CRAN Package Check Results for Package dynOmics

Last updated on 2020-09-25 07:49:51 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2 4.46 48.51 52.97 WARN
r-devel-linux-x86_64-debian-gcc 1.2 3.75 37.35 41.10 WARN
r-devel-linux-x86_64-fedora-clang 1.2 73.31 WARN
r-devel-linux-x86_64-fedora-gcc 1.2 64.44 WARN
r-devel-windows-ix86+x86_64 1.2 12.00 227.00 239.00 OK
r-patched-linux-x86_64 1.2 4.27 45.66 49.93 WARN
r-patched-solaris-x86 1.2 120.10 WARN
r-release-linux-x86_64 1.2 4.78 45.32 50.10 WARN
r-release-macos-x86_64 1.2 OK
r-release-windows-ix86+x86_64 1.2 30.00 265.00 295.00 OK
r-oldrel-macos-x86_64 1.2 OK
r-oldrel-windows-ix86+x86_64 1.2 9.00 235.00 244.00 OK

Check Details

Version: 1.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: 'lmms'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'DynOmicsUserManual.Rmd' using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     * Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     * Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/tmp/Rtmp3vXXE8/RLIBS_6dd3140f6221'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building 'DynOmicsUserManual.Rmd'
    
    SUMMARY: processing the following file failed:
     'DynOmicsUserManual.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DynOmicsUserManual.Rmd’ using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/home/hornik/tmp/scratch/RtmpXQ9Ack/RLIBS_721212724a4'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building ‘DynOmicsUserManual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DynOmicsUserManual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘DynOmicsUserManual.Rmd’ using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/tmp/Rtmp3LTKdc/RLIBS_37224f736042ac'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building ‘DynOmicsUserManual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DynOmicsUserManual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘DynOmicsUserManual.Rmd’ using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/data/gannet/ripley/R/packages/tests-devel/dynOmics.Rcheck'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building ‘DynOmicsUserManual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DynOmicsUserManual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DynOmicsUserManual.Rmd’ using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/tmp/RtmpWUpeLR/RLIBS_2d3d61b797ab'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building ‘DynOmicsUserManual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DynOmicsUserManual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-linux-x86_64

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DynOmicsUserManual.Rmd’ using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/tmp/RtmpMdaWnm/RLIBS_186e78023be'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building ‘DynOmicsUserManual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DynOmicsUserManual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘DynOmicsUserManual.Rmd’ using knitr
    Loading required package: ggplot2
    dynOmics-package package:dynOmics R Documentation
    
    _<08>F_<08>a_<08>s_<08>t _<08>F_<08>o_<08>u_<08>r_<08>i_<08>e_<08>r _<08>t_<08>r_<08>a_<08>n_<08>s_<08>f_<08>o_<08>r_<08>m _<08>t_<08>o _<08>e_<08>s_<08>t_<08>i_<08>m_<08>a_<08>t_<08>e _<08>d_<08>e_<08>l_<08>a_<08>y_<08>s _<08>i_<08>n _<08>e_<08>x_<08>p_<08>r_<08>e_<08>s_<08>s_<08>i_<08>o_<08>n _<08>i_<08>n_<08>i_<08>t_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n _<08>t_<08>o
    _<08>i_<08>d_<08>e_<08>n_<08>t_<08>i_<08>f_<08>y _<08>a_<08>s_<08>s_<08>o_<08>c_<08>i_<08>a_<08>t_<08>i_<08>o_<08>n_<08>s _<08>b_<08>e_<08>t_<08>w_<08>e_<08>e_<08>n _<08>t_<08>i_<08>m_<08>e _<08>c_<08>o_<08>u_<08>r_<08>s_<08>e '_<08>o_<08>m_<08>i_<08>c_<08>s' _<08>d_<08>a_<08>t_<08>a.
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     The package provides functions to identify associations within one
     or between two time course 'omics' data and visualise the
     associations : associateData to estimate the delays and identify
     associations of data sets containing time course 'omics'
     experiments; plot.associations: to visualise associated profiles.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     Package: dynOmics
     Type: Package
     Version: 1.2
     Date: 2018-06-12
     License: GPL-2
     LazyLoad: yes
    
     Functions for associating data: 'associateData'
     Functions for summarization: 'summary.associations'
     Functions for plots: 'plot.associations'
    
    _<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
    
     Jasmin Straube with contributions from Kim-Anh Le Cao, Emma Huang
     and Anne Bernard
    
     Maintainer: Jasmin Straube <j.straube@qimrberghofer.edu.au>
    
    
    Metabolites package:dynOmics R Documentation
    
    _<08>M_<08>e_<08>t_<08>a_<08>b_<08>o_<08>l_<08>i_<08>t_<08>e _<08>a_<08>n_<08>d _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Metabolites)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression of 5 metabolites
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Metabolites. data matrix with 7 rows and 5 columns. Each row
     represents an experimental time sample, and each column a
     single metabolite.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Metabolite Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Transcripts package:dynOmics R Documentation
    
    _<08>T_<08>r_<08>a_<08>n_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t _<08>S_<08>i_<08>m_<08>u_<08>l_<08>a_<08>t_<08>i_<08>o_<08>n _<08>D_<08>a_<08>t_<08>a
    
    _<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
    
     Simulated data were received from Redestig et al., 2011.
     Metabolite and transcript levels were obtained using an impulse
     model (Chechik and Koller, 2009). Functions were used to model
     five different metabolite patterns and for each metabolite 50
     associated transcript levels. Time lags were introduced in the
     range from -2 to 2 with the probability 0.1, 0.2, 0.4, 0.2, 0.1.
     Simulated profiles have seven time points and normal distributed
     noise was introduced with mean zero and standard deviation 0.1.
    
    _<08>U_<08>s_<08>a_<08>g_<08>e:
    
     data(Transcripts)
    
    _<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
    
     This data set contains the simulated expression 250 transcripts
     for 7 time points.
    
    _<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
    
     • Transcripts. data matrix with 7 rows and 250 columns. Each
     row represents an experimental time sample, and each column a
     single transcript.
    
    _<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
    
     The Transcript Simulation Data is based on the the paper of
     Redestig _et al._ (2011).
    
    _<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
    
     Redestig,H. and Costa,I.G. Detection and interpretation of
     metabolite-transcript coresponses using combined profiling data.
     _Bioinformatics_ *27*(13) (2011), pp. i357 65.
    
    
    Warning: Removed 126 row(s) containing missing values (geom_path).
    Loading required package: lmms
    Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
     there is no package called 'lmms'
    Installing package into '/tmp/Rtmp998ObK/RLIBS_201c1cf4d7f7'
    (as 'lib' is unspecified)
    Quitting from lines 168-177 (DynOmicsUserManual.Rmd)
    Error: processing vignette 'DynOmicsUserManual.Rmd' failed with diagnostics:
    trying to use CRAN without setting a mirror
    --- failed re-building ‘DynOmicsUserManual.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘DynOmicsUserManual.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-linux-x86_64