Last updated on 2018-04-26 06:47:40 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.0 | 3.17 | 146.10 | 149.27 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.10.0 | 3.08 | 537.44 | 540.52 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.10.0 | 475.33 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.10.0 | 462.58 | OK | |||
| r-devel-windows-ix86+x86_64 | 0.10.0 | 11.00 | 163.00 | 174.00 | OK | --no-vignettes |
| r-patched-linux-x86_64 | 0.10.0 | 3.40 | 173.91 | 177.31 | ERROR | |
| r-patched-solaris-x86 | 0.10.0 | 729.80 | OK | --no-build-vignettes | ||
| r-release-linux-x86_64 | 0.10.0 | 3.53 | 188.45 | 191.98 | ERROR | |
| r-release-windows-ix86+x86_64 | 0.10.0 | 11.00 | 163.00 | 174.00 | OK | --no-vignettes |
| r-release-osx-x86_64 | 0.10.0 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.10.0 | 5.00 | 277.00 | 282.00 | OK | --no-vignettes |
| r-oldrel-osx-x86_64 | 0.10.0 | NOTE |
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘compute.animation_tests.R’ [2s/2s]
Running ‘d3_animation_tests.R’ [4s/4s]
Running ‘effects_tests.R’ [7s/7s]
Running ‘filmstrip_tests.R’ [2s/2s]
Running ‘layout_tests.R’ [1s/1s]
Running ‘networkAnimationTest.R’ [2s/2s]
Running ‘proximity.timeline_test.R’ [1s/2s]
Running the tests in ‘tests/proximity.timeline_test.R’ failed.
Complete output:
> # some tests tfor the proximity.timeline function
> require(ndtv)
Loading required package: ndtv
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: 'statnet.common'
The following object is masked from 'package:base':
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
> require(testthat)
Loading required package: testthat
>
> test<-network.initialize(10)
> add.edges.active(test,head=1:9,tail=2:10,onset=0,terminus=10)
> add.edges.active(test,head=1,tail=3,onset=1,terminus=2)
> proximity.timeline(test)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
rendering splines for each vertex ...
>
> data(McFarland_cls33_10_16_96)
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),vertex.cex=(cls33_10_16_96%v%'type'=='instructor')*4+1,labels.at=45)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
>
> # test algorithm types
> # isoMDS is default, so already tested
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='sammon')
collapsing slice networks ...
computing vertex positions using 1D sammon layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='cmdscale')
collapsing slice networks ...
computing vertex positions using 1D cmdscale layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='gvNeato')
collapsing slice networks ...
computing vertex positions using 1D gvNeato layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
There were 18 warnings (use warnings() to see them)
> # only check MDSJ if allready installed
> has.mdsj<-ndtv:::check.mdsj(ask=FALSE)
The MDSJ Java library does not appear to be installed. The ndtv package can use MDSJ to provide a fast accurate layout algorithm. It can be downloaded from http://algo.uni-konstanz.de/software/mdsj/
Error in install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ndtv/java/does not appear to have write permissions
Calls: <Anonymous> -> install.mdsj
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.10.0
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: ‘statnet.common’
The following object is masked from ‘package:base’:
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
No slice.par found, using
Calculating layout for network slice from time 1 to 2
Calculating layout for network slice from time 2 to 3
Calculating layout for network slice from time 3 to 4
Calculating layout for network slice from time 4 to 5
Calculating layout for network slice from time 5 to 6
Calculating layout for network slice from time 6 to 7
Calculating layout for network slice from time 7 to 8
Calculating layout for network slice from time 8 to 9
Calculating layout for network slice from time 9 to 10
Calculating layout for network slice from time 10 to 11
Calculating layout for network slice from time 11 to 12
Calculating layout for network slice from time 12 to 13
rendering 10 frames for slice 0
rendering 10 frames for slice 1
rendering 10 frames for slice 2
rendering 10 frames for slice 3
rendering 10 frames for slice 4
rendering 10 frames for slice 5
rendering 10 frames for slice 6
rendering 10 frames for slice 7
rendering 10 frames for slice 8
rendering 10 frames for slice 9
rendering 10 frames for slice 10
rendering 10 frames for slice 11
Loading required package: tergm
Loading required package: ergm
ergm: version 3.8.0, created on 2017-08-18
Copyright (c) 2017, Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Carter T. Butts, University of California -- Irvine
Steven M. Goodreau, University of Washington
Pavel N. Krivitsky, University of Wollongong
Martina Morris, University of Washington
with contributions from
Li Wang
Kirk Li, University of Washington
Skye Bender-deMoll, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").
NOTE: Versions before 3.6.1 had a bug in the
implementation of the bd() constriant which distorted
the sampled distribution somewhat. In addition,
Sampson's Monks datasets had mislabeled vertices. See
the NEWS and the documentation for more details.
tergm: version 3.4.1, created on 2017-09-12
Copyright (c) 2017, Pavel N. Krivitsky, University of Wollongong
Mark S. Handcock, University of California -- Los Angeles
with contributions from
David R. Hunter, Penn State University
Steven M. Goodreau, University of Washington
Martina Morris, University of Washington
Nicole Bohme Carnegie, New York University
Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Skye Bender-deMoll
Li Wang
Kirk Li, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("tergm").
Starting maximum likelihood estimation via MCMLE:
Iteration 1 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.254.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.004823.
Step length converged twice. Stopping.
This model was fit using MCMC. To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Error: processing vignette ‘ndtv.Rnw’ failed with diagnostics:
chunk 9 (label = mdsj_actual_download)
Error in ndtv:::install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/ndtv/java/does not appear to have write permissions
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘compute.animation_tests.R’ [1s/3s]
Running ‘d3_animation_tests.R’ [3s/4s]
Running ‘effects_tests.R’ [5s/8s]
Running ‘filmstrip_tests.R’ [2s/3s]
Running ‘layout_tests.R’ [1s/1s]
Running ‘networkAnimationTest.R’ [1s/3s]
Running ‘proximity.timeline_test.R’ [1s/3s]
Running the tests in ‘tests/proximity.timeline_test.R’ failed.
Complete output:
> # some tests tfor the proximity.timeline function
> require(ndtv)
Loading required package: ndtv
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: 'statnet.common'
The following object is masked from 'package:base':
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
> require(testthat)
Loading required package: testthat
>
> test<-network.initialize(10)
> add.edges.active(test,head=1:9,tail=2:10,onset=0,terminus=10)
> add.edges.active(test,head=1,tail=3,onset=1,terminus=2)
> proximity.timeline(test)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
rendering splines for each vertex ...
>
> data(McFarland_cls33_10_16_96)
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),vertex.cex=(cls33_10_16_96%v%'type'=='instructor')*4+1,labels.at=45)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
>
> # test algorithm types
> # isoMDS is default, so already tested
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='sammon')
collapsing slice networks ...
computing vertex positions using 1D sammon layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='cmdscale')
collapsing slice networks ...
computing vertex positions using 1D cmdscale layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='gvNeato')
collapsing slice networks ...
computing vertex positions using 1D gvNeato layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
There were 18 warnings (use warnings() to see them)
> # only check MDSJ if allready installed
> has.mdsj<-ndtv:::check.mdsj(ask=FALSE)
The MDSJ Java library does not appear to be installed. The ndtv package can use MDSJ to provide a fast accurate layout algorithm. It can be downloaded from http://algo.uni-konstanz.de/software/mdsj/
Error in install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ndtv/java/does not appear to have write permissions
Calls: <Anonymous> -> install.mdsj
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.10.0
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: ‘statnet.common’
The following object is masked from ‘package:base’:
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
No slice.par found, using
Calculating layout for network slice from time 1 to 2
Calculating layout for network slice from time 2 to 3
Calculating layout for network slice from time 3 to 4
Calculating layout for network slice from time 4 to 5
Calculating layout for network slice from time 5 to 6
Calculating layout for network slice from time 6 to 7
Calculating layout for network slice from time 7 to 8
Calculating layout for network slice from time 8 to 9
Calculating layout for network slice from time 9 to 10
Calculating layout for network slice from time 10 to 11
Calculating layout for network slice from time 11 to 12
Calculating layout for network slice from time 12 to 13
rendering 10 frames for slice 0
rendering 10 frames for slice 1
rendering 10 frames for slice 2
rendering 10 frames for slice 3
rendering 10 frames for slice 4
rendering 10 frames for slice 5
rendering 10 frames for slice 6
rendering 10 frames for slice 7
rendering 10 frames for slice 8
rendering 10 frames for slice 9
rendering 10 frames for slice 10
rendering 10 frames for slice 11
Loading required package: tergm
Loading required package: ergm
ergm: version 3.8.0, created on 2017-08-18
Copyright (c) 2017, Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Carter T. Butts, University of California -- Irvine
Steven M. Goodreau, University of Washington
Pavel N. Krivitsky, University of Wollongong
Martina Morris, University of Washington
with contributions from
Li Wang
Kirk Li, University of Washington
Skye Bender-deMoll, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").
NOTE: Versions before 3.6.1 had a bug in the
implementation of the bd() constriant which distorted
the sampled distribution somewhat. In addition,
Sampson's Monks datasets had mislabeled vertices. See
the NEWS and the documentation for more details.
tergm: version 3.4.1, created on 2017-09-12
Copyright (c) 2017, Pavel N. Krivitsky, University of Wollongong
Mark S. Handcock, University of California -- Los Angeles
with contributions from
David R. Hunter, Penn State University
Steven M. Goodreau, University of Washington
Martina Morris, University of Washington
Nicole Bohme Carnegie, New York University
Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Skye Bender-deMoll
Li Wang
Kirk Li, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("tergm").
Starting maximum likelihood estimation via MCMLE:
Iteration 1 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.3152.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.02348.
Step length converged twice. Stopping.
This model was fit using MCMC. To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Error: processing vignette ‘ndtv.Rnw’ failed with diagnostics:
chunk 9 (label = mdsj_actual_download)
Error in ndtv:::install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ndtv/java/does not appear to have write permissions
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘compute.animation_tests.R’ [2s/3s]
Running ‘d3_animation_tests.R’ [4s/7s]
Running ‘effects_tests.R’ [7s/9s]
Running ‘filmstrip_tests.R’ [2s/4s]
Running ‘layout_tests.R’ [1s/2s]
Running ‘networkAnimationTest.R’ [2s/3s]
Running ‘proximity.timeline_test.R’ [1s/3s]
Running the tests in ‘tests/proximity.timeline_test.R’ failed.
Complete output:
> # some tests tfor the proximity.timeline function
> require(ndtv)
Loading required package: ndtv
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: 'statnet.common'
The following object is masked from 'package:base':
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
> require(testthat)
Loading required package: testthat
>
> test<-network.initialize(10)
> add.edges.active(test,head=1:9,tail=2:10,onset=0,terminus=10)
> add.edges.active(test,head=1,tail=3,onset=1,terminus=2)
> proximity.timeline(test)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
rendering splines for each vertex ...
>
> data(McFarland_cls33_10_16_96)
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),vertex.cex=(cls33_10_16_96%v%'type'=='instructor')*4+1,labels.at=45)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
>
> # test algorithm types
> # isoMDS is default, so already tested
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='sammon')
collapsing slice networks ...
computing vertex positions using 1D sammon layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='cmdscale')
collapsing slice networks ...
computing vertex positions using 1D cmdscale layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='gvNeato')
collapsing slice networks ...
computing vertex positions using 1D gvNeato layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
There were 18 warnings (use warnings() to see them)
> # only check MDSJ if allready installed
> has.mdsj<-ndtv:::check.mdsj(ask=FALSE)
The MDSJ Java library does not appear to be installed. The ndtv package can use MDSJ to provide a fast accurate layout algorithm. It can be downloaded from http://algo.uni-konstanz.de/software/mdsj/
Error in install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ndtv/java/does not appear to have write permissions
Calls: <Anonymous> -> install.mdsj
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.10.0
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: ‘statnet.common’
The following object is masked from ‘package:base’:
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
No slice.par found, using
Calculating layout for network slice from time 1 to 2
Calculating layout for network slice from time 2 to 3
Calculating layout for network slice from time 3 to 4
Calculating layout for network slice from time 4 to 5
Calculating layout for network slice from time 5 to 6
Calculating layout for network slice from time 6 to 7
Calculating layout for network slice from time 7 to 8
Calculating layout for network slice from time 8 to 9
Calculating layout for network slice from time 9 to 10
Calculating layout for network slice from time 10 to 11
Calculating layout for network slice from time 11 to 12
Calculating layout for network slice from time 12 to 13
rendering 10 frames for slice 0
rendering 10 frames for slice 1
rendering 10 frames for slice 2
rendering 10 frames for slice 3
rendering 10 frames for slice 4
rendering 10 frames for slice 5
rendering 10 frames for slice 6
rendering 10 frames for slice 7
rendering 10 frames for slice 8
rendering 10 frames for slice 9
rendering 10 frames for slice 10
rendering 10 frames for slice 11
Loading required package: tergm
Loading required package: ergm
ergm: version 3.8.0, created on 2017-08-18
Copyright (c) 2017, Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Carter T. Butts, University of California -- Irvine
Steven M. Goodreau, University of Washington
Pavel N. Krivitsky, University of Wollongong
Martina Morris, University of Washington
with contributions from
Li Wang
Kirk Li, University of Washington
Skye Bender-deMoll, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").
NOTE: Versions before 3.6.1 had a bug in the
implementation of the bd() constriant which distorted
the sampled distribution somewhat. In addition,
Sampson's Monks datasets had mislabeled vertices. See
the NEWS and the documentation for more details.
tergm: version 3.4.1, created on 2017-09-12
Copyright (c) 2017, Pavel N. Krivitsky, University of Wollongong
Mark S. Handcock, University of California -- Los Angeles
with contributions from
David R. Hunter, Penn State University
Steven M. Goodreau, University of Washington
Martina Morris, University of Washington
Nicole Bohme Carnegie, New York University
Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Skye Bender-deMoll
Li Wang
Kirk Li, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("tergm").
Starting maximum likelihood estimation via MCMLE:
Iteration 1 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.2829.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.01097.
Step length converged twice. Stopping.
This model was fit using MCMC. To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Error: processing vignette ‘ndtv.Rnw’ failed with diagnostics:
chunk 9 (label = mdsj_actual_download)
Error in ndtv:::install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ndtv/java/does not appear to have write permissions
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘compute.animation_tests.R’ [2s/3s]
Running ‘d3_animation_tests.R’ [4s/6s]
Running ‘effects_tests.R’ [7s/9s]
Running ‘filmstrip_tests.R’ [2s/3s]
Running ‘layout_tests.R’ [1s/2s]
Running ‘networkAnimationTest.R’ [2s/3s]
Running ‘proximity.timeline_test.R’ [1s/2s]
Running the tests in ‘tests/proximity.timeline_test.R’ failed.
Complete output:
> # some tests tfor the proximity.timeline function
> require(ndtv)
Loading required package: ndtv
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: 'statnet.common'
The following object is masked from 'package:base':
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
> require(testthat)
Loading required package: testthat
>
> test<-network.initialize(10)
> add.edges.active(test,head=1:9,tail=2:10,onset=0,terminus=10)
> add.edges.active(test,head=1,tail=3,onset=1,terminus=2)
> proximity.timeline(test)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
rendering splines for each vertex ...
>
> data(McFarland_cls33_10_16_96)
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),vertex.cex=(cls33_10_16_96%v%'type'=='instructor')*4+1,labels.at=45)
collapsing slice networks ...
computing vertex positions using 1D isoMDS layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
>
> # test algorithm types
> # isoMDS is default, so already tested
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='sammon')
collapsing slice networks ...
computing vertex positions using 1D sammon layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='cmdscale')
collapsing slice networks ...
computing vertex positions using 1D cmdscale layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
> proximity.timeline(cls33_10_16_96,onsets=seq(0,45,5),termini=seq(2.5,47.5,5),mode='gvNeato')
collapsing slice networks ...
computing vertex positions using 1D gvNeato layout ...
computing positions for slice 1
computing positions for slice 2
computing positions for slice 3
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
rendering splines for each vertex ...
There were 18 warnings (use warnings() to see them)
> # only check MDSJ if allready installed
> has.mdsj<-ndtv:::check.mdsj(ask=FALSE)
The MDSJ Java library does not appear to be installed. The ndtv package can use MDSJ to provide a fast accurate layout algorithm. It can be downloaded from http://algo.uni-konstanz.de/software/mdsj/
Error in install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/ndtv/java/does not appear to have write permissions
Calls: <Anonymous> -> install.mdsj
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.10.0
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Martina Morris, University of Washington
Skye Bender-deMoll, University of Washington
For citation information, type citation("network").
Type help("network-package") to get started.
Loading required package: networkDynamic
networkDynamic: version 0.9.0, created on 2016-01-12
Copyright (c) 2016, Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Pavel N. Krivitsky, University of Wollongong
Skye Bender-deMoll, University of Washington
with contributions from
Zack Almquist, University of California -- Irvine
David R. Hunter, Penn State University
Li Wang
Kirk Li, University of Washington
Steven M. Goodreau, University of Washington
Jeffrey Horner
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("networkDynamic").
Loading required package: animation
Loading required package: sna
Loading required package: statnet.common
Attaching package: ‘statnet.common’
The following object is masked from ‘package:base’:
order
sna: Tools for Social Network Analysis
Version 2.4 created on 2016-07-23.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
For citation information, type citation("sna").
Type help(package="sna") to get started.
ndtv: version 0.10.0, created on 2016-5-6
Copyright (c) 2016, Skye Bender-deMoll, University of Washington
with contributions from
Martina Morris, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ndtv").
No slice.par found, using
Calculating layout for network slice from time 1 to 2
Calculating layout for network slice from time 2 to 3
Calculating layout for network slice from time 3 to 4
Calculating layout for network slice from time 4 to 5
Calculating layout for network slice from time 5 to 6
Calculating layout for network slice from time 6 to 7
Calculating layout for network slice from time 7 to 8
Calculating layout for network slice from time 8 to 9
Calculating layout for network slice from time 9 to 10
Calculating layout for network slice from time 10 to 11
Calculating layout for network slice from time 11 to 12
Calculating layout for network slice from time 12 to 13
rendering 10 frames for slice 0
rendering 10 frames for slice 1
rendering 10 frames for slice 2
rendering 10 frames for slice 3
rendering 10 frames for slice 4
rendering 10 frames for slice 5
rendering 10 frames for slice 6
rendering 10 frames for slice 7
rendering 10 frames for slice 8
rendering 10 frames for slice 9
rendering 10 frames for slice 10
rendering 10 frames for slice 11
Loading required package: tergm
Loading required package: ergm
ergm: version 3.8.0, created on 2017-08-18
Copyright (c) 2017, Mark S. Handcock, University of California -- Los Angeles
David R. Hunter, Penn State University
Carter T. Butts, University of California -- Irvine
Steven M. Goodreau, University of Washington
Pavel N. Krivitsky, University of Wollongong
Martina Morris, University of Washington
with contributions from
Li Wang
Kirk Li, University of Washington
Skye Bender-deMoll, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").
NOTE: Versions before 3.6.1 had a bug in the
implementation of the bd() constriant which distorted
the sampled distribution somewhat. In addition,
Sampson's Monks datasets had mislabeled vertices. See
the NEWS and the documentation for more details.
tergm: version 3.4.1, created on 2017-09-12
Copyright (c) 2017, Pavel N. Krivitsky, University of Wollongong
Mark S. Handcock, University of California -- Los Angeles
with contributions from
David R. Hunter, Penn State University
Steven M. Goodreau, University of Washington
Martina Morris, University of Washington
Nicole Bohme Carnegie, New York University
Carter T. Butts, University of California -- Irvine
Ayn Leslie-Cook, University of Washington
Skye Bender-deMoll
Li Wang
Kirk Li, University of Washington
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("tergm").
Starting maximum likelihood estimation via MCMLE:
Iteration 1 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.3131.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.01726.
Step length converged twice. Stopping.
This model was fit using MCMC. To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Error: processing vignette ‘ndtv.Rnw’ failed with diagnostics:
chunk 9 (label = mdsj_actual_download)
Error in ndtv:::install.mdsj(mdsj.dir) :
Unable to install MDSJ because the package path /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/ndtv/java/does not appear to have write permissions
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.10.0
Check: re-building of vignette outputs
Result: NOTE
Error in re-building vignettes:
...
computing positions for slice 4
computing positions for slice 5
computing positions for slice 6
computing positions for slice 7
computing positions for slice 8
computing positions for slice 9
computing positions for slice 10
computing positions for slice 11
rendering splines for each vertex ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
Running 'texi2dvi' on 'ndtv.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.6 \usepackage
{color}^^M
! ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Flavor: r-oldrel-osx-x86_64