwith sTiles_install_library() or supplied by the user"
stmgp,,,TRUE,PLINK must be installed
stpphawkes,gsl,,TRUE,GNU GSL
strawr,curl,,TRUE,libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb)
streambugs,,,TRUE,C99
streamMOA,,,TRUE,Java
stressor,,,TRUE,python(>=3.8.10)
string2path,cargo,,TRUE,
stringi,,,TRUE,"ICU4C, optional)"
submitr,,,FALSE,"SSH client, HTCondor (https://htcondor.org)"
subtitles,,,FALSE,"ffmpeg, libass"
sudachir,,,TRUE,Python
summata,,,FALSE,"All optional. A 'LaTeX' distribution providingpdflatex or xelatex, and kpsewhich, for PDF output fromtable2pdf(); pdfcrop for auto-sized PDF output; Ghostscript forthe optional font embedding in forestsave(). Each featurereports the absence of its tool and the remainder of thepackage is unaffected."
sundialr,,,FALSE,cmake
SuperGauss,fftw,,TRUE,fftw3
surveyvoi,jags fftw gmp mpfr,,TRUE,"JAGS (optional), fftw3, gmp, gmpxx, mpfr, autoconf,automake"
survSNP,gsl,,TRUE,GNU GSL
svDialogs,,zenity yad,TRUE,"zenity, yad"
svglite,libpng,,TRUE,libpng
svKomodo,,,TRUE,Komodo Edit(https://www.activestate.com/products/komodo-ide/)
switchr,,git subversion,TRUE,"git, svn"
SymbolicDeterminants,,,TRUE,
symengine,cmake gmp mpfr,,TRUE,"cmake, gmp, mpfr"
symSEM,,,TRUE,Python
SymTS,gsl,,TRUE,
sysfonts,libpng freetype,,TRUE,"zlib, libpng, FreeType"
systemfonts,freetype,,TRUE,"fontconfig, freetype2"
tables,,,TRUE,pandoc for vignettes
tabr,,lilypond,TRUE,LilyPond v2.22.1-2+ (needed for rendering sheetmusic or writing MIDI files)
tabulapdf,,,TRUE,"Java: openjdk-11-jdk (deb),java-11-openjdk.x86_64 (rpm), openjdk@11 (brew)"
tabular,,,FALSE,"Quarto command line tool(<https://github.com/quarto-dev/quarto-cli>), needed only tobuild the package vignettes. Optional for PDF output: a TeXdistribution (e.g. TinyTeX) or Typst(<https://github.com/typst/typst>, standalone or the copybundled with Quarto); see check_latex() and check_typst()."
talib,,,FALSE,CMake
tantivyr,,,FALSE,"Cargo (Rust's package manager), rustc"
tapkee,,,TRUE,'tapkee' (http://tapkee.lisitsyn.me/)
TAQMNGR,,,TRUE,
targeted,,,TRUE,Quarto command line tools(https://github.com/quarto-dev/quarto-cli).
tarpolyglot,,,FALSE,"The external language toolchains are optional andeach is only required by its matching targets constructor: aPython installation for tar_target_py(), a Julia installationfor tar_target_jl(), and a Rust toolchain with Cargo fortar_target_rs() (on Windows, the GNU toolchain, to match R'sABI). A pipeline that uses a single language needs only thatlanguage's toolchain, and a pipeline that uses none of theseconstructors needs no external toolchain at all."
taxodist,,,FALSE,internet access for online taxonomy retrieval
tcltk2,xvfb,,TRUE,"Tcl/Tk, Tktable, optional)"
TDA,gmp,,TRUE,"gmp,"
TDCM,,,TRUE,pandoc
teems,,,FALSE,Docker (https://www.docker.com)
telegramR,,,FALSE,"OpenSSL: libssl-dev (deb), openssl-devel(rpm), openssl@3 (brew)"
tensorflow,,,TRUE,TensorFlow (https://www.tensorflow.org/)
tera,,,FALSE,"Cargo (Rust's package manager), rustc"
tergo,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
terminalgraphics,,,TRUE,A terminal emulator supporting the TerminalGraphics Protocol(<https://sw.kovidgoyal.net/kitty/graphics-protocol/>) orSixel.
terra,gdal geos proj sqlite,,TRUE,"GDAL, GEOS, PROJ, TBB, sqlite3"
tesseract,tesseract leptonica,,TRUE,Tesseract(libtesseract-dev /tesseract-devel) and Leptonica (libleptonica-dev /leptonica-devel). On Debian you need to install the Englishtraining data separately (tesseract-ocr-eng)
TexExamRandomizer,,latexmk,TRUE,
texor,,,TRUE,pandoc - https://pandoc.org
texPreview,,tex-standalone,TRUE,
texreg,,pandoc,TRUE,"pandoc suggested for using wordregfunction; LaTeX packages tikz, booktabs, dcolumn, rotating,thumbpdf, longtable, paralist for the vignette"
text,,,TRUE,Python
TextAnalysisR,,,FALSE,Python with spaCy forlemmatization and sentence-transformers for embeddings(optional)
textrecipes,,,TRUE,""""""
textshaping,freetype harfbuzz fribidi,,TRUE,"freetype2, harfbuzz, fribidi"
textTinyR,,,TRUE,libarmadillo: apt-get install -y libarmadillo-dev(deb)
tfaddons,,,TRUE,
tfautograph,,,TRUE,TensorFlow (https://www.tensorflow.org/)
tfdatasets,,,TRUE,TensorFlow(https://www.tensorflow.org/)
tfestimators,,,TRUE,TensorFlow (https://www.tensorflow.org/)
tfevents,protobuf,,TRUE,"libprotobuf, protobuf-compiler"
tfhub,,,TRUE,TensorFlow(https://www.tensorflow.org/)
tfio,,,TRUE,TensorFlow(https://www.tensorflow.org/)and TensorFlow IO(https://github.com/tensorflow/io)
tfprobability,,,TRUE,TensorFlow Probability(https://www.tensorflow.org/probability)
theeuh,,,FALSE,"ONNX Runtime, optional at runtime)"
theorytools,,,TRUE,Python
Thermimage,,exiftool ffmpeg-bin imagemagick-bin,TRUE,"exiftool, perl, ffmpeg, imagemagick"
tidycwl,,pandoc,TRUE,"PhantomJS (https://phantomjs.org), pandoc - https://pandoc.org."
tidyGenR,,,TRUE,cutadapt(https://cutadapt.readthedocs.io/en/stable/)
tidymedia,,,FALSE,"FFmpeg (https://ffmpeg.org/), MediaInfo(https://mediaarea.net/en/MediaInfo)"
tidync,,,TRUE,netcdf udunits-2
tiff,libjpeg libtiff,,TRUE,tiff and jpeg libraries
tikzDevice,,tex-pgf,TRUE,pgf
tiledb,tiledb,,TRUE,"A  compiler is required; on macOS compilationversionor later is required. Optionally cmake (only whenTileDB source build selected), curl (only when TileDB sourcebuild selected)), and git (only when TileDB source buildselected); on x86_64 and M1 platforms pre-built TileDB Embeddedlibraries are available at GitHub and are used if no TileDBinstallation is detected, and no other option to build ordownload was specified by the user."
tiler,,gdal-python,TRUE,"Python, python-gdal library (For Windows,gdal installed via OSGeo4W <https://trac.osgeo.org/osgeo4w/>recommended) clipboard"
timechange,,,TRUE,A system with zoneinfo data (e.g./usr/share/zoneinfo). On Windows the zoneinfo included with Ris used.
tinyimg,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
tkImgR,xvfb,tkimg,TRUE,"Tcl/Tk. To read and write other formatsthan PPM/PGM, PNG and GIF it is required the 'tkImg' for'Tcl/Tk' (https://sourceforge.net/projects/tkimg/), or thedebian 'libtk-img' package (Ubuntu) or the RPM 'tkimg' package(Fedora or openSUSE)."
tkrplot,,,TRUE,Windows or X11
tkRplotR,xvfb,,TRUE,Tcl/Tk
TMB,,g++,TRUE,
tok,cargo,,FALSE,"Cargo (Rust's package manager), rustc"
tomledit,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
TooManyCellsR,,,TRUE,'TooManyCells'(https://github.com/GregorySchwartz/too-many-cells)
topicmodels,gsl,,TRUE,GNU Scientific Library version
topicmodels.etm,,,TRUE,LibTorch (https://pytorch.org/)
topics,,,TRUE,Python
torch,,,TRUE,LibTorch (https://pytorch.org/); Only x86_64platforms are currently supported except for ARM system runningmacOS.
trackdem,,python3 ffmpeg-bin exiftool,TRUE,"Python, Libav, ExifTool"
TreeBUGS,,,TRUE,JAGS (https://mcmc-jags.sourceforge.io/)
TreeDist,,,TRUE,pandoc-citeproc
tsapp,,,TRUE,"under Linux, fftwtools needs libfftw3-dev"
TTAinterfaceTrendAnalysis,xvfb,,TRUE,
tth,,,TRUE,USE_C17
TTR.PGM,,,TRUE,CXX17
tvbounds,,,FALSE,For tvbounds_counterfactual(): Julia andthe Artelys KNITRO solver with a valid license.
TVMM,xvfb,,TRUE,
twc,,,TRUE,"PROJ, https://proj.org/download.html), GDAL(>=, https://gdal.org/download.html), NetCDF(>=,https://www.unidata.ucar.edu/software/netcdf/)."
tynding,,,TRUE,
typr,,,TRUE,Typst command line tool(<https://github.com/typst/typst>) or Quarto command line tool(<https://github.com/quarto-dev/quarto-cli>).
ubiquity,,perl,TRUE,Perl
udunits2,udunits,,TRUE,udunits fromhttps://www.unidata.ucar.edu/software/udunits/
UHM,,,TRUE,JAGSx.y
uHMM,xvfb,,TRUE,
unigd,libtiff libpng,,TRUE,"Cairo (optional, for raster output), libtiff(optional, for TIFF output), libpng, zlib"
units,udunits,,TRUE,udunits-2
unix,,,TRUE,"POSIX.1-2001, AppArmor (optional)"
unmconf,,,TRUE,JAGS(http://mcmc-jags.sourceforge.net)
Uno,,,FALSE,"CMake,"
unsum,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
untb,,pari,TRUE,PARI/GP[strongly recommended forlogkda()]
uqsa,,,TRUE,
URooTab,,,TRUE,EViews
ustats,,,FALSE,"Python; Python packages: u-stats, numpy,torch (installed automatically on first use, or viasetup_ustats())"
uuidx,,,FALSE,"Cargo (Rust's package manager), rustc"
V8,v8,,TRUE,"On Linux you can build against libv8-dev (Debian)or v8-devel (Fedora). We also provide static libv8 binaries formost platforms, see the README for details."
valection,,,TRUE,
vapour,gdal proj sqlite,,TRUE,"libgdal-dev, GDAL, PROJ"
varitas,,perl bwa,TRUE,"perl, bedtools, bwa"
varPro,,,TRUE,OpenMP
vaultr,,,TRUE,vault
VBLPCM,gsl,,TRUE,Gnu Scientific Library
VCFArrow,,,FALSE,zlib
vcfppR,curl,,TRUE,"libcurl: libcurl-devel (rpm) orlibcurl4-openssl-dev (deb), ."
vcfR,devscripts,,TRUE,
vdiffr,libpng,,TRUE,libpng
VectorForgeML,,,TRUE,OpenMP (optional)
vegawidget,,,TRUE,To use image functions for MacOS: X11
venneuler,,,TRUE,Javaor higher
VertexWiseR,,,FALSE,"Miniconda3 (v26.7.1), Python (<= v3.12), BrainStat(v0.4.2), vtk (v9.3.1), numpy (<= v1.26.4), nilearn (<=v0.12.0), netneurotools (<= v0.2.5)"
virtuoso,,,TRUE,"virtuoso-opensource (Linux). For Mac & Windows,this package can automate Virtuoso installation."
visreg,,,FALSE,Quarto command line tool
vitae,,,TRUE,pandoc - http://pandoc.org
VMDecomp,,,TRUE,"libarmadillo: apt-get install -y libarmadillo-dev(deb), libblas: apt-get install -y libblas-dev (deb),liblapack: apt-get install -y liblapack-dev (deb),libarpack++2: apt-get install -y libarpack++2-dev (deb),: apt-get install -y  (deb)"
vmr,,vagrant,TRUE,Vagrant <https://www.vagrantup.com>
vol2birdR,gsl hdf5 proj,,TRUE,"GSL, HDF5, PROJ"
vostokR,,,FALSE,OpenMP (optional)
warbleR,,,FALSE,"fftw3,  sox, Ghostscript, libsndfile, FLAC(optional)"
watcher,fswatch,,FALSE,"'libfswatch' (optional, bundled copy compiledotherwise)"
waysign,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
webdriver,,,TRUE,PhantomJS (http://phantomjs.org/)
WebGestaltR,,,FALSE,"Cargo (Rust's package manager), rustc v1.63.0+"
webp,libwebp,,TRUE,libwebp
webshot,,imagemagick-bin,TRUE,"PhantomJS for taking screenshots, ImageMagick orGraphicsMagick and OptiPNG for manipulating images."
websocket,openssl,,TRUE,OpenSSL
weightederm,,,FALSE,"Python, weightederm Python package"
wgaim,,,TRUE,asreml-Rx
WH,,,TRUE,LAPACK
whirl,,,TRUE,Quarto command line tool(<https://github.com/quarto-dev/quarto-cli>).
whitebox,,,TRUE,WhiteboxTools(https://github.com/jblindsay/whitebox-tools/releases/latest)
worcs,,,TRUE,pandoc - https://pandoc.org
wordnet,,wordnet,TRUE,Java; WordNet database files (directdownload:<https://wordnetcode.princeton.edu/3.0/WNdb-3.0.tar.gz>; Debianand Fedora package: wordnet)
workflowr,,,TRUE,pandoc - https://pandoc.org
writexl,,,TRUE,zlib
WriteXLS,,perl,TRUE,Perl
x13binary,,,TRUE,Fortran sources included in `tools/x13as_html`require a Fortran compiler
xactonomial,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
xbioclim,,,FALSE,"optionally GDAL withgdal-config, CUDA toolkit with nvcc for GPUacceleration"
xdvir,freetype,,TRUE,freetype2
xlcharts,,,TRUE,"Python, Conda"
XLConnect,,,TRUE,Java
xlsx,,,TRUE,java
xlsxjars,,,TRUE,java
XML,libxml2,,TRUE,libxml2
xml2,libxml2,,TRUE,"libxml2: libxml2-dev (deb), libxml2-devel (rpm)"
xmlrectr,,,FALSE,"libxml2 development files, pkg-config; on Windowsuse the matching Rtools toolchain"
xmpdf,,ghostscript exiftool,TRUE,'ghostscript' or 'pdftk' for editing pdf bookmarksand/or documentation info entries. 'exiftool' for editing pdfdocumentation info entries and/or xmp metadata.
xslt,libxslt,,TRUE,"libxslt: libxslt1-dev (deb), libxslt-devel (rpm)"
yaml12,cargo,,FALSE,"Cargo (Rust's package manager), rustc,xz. On Windows ARM64, source installs also require MicrosoftC++ Build Tools with ARM64 components."
yamlme,,,TRUE,pandoc - http://pandoc.org
ymd,cargo,,TRUE,"Cargo (Rust's package manager), rustc, xz"
zmij,,,FALSE,"Cargo (Rust's package manager), rustc, xz"
zoomerjoin,cargo,,TRUE,"Cargo (Rust's package manager), rustc"
zot,,,TRUE,
zucrypt,,,FALSE,"A C99 compiler. No system cryptographic library isused, no CMake, Python or Perl is required, and nothing isdownloaded or generated during installation: the backend isbuilt from vendored sources, with an explicit object list inportable make."
zuexact,,,FALSE,C99