2015-01-03 19:56:29 UTC; Steven Harris Ranney
2018-01-10 08:38:11 UTC; Benjamin Schlegel
2012-06-11 14:36:21 UTC; Sophie Baillargeon
2010-01-31 13:29:31 UTC; Jens Henrik Badsberg
2017-12-06 14:42:27 UTC; Benjamin Schlegel
2016-10-16 07:32:22 UTC; Engineering Broker
2017-08-13 21:27:45 UTC; NvTomus InDemonic
2015-02-26 17:45:29 UTC; Sophie Baillargeon
2015-08-23 02:08:23 UTC; Fernando de Villar
2017-09-19 16:00:57 UTC; Alberto Vico Moreno
2016-02-23 18:10:11 UTC; LARMARANGE Joseph
2017-07-05 08:50:23 UTC; Gabriele Rovigatti
2014-08-28 18:37:46 UTC; Sophie Baillargeon
2017-01-03 15:34:03 UTC; Guybrush Threepwood
2016-07-26 19:41:07 UTC; Timothy Schwinghamer
2017-08-15 05:32:43 UTC; Aurnov Chattopadhyay
2014-10-17 18:39:03 UTC; Christiane Dargatz
2016-03-19 23:54:53 UTC; Sophie Baillargeon

Image Magick (for reading non PPM format), dcraw
(for reading RAW images).
Optionally Latte-integrale, Bertini, and Macaulay2.
Cygwin is required for each of the above for Windows users. See
INSTALL file for details.
None, but greater than 12 GB of RAM highly
recommended.
ImageMagick (http://imagemagick.org) or
GraphicsMagick (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()
Java JDK 1.2 or higher (for JRI/REngine JDK 1.4 or
higher), GNU make
Requires external zip utility, available in path.
On windows, it's sufficient to install RTools.
JAGS (>= 3.4.0) (see
http://mcmc-jags.sourceforge.net)
OpenCL library; single-precision AMD or Nvidia GPU;
Preferred genomic operations engine: 'BEDTools',
'BEDOPS' and 'Tabix'.
Hugo (<https://gohugo.io>) and Pandoc
(<http://pandoc.org>)
OpenBUGS (>= 3.2.2), hence Windows or Linux
MAGeCK (=0.51, from
http://sourceforge.net/p/mageck/wiki/Home/), bowtie2
(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
OpenCL library; double-precision AMD or Nvidia GPU;
GNU make
Python (>= 2.7.0); spaCy <https://spacy.io/> (>=
1.8); Java (>= 7.0); Stanford CoreNLP
<http://nlp.stanford.edu/software/corenlp.shtml> (>= 3.7.0)
xclip (https://github.com/astrand/xclip) or xsel
(http://www.vergenet.net/~conrad/software/xsel/) for accessing
the X11 clipboard
Java (>= 7.0); Stanford CoreNLP
<http://nlp.stanford.edu/ software/corenlp.shtml> (>= 3.5.2)
couchDB instance to connect to and work with.
nvcc (release >= 3.1) (NVIDIA Cuda Compiler
driver); Linux operating system; GNU make.
libcurl: libcurl-devel (rpm) or
libcurl4-openssl-dev (deb).
none, one or more of JAGS (>= 3.0.0), WinBUGS (>=
1.4), OpenBUGS (>= 3.2.2)
GLPK library package (e.g., libglpk-dev on
Debian/Ubuntu)
Xft or zlib (only needed for platforms other than
OSX and Windows)
Requires the OpenMP library for parallel computing.
If the OpenMP library is not available, the code is executed
sequentially and a warning is printed.
Python (>= 2.7 or >= 3.5) and elex package
python3, rPython (see file README). To make full
use of the vignette's examples you need 'pandoc'
(http://pandoc.org) installed, although it's not a requirement.
GNU Scientific Library (GSL). Note: users should
have GSL installed.
Python (>= 2.4), difflib, fuzzywuzzy ( >=0.15.0 ),
python-Levenshtein ( >=0.12.0 ). Detailed installation
instructions for each operating system can be found in the
README file.
Debian or Ubuntu system with access to Goto Blas,
Intel MKL, Atlas development build as well as a Nvidia GPU with
CUDA support
The SequenomMarkers() marker design function
requires 'vcftools' and 'Perl' on 'windows', and, in addition,
'awk' and 'bash' on '*nix'.
MongoDB (>= 3.4.0), Python (>= 2.7). Installation
instructions and links can be found in the README file.
zlib headers and library. OpenSSL headers and
library. LibSSH2 (optional on non-Windows) to enable the SSH
transport.
Compiling vignette requires JAGS
(http://mcmc-jags.sourceforge.net)
GPGME: libgpgme11-dev (deb), gpgme-devel (rpm)
gpgme (brew). On Linux 'haveged' is recommended for generating
entropy when using the GPG key generator.
C++11 (supporting at least std=c++0x), OpenCL
shared library (provided by an SDK such as AMD/NVIDIA) and
OpenCL headers including the C++ header file (provided by
Khronos if not by SDK)
Python (>= 2.7.0) with header files and shared
library; TensorFlow (>= 1.0.0; https://www.tensorflow.org/)
libhdf5 (>= 1.8.12) with C++ interface
(--enable-cxx=yes) and v18 API enabled
Apache Hadoop >= 2.6.0
(https://hadoop.apache.org/releases.html#Download); Obsolete:
Hadoop core >= 0.19.1 and <= 1.0.3 or CDH3
(http://www.cloudera.com); standard unix tools (e.g., chmod)
ImageMagick (http://imagemagick.org) or
GraphicsMagick (http://www.graphicsmagick.org)
A C library with the fesetround/fegetround
functions.
Impala driver to support a 'DBI'-compatible R
interface
JAVA JDK 1.7 or higher for rcdk, OpenBabel (>=
2.3.1) with headers, http://openbabel.org
libjq: jq-devel (rpm) or libjq-dev (deb)
libsecret on Linux (libsecret-1-dev on
Debian/Ubuntu, libsecret-devel on Fedora/CentOS)
CUDA 8.0 tookit, OpenMP 4.0 capable compiler
Package vignettes based on R Markdown v2 or
reStructuredText require Pandoc (http://pandoc.org). The
function rst2pdf() require rst2pdf
(https://github.com/rst2pdf/rst2pdf).
ImageJ (>=1.48), ij.jar (see
http://imagej.nih.gov/ij/), Java (>=1.6.0)
libxml2: libxml2-dev (deb), libxml2-devel (rpm)
GNU make SAGA GIS GRASS GIS (7.x.x) Orfeo ToolBox
JAGS (>= 3.0.0) (see
http://mcmc-jags.sourceforge.net)
At least trial version of LocalSolver to be
downloaded from http://www.localsolver.com/download.html
A system with zoneinfo data (e.g.
/usr/share/zoneinfo) as well as a recent-enough C++11 compiler
(such as g++-4.8 or later). On Windows the zoneinfo included
with R is used.
ImageMagick++: ImageMagick-c++-devel (rpm) or
libmagick++-dev (deb)
ADMB version 11 <http://admb-project.org/> for
use.admb=TRUE; see readme.txt
Maxent.jar software, Java Runtime Environment (JRE)
Imports the `curl` and `XML` packages. These have
system requirements on `libxml2-devel`, `libcurl-devel` and
`openssl-devel`.
JAGS (>= 4.1) for the script version, both JAGS and
GTK+ for the GUI version. For install instructions, see README
file.
MonetDB, available from http://www.monetdb.org or
MonetDBLite R package
jags (>= 4.0.0) (see
http://mcmc-jags.sourceforge.net)
A valid account MUST be registered with Microsoft's
Cognitive Services website
<https://www.microsoft.com/cognitive-services/> in order to
obtain a (free) API key. Without an API key, this package will
not work properly.
pandoc, ipython (>= 3.0) or jupyter,
ipython/jupyter notebook optional dependencies, pywin32 (on
windows)
A compiler with C++11 support for the thread
library, Requires Rtools >= 33 (i.e. R >= 3.3.0) to build on
Windows.
CUDA >= v7.0, Nvidia GPU (e.g. GeForce or Tesla)
with compute capability >= 3.0 (Kepler)
C++11, GNU make, An ODBC3 driver manager and
drivers.
pandoc (http://johnmacfarlane.net/pandoc) for
exporting markdown files to other formats.
For the MERLIN wrapper, MERLIN
(http://csg.sph.umich.edu/abecasis/Merlin/) must be installed
and pointed to in the PATH environment variable.
The 'Japanese.Rnw' vignette requires uplatex and
dvipdfmx.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. MS-MPI (Microsoft HPC Pack 2012) or MPICH2 (>=
1.4.1p1) on Windows.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. MS-MPI (Microsoft HPC Pack 2012 R2 MS-MPI
Redistributable Package) on Windows.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. MS-MPI (Microsoft MPI v7.1 (SDK) and Microsoft HPC
Pack 2012 R2 MS-MPI Redistributable Package) on Windows.
OpenMPI (>= 1.5.4) on Solaris, Linux and Mac.
(Parallel) HDF5 and (Parallel) NetCDF4 (4.1 or later)
libraries. No MPI library required on Windows.
OpenMPI (>= 1.5.4) on Solaris, Linux, Mac, and
FreeBSD. No MPI library required on Windows yet.
ssh (OpenSSH) or plink (PuTTY) on Solaris, Linux,
and Mac.
Linux, Mac OSX, and Windows, or 'ZeroMQ' library >=
4.0.4. Solaris 10 needs 'ZeroMQ' library 4.0.7 and 'OpenCSW'.
Poppler C++ API: libpoppler-cpp-dev (deb) or
poppler-cpp-devel (rpm). The unit tests also require the
'poppler-data' package (rpm/deb)
Phoenix NLME with Phoenix Modeling Language (PML)
license
For Windows users, Rtools (see
https://cran.r-project.org/bin/windows/Rtools/).
Python 2.7.x or Python 3.2.x-3.4.x, NumPy (Python
scientific computing package)
pandoc (>= 1.12.3) -
http://johnmacfarlane.net/pandoc
JAGS (>= 3.2.0) (see
http://mcmc-jags.sourceforge.net)
A POSIX system. Currently Linux and OS X are known
to work. GNU make.
proj 4.4.6 or higher (http://proj.maptools.org/)
pandoc (http://pandoc.org) for building Vignettes
and output reports as HTML
Pasting to clipboard requires the xclip command on
BSD and Linux or the pbcopy command on Mac OS.
Python (>= 2.7.0) with header files and shared
library (UNIX) / static library (Windows)
Qt4 libraries and headers (http://qt.nokia.com),
cmake (http://www.cmake.org)
OpenBugs for functions bugs() and openbugs() or
WinBUGS 1.4 for function bugs()
linux (>= 3.0), libapparmor-dev (optional)
Java JRE 1.6 or higher ; Xuggle-xuggler-5.4.jar in
library paths and class paths.
A valid Bloomberg installation. The API headers and
dynamic library are downloaded from
<https://github.com/Rblp/blp> during the build step. See
<https://bloomberg.github.io/blpapi-docs/cpp/3.8> as well as
<http://www.bloomberglabs.com/api/> for API documentation. A
compiler recent enough for (at least partial) C++11 support;
g++-4.6.* or later should be sufficient and g++-4.9.* or later
is preferred.
GMP (GNU MP bignum library from
<http://gmplib.org/>)
A Debian-based system with the libapt-pkg-dev
package
A 64-bit POSIX OS such as Linux or OS X with IANA
time zone data in /usr/share/zoneinfo as well as a
recent-enough C++11 compiler (such as g++-4.9 or later which
preferred, g++-4.8 works too). On Windows the zoneinfo included
with R is used; and time parsing support is enabled via a
backport of std::get_time from the LLVM libc++ library.
On Linux and MacOS GNU make, pcre (>= 7) and glib2
(>= 2).
A POSIX system. Currently Linux and OS X are known
to work.
A C++11 compiler. Versions 4.8.*, 4.9.* or later of
GCC will be fine.
GNU make, Windows: cmd.exe and cscript.exe,
Solaris: g++ is required
The hiredis library (eg via package libhiredis-dev
on Debian/Ubuntu, hiredis-devel on Fedora/RedHat, or directly
from source from https://github.com/redis/hiredis) is required.
MsgPack support is activated if the (optional) RcppMsgPack
package is detected.
C++11, Boost 1.52 or later (via BH package)
A C++11 compiler; g++ (>= 4.8.*) should be fine.
DieHarder library (>= 3.31.1) from
http://www.phy.duke.edu/~rgb/General/dieharder.php, GNU GSL for
the GSL random-number generators
mono 4.x or higher on OSX / Linux, .NET 4.x or
higher on Windows, 'msbuild' and 'nuget' available in the path
MOSEK (http://www.mosek.com) and MOSEK License for
use of Rmosek, optional use of the pogs optimizer may require
CUDA/GPU accoutrements.
(Python and gym only required if gym environments
are used)
Subversion for install_svn, git for install_git
for building from source: GDAL >= 1.6.3, library
from http://trac.osgeo.org/gdal/wiki/DownloadSource and PROJ.4
(proj >= 4.4.9) from http://download.osgeo.org/proj/; GDAL OSX
frameworks built by William Kyngesburye at
http://www.kyngchaos.com/ may be used for source installs on
OSX.
GEOS (>= 3.2.0); for building from source: GEOS
from http://trac.osgeo.org/geos/; GEOS OSX frameworks built by
William Kyngesburye at http://www.kyngchaos.com/ may be used
for source installs on OSX.
OpenGL, GLU Library, XQuartz (on OSX), zlib
(optional), libpng (>=1.2.9, optional), FreeType (optional),
pandoc (>=1.14, needed for vignettes)
R built as a shared or static library, 'MPI'
library.
Java (>= 1.5), zlib headers and library.
Oracle Java 7,Apache Kafka 2.8.0-0.8.1.1
libmariadb-client-lgpl-dev or libmysqlclient-dev
(deb), mariadb-connector-c-devel or mariadb-devel (rpm),
mariadb-connector-c or mysql-connector-c (brew)
notepad.exe, mark.exe (>= 8.0) (or mark32.exe and
mark64.exe) and rel_32.exe (see README.txt)
libmariadb-client-dev | libmariadb-client-lgpl-dev
| libmysqlclient-dev (deb), mariadb-devel (rpm), mariadb |
mysql-connector-c (brew), mysql56_dev (csw)
The tools to run 'R CMD SHLIB' on 'Fortran' code.
The used 'Fortran' compiler must support pointer initialization
which is a feature of the 2008 standard.
SYMPHONY (>= 5.6.16) libraries and headers
Oracle Instant Client or Oracle Database Client
Poppler Glib interface headers and libraries
(<http://poppler.freedesktop.org/>) [Debian/Ubuntu:
libpoppler-glib-dev, Fedora: poppler-glib-devel]
libpq >= 9.0: libpq-dev (deb) or postgresql-devel
(rpm)
C++11, GNU make, Windows: cmd.exe and cscript.exe
ProtoBuf libraries and compiler version 2.2.0 or
later; version 3.0.0 or later is supported as well. On
Debian/Ubuntu these can be installed as libprotoc-dev,
libprotobuf-dev and protobuf-compiler, while on Fedora/CentOS
protobuf-devel and protobuf-compiler are needed.
A user API key (which one can request from the
website at <http://www.pushbullet.com>), and one or more
devices to push messages to which may be any one of an (Android
or iOS) phone, a (Chrome or Firefox, or Opera or Safari)
browser or the (Windows or Mac) desktop application provided
the corresponding Pushbullet 'app' has been installed on any
one of these.
Windows, Python (>= 2.4.0), ArcGIS (>= 9.2)
Python (>= 2.7) and Python headers and libraries
(See the INSTALL file)
QuantLib library (>= 1.8.0) from
http://quantlib.org, Boost library from http://www.boost.org
need the RDRAND instruction on Intel CPU. and C
compiler must be able to compile a GNU-style in-line assembler.
NW RFC SDK downloaded from http://service.sap.com
Tcl/Tk (>= 8.5), Tktable (>= 2.9, optional)
The Boost 'program_options' library
(http://boost.org) is required.
Python (>=2.6) in path and NumPy module installed,
ghostscript (>=9.0)
ZeroMQ >= 3.0.0: libzmq3-dev (deb) or zeromq3-devel
(rpm)
GLPK library, including -dev or -devel part
zlib headers and libraries, optionally also bzip2
and POSIX-compliant regex functions.
(PDF)LaTeX (https://www.latex-project.org/) with
'pdfpages' package for studentGrowthPlot option in visualizeSGP
to bind together student growth plots into school catalogs
Python (>= 2.7) and Python headers and libraries
(See the README.md file)
For playing sounds, a command line system tool for
playing wav-files is required.
little-endian processor required for some functions
(see README)
pandoc (http://pandoc.org) for generating and
exporting markdown reports to other formats.
Komodo Edit (http://www.openkomodo.com), SciViews-K
(http://www.sciviews.org/SciViews-K)
Tesseract >= 3.03 (libtesseract-dev /
tesseract-devel) and Leptonica (libleptonica-dev /
leptonica-devel). On Debian you need to install the English
training data separately (tesseract-ocr-eng)
The package requires the following two components :
A C++11 compiler and on a unix OS the boost-locale headers and
libraries ( boost >= 1.55.0 , www.boost.org ). Debian/Ubuntu:
libboost-locale-dev, Fedora : yum install boost-devel, OSX/brew
: detailed installation instructions can be found in the README
file
exiftool
(http://www.sno.phy.queensu.ca/~phil/exiftool/), perl, ffmpeg,
imagemagick
Teradata Aster Database 5.20 (AD5.20) or higher,
Teradata Aster Analytical Foundation 5.20 (AA5.20) or higher.
GNU Scientific Library version >= 1.8, C++11
PARI/GP >= 2.3.0 [strongly recommended for
logkda()]
nvcc (release >= 7.1) (NVIDIA Cuda Compiler driver)
libmagic (>= 5.14) for Unix/Linux/macOS; Rtools
3.3+ for Windows
PhantomJS (http://phantomjs.org) for taking
screenshots, ImageMagick (http://www.imagemagick.org) or
GraphicsMagick (http://www.graphicsmagick.org) and OptiPNG
(http://optipng.sourceforge.net) for manipulating images.
Java (>= 5.0); WordNet database files (direct
download:
<http://wordnetcode.princeton.edu/3.0/WNdb-3.0.tar.gz>; Debian
and Fedora package: wordnet)
Perl (>= 5.0), Unitex (>= 3.0
http://www-igm.univ-mlv.fr/~unitex/)
The standalone program xgobi must be installed
additionally, see file README, or INSTALL.windows under Windows
libxslt: libxslt1-dev (deb), libxslt-devel (rpm)