Last data update: 2014.03.03

destiny

Package: destiny
Type: Package
Title: Creates diffusion maps
Version: 1.2.1
Date: 2014-12-19
Authors@R: c(
person('Philipp', 'Angerer', NULL, 'philipp.angerer@helmholtz-muenchen.de', c('cre', 'aut')),
person('Laleh', 'Haghverdi', NULL, 'laleh.haghverdi@helmholtz-muenchen.de', 'ctb'),
person('Maren', 'Büttner', NULL, 'maren.buettner@helmholtz-muenchen.de', 'ctb'),
person('Fabian', 'Theis', NULL, 'fabian.theis@helmholtz-muenchen.de', 'ctb'),
person('Carsten', 'Marr', NULL, 'carsten.marr@helmholtz-muenchen.de', 'ctb'),
person('Florian', 'Büttner', NULL, 'f.buettner@helmholtz-muenchen.de', 'ctb'))
Description: Create and plot diffusion maps.
License: GPL
Encoding: UTF-8
Depends: R (>= 3.2.0), methods, Biobase
Imports: graphics, Rcpp (>= 0.10.3), RcppEigen, BiocGenerics, Matrix,
Hmisc, FNN, VIM, proxy, igraph, scatterplot3d
LinkingTo: Rcpp, RcppEigen
SystemRequirements: C++11
NeedsCompilation: yes
Enhances: rgl
Suggests: RColorBrewer, ggplot2, nbconvertR
VignetteBuilder: nbconvertR
biocViews: CellBiology, CellBasedAssays, Clustering, Software,
Visualization
Collate: 'RcppExports.R' 'censoring.r' 'destiny-package.r'
's4-null-unions.r' 'dist-matrix-coerce.r' 'sigmas.r'
'diffusionmap.r' 'diffusionmap-coercions.r'
'diffusionmap-methods.r' 'plothelpers.r'
'diffusionmap-plotting.r' 'utils.r' 'expressionset-helpers.r'
'guo-data.r' 'predict.r' 'sigmas-plotting.r' 'update-methods.r'
RoxygenNote: 5.0.1
Packaged: 2016-05-12 05:33:11 UTC; biocbuild
Author: Philipp Angerer [cre, aut],
Laleh Haghverdi [ctb],
Maren Büttner [ctb],
Fabian Theis [ctb],
Carsten Marr [ctb],
Florian Büttner [ctb]
Maintainer: Philipp Angerer <philipp.angerer@helmholtz-muenchen.de>

● BiocViews: CellBasedAssays, CellBiology, Clustering, Software, Visualization
● 13 images, 16 functions, 0 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'destiny' ...
** libs
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"  -g -fpic  -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/bits/locale_classes.h:40,
                 from /usr/include/c++/5/bits/ios_base.h:41,
                 from /usr/include/c++/5/ios:42,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iterator:64,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/bits/locale_classes.h:40,
                 from /usr/include/c++/5/bits/ios_base.h:41,
                 from /usr/include/c++/5/ios:42,
                 from /usr/include/c++/5/ostream:38,
                 from /usr/include/c++/5/iterator:64,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:25,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"  -g -fpic  -g -O2 -c censoring.cpp -o censoring.o
In file included from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from censoring.cpp:7:
/home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from censoring.cpp:6:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppEigen/include"  -g -fpic  -g -O2 -c no_censoring.cpp -o no_censoring.o
In file included from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from no_censoring.cpp:5:
/home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: warning: 'template<class _Operation> class std::binder2nd' is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^
In file included from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigenForward.h:30,
                 from /home/ddbj/local/lib64/R/library/RcppEigen/include/RcppEigen.h:25,
                 from no_censoring.cpp:5:
/home/ddbj/local/lib64/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: warning: 'template<class _Operation> class std::binder1st' is deprecated [-Wdeprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^
In file included from /usr/include/c++/5/bits/stl_function.h:1128:0,
                 from /usr/include/c++/5/string:48,
                 from /usr/include/c++/5/stdexcept:39,
                 from /usr/include/c++/5/array:38,
                 from /usr/include/c++/5/tuple:39,
                 from /usr/include/c++/5/unordered_map:41,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/platform/compiler.h:153,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp/r/headers.h:48,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/RcppCommon.h:29,
                 from /home/ddbj/local/lib64/R/library/Rcpp/include/Rcpp.h:27,
                 from no_censoring.cpp:4:
/usr/include/c++/5/backward/binders.h:108:11: note: declared here
     class binder1st
           ^
g++ -std=c++11 -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o destiny.so RcppExports.o censoring.o no_censoring.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/destiny/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'plot' from package 'graphics' in package 'destiny'
** help
*** installing help indices
  converting help for package 'destiny'
    finding HTML links ... done
    DiffusionMap-class                      html  
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/DiffusionMap-class.Rd:49: missing file link 'ExpressionSet'
    DiffusionMap-coercions                  html  
    DiffusionMap-methods                    html  
    ExpressionSet-helpers                   html  
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/ExpressionSet-helpers.Rd:10: missing file link 'ExpressionSet'
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/ExpressionSet-helpers.Rd:34: missing file link 'ExpressionSet'
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/ExpressionSet-helpers.Rd:20: missing file link 'ExpressionSet'
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/ExpressionSet-helpers.Rd:31: missing file link 'ExpressionSet'
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/ExpressionSet-helpers.Rd:49: missing file link 'ExpressionSet'
    Sigmas-class                            html  
    colorlegend                             html  
    cube.helix                              html  
    destiny                                 html  
    dm.predict                              html  
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/dm.predict.Rd:12: missing file link 'ExpressionSet'
    find.dm.k                               html  
    find.sigmas                             html  
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/find.sigmas.Rd:13: missing file link 'ExpressionSet'
    guo                                     html  
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/guo.Rd:10: missing file link 'ExpressionSet'
Rd warning: /tmp/Rtmpl7W8gB/R.INSTALL1cac3ff6cc66/destiny/man/guo.Rd:16: missing file link 'ExpressionSet'
    lWhich                                  html  
    plot.DiffusionMap                       html  
    plot.Sigmas                             html  
    updateObject-DiffusionMap-method        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (destiny)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO