CRAN Package Check Results for Package FLightR

Last updated on 2018-05-27 07:50:48 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.4.6 9.42 192.42 201.84 OK
r-devel-linux-x86_64-debian-gcc 0.4.6 7.35 135.66 143.01 ERROR
r-devel-linux-x86_64-fedora-clang 0.4.6 176.87 NOTE
r-devel-linux-x86_64-fedora-gcc 0.4.6 226.92 NOTE
r-devel-windows-ix86+x86_64 0.4.6 10.00 212.00 222.00 OK
r-patched-linux-x86_64 0.4.6 7.57 175.16 182.73 ERROR
r-patched-solaris-x86 0.4.6 340.30 NOTE
r-release-linux-x86_64 0.4.6 7.97 178.71 186.68 OK
r-release-windows-ix86+x86_64 0.4.6 15.00 278.00 293.00 OK
r-release-osx-x86_64 0.4.6 NOTE
r-oldrel-windows-ix86+x86_64 0.4.6 14.00 202.00 216.00 OK
r-oldrel-osx-x86_64 0.4.6 NOTE

Check Details

Version: 0.4.6
Check: examples
Result: ERROR
    Running examples in ‘FLightR-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: plot_util_distr
    > ### Title: plots resulting track over map with uncertainty shown by spave
    > ### utilisation distribution
    > ### Aliases: plot_util_distr
    >
    > ### ** Examples
    >
    > File<-system.file("extdata", "Godwit_TAGS_format.csv", package = "FLightR")
    > # to run example fast we will cut the real data file by 2013 Aug 20
    > Proc.data<-get.tags.data(File, end.date=as.POSIXct('2013-06-25', tz='GMT'))
    Detected Intigeo_Mode_1 tag
    Data found to be logtransformed
    tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    > Calibration.periods<-data.frame(
    + calibration.start=as.POSIXct(c(NA, "2014-05-05")),
    + calibration.stop=as.POSIXct(c("2013-08-20", NA)),
    + lon=5.43, lat=52.93)
    > #use c() also for the geographic coordinates, if you have more than one calibration location
    > # (e. g., lon=c(5.43, 6.00), lat=c(52.93,52.94))
    >
    > # NB Below likelihood.correction is set to FALSE for fast run!
    > # Leave it as default TRUE for real examples
    > Calibration<-make.calibration(Proc.data, Calibration.periods, likelihood.correction=FALSE)
    
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    calibration method used: parametric.slope
    >
    > Grid<-make.grid(left=0, bottom=50, right=10, top=56,
    + distance.from.land.allowed.to.use=c(-Inf, Inf),
    + distance.from.land.allowed.to.stay=c(-Inf, Inf))
    >
    > all.in<-make.prerun.object(Proc.data, Grid, start=c(5.43, 52.93),
    + Calibration=Calibration, threads=1)
    likelihood correction turned off as no correction found in the calibration
    estimating dusks
    doing 1
    estimating dawns
    doing 1
    processing results
    > # here we will run only 1e4 partilces for a very short track.
    > # One should use 1e6 particles for the full run
    > Result<-run.particle.filter(all.in, threads=1,
    + nParticles=1e3, known.last=TRUE,
    + precision.sd=25, check.outliers=FALSE)
    smart filter is OFF
    
    
    ##########################
     Time.Period 1 of 13
    generating new particlesESS is 1000
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 2 of 13
    generating new particlesESS is 696.991 - resampling 1
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 3 of 13
    generating new particlesESS is 719.8262 - resampling 2
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 4 of 13
    generating new particlesESS is 867.7164 - resampling 3
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 5 of 13
    generating new particlesESS is 841.8246 - resampling 4
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 6 of 13
    generating new particlesESS is 871.8335 - resampling 5
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 7 of 13
    generating new particlesESS is 889.5587 - resampling 6
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 8 of 13
    generating new particlesESS is 872.5115 - resampling 7
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 9 of 13
    generating new particlesESS is 930.8292 - resampling 8
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 10 of 13
    generating new particlesESS is 928.2488 - resampling 9
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 11 of 13
    generating new particlesESS is 887.9647 - resampling 10
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 12 of 13
    generating new particlesESS is 897.0272 - resampling 11
     unique P in point leaving stack 1
    creating stack
    
    
    ##########################
     Time.Period 13 of 13
    generating new particlesESS is 645.7516 - resampling 12
     unique P in point leaving stack 1
    creating stack
    adding last points form the stack to the resutls
    +----------------------------------+
    | estimated negative Log Likelihood is -2.356323
    +----------------------------------+
    estimating results object
    estimating quantiles for positions
    adding 95% credibility intervals to medians
     estimating distances
     estimating directions
     estimating mean directions and kappas
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
    DONE!
    >
    > plot_util_distr(Result, zoom=6, save=FALSE)
    function will plot 13 twilights
    function will plot 13 twilights
    function will plot 13 twilights
    Warning: bounding box given to google - spatial extent only approximate.
    converting bounding box to center/zoom specification. (experimental)
    Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
     cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=53.099988,5.25&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
    Error in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
     cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=53.099988,5.25&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
    Calls: plot_util_distr ... do.call -> <Anonymous> -> get_googlemap -> download.file
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.4.6
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘rgdal’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.4.6
Check: tests
Result: ERROR
     Running ‘testthat.R’ [89s/114s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(FLightR)
     This is FLightR 0.4.6
     NB: All functions that started from plot.**.**() are renamed to plot_**_** in order to pass CRAN check
    
     > test_check("FLightR")
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
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     calibration method used: parametric.slope
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
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     calibration method used: parametric.slope
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
     stage 1...
     stage 2...
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
     checking dawn 1
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     checking dusk 11
     checking dusk 12
     checking dusk 13
     checking dusk 14
     checking dusk 15
     calibration method used: parametric.slope
     likelihood correction turned off as no correction found in the calibration
     estimating dusks
     doing 1
     doing 11
     estimating dawns
     doing 1
     doing 11
     processing results
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
     checking dawn 1
     checking dawn 2
     checking dawn 3
     checking dawn 4
     checking dawn 5
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     checking dusk 10
     checking dusk 11
     checking dusk 12
     checking dusk 13
     checking dusk 14
     checking dusk 15
     calibration method used: parametric.slope
     likelihood correction turned off as no correction found in the calibration
     estimating dusks
     doing 1
     doing 11
     estimating dawns
     doing 1
     doing 11
     processing results
     smart filter is OFF
    
    
     ##########################
     Time.Period 1 of 27
     generating new particlesESS is 1000
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 2 of 27
     generating new particlesESS is 484.8809 - resampling 1
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 3 of 27
     generating new particlesESS is 353.1679 - resampling 2
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 4 of 27
     generating new particlesESS is 833.2095 - resampling 3
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 5 of 27
     generating new particlesESS is 836.2745 - resampling 4
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 6 of 27
     generating new particlesESS is 849.2699 - resampling 5
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 7 of 27
     generating new particlesESS is 862.5026 - resampling 6
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 8 of 27
     generating new particlesESS is 830.166 - resampling 7
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 9 of 27
     generating new particlesESS is 913.4229 - resampling 8
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 10 of 27
     generating new particlesESS is 908.7612 - resampling 9
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 11 of 27
     generating new particlesESS is 882.9262 - resampling 10
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 12 of 27
     generating new particlesESS is 879.55 - resampling 11
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 13 of 27
     generating new particlesESS is 524.3876 - resampling 12
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 14 of 27
     generating new particlesESS is 865.4295 - resampling 13
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 15 of 27
     generating new particlesESS is 927.6183 - resampling 14
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 16 of 27
     generating new particlesESS is 889.7589 - resampling 15
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 17 of 27
     generating new particlesESS is 886.6172 - resampling 16
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 18 of 27
     generating new particlesESS is 886.8583 - resampling 17
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 19 of 27
     generating new particlesESS is 948.3973 - resampling 18
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 20 of 27
     generating new particlesESS is 919.8342 - resampling 19
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 21 of 27
     generating new particlesESS is 844.4323 - resampling 20
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 22 of 27
     generating new particlesESS is 909.5005 - resampling 21
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 23 of 27
     generating new particlesESS is 931.0699 - resampling 22
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 24 of 27
     generating new particlesESS is 913.7502 - resampling 23
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 25 of 27
     generating new particlesESS is 842.963 - resampling 24
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 26 of 27
     generating new particlesESS is 961.3127 - resampling 25
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 27 of 27
     generating new particlesESS is 726.1329 - resampling 26
     unique P in point leaving stack 1
     creating stack
     adding last points form the stack to the resutls
     +----------------------------------+
     | estimated negative Log Likelihood is -11.63468
     +----------------------------------+
     estimating results object
     estimating quantiles for positions
     adding 95% credibility intervals to medians
     estimating distances
     estimating directions
     estimating mean directions and kappas
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
     DONE!
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
     checking dawn 1
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     checking dusk 1
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     checking dusk 6
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     checking dusk 8
     checking dusk 9
     checking dusk 10
     checking dusk 11
     checking dusk 12
     checking dusk 13
     checking dusk 14
     checking dusk 15
     calibration method used: parametric.slope
     likelihood correction turned off as no correction found in the calibration
     estimating dusks
     doing 1
     doing 11
     estimating dawns
     doing 1
     doing 11
     processing results
     smart filter is OFF
    
    
     ##########################
     Time.Period 1 of 27
     generating new particlesESS is 1000
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 2 of 27
     generating new particlesESS is 439.0429 - resampling 1
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 3 of 27
     generating new particlesESS is 307.7932 - resampling 2
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 4 of 27
     generating new particlesESS is 727.6605 - resampling 3
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 5 of 27
     generating new particlesESS is 710.6271 - resampling 4
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 6 of 27
     generating new particlesESS is 781.9006 - resampling 5
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 7 of 27
     generating new particlesESS is 837.1334 - resampling 6
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 8 of 27
     generating new particlesESS is 833.198 - resampling 7
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 9 of 27
     generating new particlesESS is 899.669 - resampling 8
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 10 of 27
     generating new particlesESS is 887.9905 - resampling 9
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 11 of 27
     generating new particlesESS is 891.3709 - resampling 10
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 12 of 27
     generating new particlesESS is 874.4597 - resampling 11
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 13 of 27
     generating new particlesESS is 569.263 - resampling 12
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 14 of 27
     generating new particlesESS is 872.654 - resampling 13
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 15 of 27
     generating new particlesESS is 936.1794 - resampling 14
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 16 of 27
     generating new particlesESS is 867.7118 - resampling 15
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 17 of 27
     generating new particlesESS is 899.8249 - resampling 16
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 18 of 27
     generating new particlesESS is 902.6497 - resampling 17
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 19 of 27
     generating new particlesESS is 943.4788 - resampling 18
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 20 of 27
     generating new particlesESS is 925.6394 - resampling 19
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 21 of 27
     generating new particlesESS is 880.1384 - resampling 20
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 22 of 27
     generating new particlesESS is 930.567 - resampling 21
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 23 of 27
     generating new particlesESS is 928.6618 - resampling 22
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 24 of 27
     generating new particlesESS is 899.2928 - resampling 23
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 25 of 27
     generating new particlesESS is 843.0832 - resampling 24
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 26 of 27
     generating new particlesESS is 945.7015 - resampling 25
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 27 of 27
     generating new particlesESS is 668.5231 - resampling 26
     unique P in point leaving stack 1
     creating stack
     adding last points form the stack to the resutls
     +----------------------------------+
     | estimated negative Log Likelihood is -11.59001
     +----------------------------------+
     estimating results object
     estimating quantiles for positions
     adding 95% credibility intervals to medians
     estimating distances
     estimating directions
     estimating mean directions and kappas
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
     DONE!
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
     checking dawn 1
     checking dawn 2
     checking dawn 3
     checking dawn 4
     checking dawn 5
     checking dawn 6
     checking dawn 7
     checking dawn 8
     checking dawn 9
     checking dawn 10
     checking dawn 11
     checking dawn 12
     checking dawn 13
     checking dusk 1
     checking dusk 2
     checking dusk 3
     checking dusk 4
     checking dusk 5
     checking dusk 6
     checking dusk 7
     checking dusk 8
     checking dusk 9
     checking dusk 10
     checking dusk 11
     checking dusk 12
     checking dusk 13
     checking dusk 14
     checking dusk 15
     calibration method used: parametric.slope
     likelihood correction turned off as no correction found in the calibration
     estimating dusks
     doing 1
     doing 11
     estimating dawns
     doing 1
     doing 11
     processing results
     smart filter is OFF
    
    
     ##########################
     Time.Period 1 of 27
     generating new particlesESS is 1000
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 2 of 27
     generating new particlesESS is 518.1807 - resampling 1
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 3 of 27
     generating new particlesESS is 324.167 - resampling 2
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 4 of 27
     generating new particlesESS is 770.7627 - resampling 3
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 5 of 27
     generating new particlesESS is 662.6424 - resampling 4
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 6 of 27
     generating new particlesESS is 765.3358 - resampling 5
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 7 of 27
     generating new particlesESS is 846.4829 - resampling 6
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 8 of 27
     generating new particlesESS is 756.958 - resampling 7
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 9 of 27
     generating new particlesESS is 881.4298 - resampling 8
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 10 of 27
     generating new particlesESS is 905.4365 - resampling 9
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 11 of 27
     generating new particlesESS is 890.0974 - resampling 10
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 12 of 27
     generating new particlesESS is 871.8822 - resampling 11
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 13 of 27
     generating new particlesESS is 554.5852 - resampling 12
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 14 of 27
     generating new particlesESS is 870.8068 - resampling 13
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 15 of 27
     generating new particlesESS is 904.8705 - resampling 14
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 16 of 27
     generating new particlesESS is 890.8773 - resampling 15
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 17 of 27
     generating new particlesESS is 906.6083 - resampling 16
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 18 of 27
     generating new particlesESS is 896.4747 - resampling 17
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 19 of 27
     generating new particlesESS is 949.7125 - resampling 18
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 20 of 27
     generating new particlesESS is 909.129 - resampling 19
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 21 of 27
     generating new particlesESS is 850.3465 - resampling 20
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 22 of 27
     generating new particlesESS is 912.3474 - resampling 21
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 23 of 27
     generating new particlesESS is 952.5628 - resampling 22
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 24 of 27
     generating new particlesESS is 901.8448 - resampling 23
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 25 of 27
     generating new particlesESS is 859.4991 - resampling 24
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 26 of 27
     generating new particlesESS is 957.9234 - resampling 25
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 27 of 27
     generating new particlesESS is 708.7787 - resampling 26
     unique P in point leaving stack 1
     creating stack
     adding last points form the stack to the resutls
     +----------------------------------+
     | estimated negative Log Likelihood is -11.73115
     +----------------------------------+
     estimating results object
     estimating quantiles for positions
     adding 95% credibility intervals to medians
     estimating distances
     estimating directions
     estimating mean directions and kappas
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
     DONE!
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
     checking dawn 1
     checking dawn 2
     checking dawn 3
     checking dawn 4
     checking dawn 5
     checking dawn 6
     checking dawn 7
     checking dawn 8
     checking dawn 9
     checking dawn 10
     checking dawn 11
     checking dawn 12
     checking dawn 13
     checking dusk 1
     checking dusk 2
     checking dusk 3
     checking dusk 4
     checking dusk 5
     checking dusk 6
     checking dusk 7
     checking dusk 8
     checking dusk 9
     checking dusk 10
     checking dusk 11
     checking dusk 12
     checking dusk 13
     checking dusk 14
     checking dusk 15
     calibration method used: parametric.slope
     likelihood correction turned off as no correction found in the calibration
     estimating dusks
     doing 1
     doing 11
     estimating dawns
     doing 1
     doing 11
     processing results
     smart filter is OFF
    
    
     ##########################
     Time.Period 1 of 27
     generating new particlesESS is 1000
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 2 of 27
     generating new particlesESS is 467.7768 - resampling 1
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 3 of 27
     generating new particlesESS is 336.5217 - resampling 2
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 4 of 27
     generating new particlesESS is 764.0731 - resampling 3
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 5 of 27
     generating new particlesESS is 580.357 - resampling 4
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 6 of 27
     generating new particlesESS is 758.0036 - resampling 5
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 7 of 27
     generating new particlesESS is 810.0917 - resampling 6
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 8 of 27
     generating new particlesESS is 802.5027 - resampling 7
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 9 of 27
     generating new particlesESS is 903.3698 - resampling 8
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 10 of 27
     generating new particlesESS is 897.5683 - resampling 9
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 11 of 27
     generating new particlesESS is 869.4761 - resampling 10
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 12 of 27
     generating new particlesESS is 859.1873 - resampling 11
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 13 of 27
     generating new particlesESS is 532.7298 - resampling 12
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 14 of 27
     generating new particlesESS is 872.381 - resampling 13
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 15 of 27
     generating new particlesESS is 919.4524 - resampling 14
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 16 of 27
     generating new particlesESS is 902.2519 - resampling 15
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 17 of 27
     generating new particlesESS is 893.8334 - resampling 16
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 18 of 27
     generating new particlesESS is 908.3454 - resampling 17
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 19 of 27
     generating new particlesESS is 945.9017 - resampling 18
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 20 of 27
     generating new particlesESS is 894.3718 - resampling 19
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 21 of 27
     generating new particlesESS is 852.1071 - resampling 20
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 22 of 27
     generating new particlesESS is 921.1117 - resampling 21
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 23 of 27
     generating new particlesESS is 943.7407 - resampling 22
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 24 of 27
     generating new particlesESS is 903.4423 - resampling 23
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 25 of 27
     generating new particlesESS is 836.7734 - resampling 24
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 26 of 27
     generating new particlesESS is 948.695 - resampling 25
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 27 of 27
     generating new particlesESS is 698.1419 - resampling 26
     unique P in point leaving stack 1
     creating stack
     adding last points form the stack to the resutls
     +----------------------------------+
     | estimated negative Log Likelihood is -11.63205
     +----------------------------------+
     estimating results object
     estimating quantiles for positions
     adding 95% credibility intervals to medians
     estimating distances
     estimating directions
     estimating mean directions and kappas
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
     DONE!
     function will plot 27 twilights
     function will plot 27 twilights
     function will plot 27 twilights
     ── 1. Error: plot_util_distr_works (@test_data_result_summary_and_plotting.R#57)
     cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=53.099988,5.25&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
     1: expect_warning(plot_util_distr(Result, zoom = 5, save = FALSE)) at testthat/test_data_result_summary_and_plotting.R:57
     2: quasi_capture(enquo(object), capture_warnings, label = label)
     3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
     4: withCallingHandlers(code, warning = function(condition) {
     out$push(condition)
     invokeRestart("muffleWarning")
     })
     5: eval_bare(get_expr(quo), get_env(quo))
     6: plot_util_distr(Result, zoom = 5, save = FALSE)
     7: do.call(ggmap::get_map, map.options)
     8: (function (location = c(lon = -95.3632715, lat = 29.7632836), zoom = "auto", scale = "auto",
     maptype = c("terrain", "terrain-background", "satellite", "roadmap", "hybrid",
     "toner", "watercolor", "terrain-labels", "terrain-lines", "toner-2010", "toner-2011",
     "toner-background", "toner-hybrid", "toner-labels", "toner-lines", "toner-lite"),
     source = c("google", "osm", "stamen", "cloudmade"), force = ifelse(source ==
     "google", TRUE, TRUE), messaging = FALSE, urlonly = FALSE, filename = "ggmapTemp",
     crop = TRUE, color = c("color", "bw"), language = "en-EN", api_key)
     {
     args <- as.list(match.call(expand.dots = TRUE)[-1])
     if ("verbose" %in% names(args)) {
     .Deprecated(msg = "verbose argument deprecated, use messaging.")
     messaging <- eval(args$verbose)
     }
     if ("center" %in% names(args)) {
     .Deprecated(msg = "center argument deprecated, use location.")
     location <- eval(args$center)
     }
     source <- match.arg(source)
     color <- match.arg(color)
     if (missing(maptype)) {
     if (source != "cloudmade") {
     maptype <- "terrain"
     }
     else {
     maptype <- 1
     }
     }
     if (source == "stamen") {
     if (!(maptype %in% c("terrain", "terrain-background", "terrain-labels", "terrain-lines",
     "toner", "toner-2010", "toner-2011", "toner-background", "toner-hybrid",
     "toner-labels", "toner-lines", "toner-lite", "watercolor"))) {
     stop("invalid stamen maptype, see ?get_stamenmap", call. = FALSE)
     }
     }
     if (source == "google" & (maptype %in% c("terrain-background", "terrain-labels",
     "terrain-lines", "toner", "toner-2010", "toner-2011", "toner-background",
     "toner-hybrid", "toner-labels", "toner-lines", "toner-lite", "watercolor"))) {
     message(paste0("maptype = \"", maptype, "\" is only available with source = \"stamen\"."))
     message(paste0("resetting to source = \"stamen\"..."))
     source <- "stamen"
     }
     location_stop <- TRUE
     if (is.character(location) && length(location) == 1) {
     location_type <- "address"
     location_stop <- FALSE
     }
     if (is.data.frame(location) && ncol(location) == 2) {
     location <- colMeans(location)
     }
     if (is.numeric(location) && length(location) == 2) {
     location_type <- "lonlat"
     location_stop <- FALSE
     if (!is.null(names(location))) {
     loc_names <- names(location)
     if (all(loc_names == c("long", "lat"))) {
     names(location) <- c("lon", "lat")
     }
     else if (all(loc_names == c("lat", "lon"))) {
     message("note : locations should be specified in the lon/lat format, not lat/lon.")
     location <- location[c("lon", "lat")]
     }
     else if (all(loc_names == c("lat", "long"))) {
     message("note : locations should be specified in the lon/lat format, not lat/lon.")
     location <- location[c("long", "lat")]
     names(location) <- c("lon", "lat")
     }
     }
     else {
     names(location) <- c("lon", "lat")
     }
     }
     if (is.numeric(location) && length(location) == 4) {
     location_type <- "bbox"
     location_stop <- FALSE
     if (length(names(location)) > 0) {
     if (!all(names(location) %in% c("left", "bottom", "right", "top"))) {
     stop("bounding boxes should have name left, bottom, right, top)",
     call. = FALSE)
     }
     location <- location[c("left", "bottom", "right", "top")]
     }
     else {
     names(location) <- c("left", "bottom", "right", "top")
     }
     }
     if (location_stop) {
     stop("improper location specification, see ?get_map.", call. = F)
     }
     if (zoom == "auto" && location_type == "bbox") {
     if (zoom == "auto") {
     lon_range <- location[c("left", "right")]
     lat_range <- location[c("bottom", "top")]
     if (missing(zoom)) {
     lonlength <- diff(lon_range)
     latlength <- diff(lat_range)
     zoomlon <- ceiling(log2(360 * 2/lonlength))
     zoomlat <- ceiling(log2(180 * 2/latlength))
     zoom <- max(zoomlon, zoomlat)
     }
     }
     }
     else if (zoom == "auto" && location_type != "bbox") {
     zoom = 10
     }
     if (scale == "auto") {
     if (source == "google")
     scale <- 2
     if (source == "osm")
     scale <- OSM_scale_lookup(zoom)
     }
     if (source == "google") {
     if (location_type == "bbox") {
     warning("bounding box given to google - spatial extent only approximate.",
     call. = FALSE, immediate. = TRUE)
     message("converting bounding box to center/zoom specification. (experimental)")
     user_bbox <- location
     location <- c(lon = mean(location[c("left", "right")]), lat = mean(location[c("bottom",
     "top")]))
     }
     map <- get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale,
     messaging = messaging, urlonly = urlonly, force = force, filename = filename,
     color = color, language = language)
     if (FALSE) {
     bb <- attr(map, "bb")
     mbbox <- c(left = bb$ll.lon, bottom = bb$ll.lat, right = bb$ur.lon, top = bb$ur.lat)
     size <- dim(map)
     if (location_type == "bbox") {
     slon <- seq(mbbox["left"], mbbox["right"], length.out = size[1])
     slat <- seq(mbbox["top"], mbbox["bottom"], length.out = size[2])
     keep_x_ndcs <- which(user_bbox["left"] <= slon & slon <= user_bbox["right"])
     keep_y_ndcs <- which(user_bbox["bottom"] <= slat & slat <= user_bbox["top"])
     map <- map[keep_y_ndcs, keep_x_ndcs]
     class(map) <- c("ggmap", "raster")
     attr(map, "bb") <- data.frame(ll.lat = user_bbox["bottom"], ll.lon = user_bbox["left"],
     ur.lat = user_bbox["top"], ur.lon = user_bbox["right"])
     }
     }
     return(map)
     }
     if (source == "osm") {
     if (location_type != "bbox") {
     gm <- get_googlemap(center = location, zoom = zoom, filename = filename)
     location <- as.numeric(attr(gm, "bb"))[c(2, 1, 4, 3)]
     }
     return(get_openstreetmap(bbox = location, scale = scale, messaging = messaging,
     urlonly = urlonly, filename = filename, color = color))
     }
     if (source == "stamen") {
     if (location_type != "bbox") {
     gm <- get_googlemap(center = location, zoom = zoom, filename = filename)
     location <- as.numeric(attr(gm, "bb"))[c(2, 1, 4, 3)]
     }
     return(get_stamenmap(bbox = location, zoom = zoom, maptype = maptype, crop = crop,
     messaging = messaging, urlonly = urlonly, filename = filename, force = force,
     color = color))
     }
     if (source == "cloudmade") {
     if (missing(api_key))
     stop("an api key must be provided for cloudmade maps, see ?get_cloudmademap.",
     call. = FALSE)
     if (location_type != "bbox") {
     gm <- get_googlemap(center = location, zoom = zoom, filename = filename)
     location <- as.numeric(attr(gm, "bb"))[c(2, 1, 4, 3)]
     }
     return(get_cloudmademap(bbox = location, zoom = zoom, maptype = maptype,
     crop = crop, messaging = messaging, urlonly = urlonly, filename = filename,
     highres = TRUE, color = color, api_key = api_key))
     }
     })(zoom = 5, col = "bw", location = c(4.6155178, 52.71809615, 5.8844822, 53.4818792
     ))
     9: get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale, messaging = messaging,
     urlonly = urlonly, force = force, filename = filename, color = color, language = language)
     10: download.file(url, destfile = tmp, quiet = !messaging, mode = "wb")
    
     Detected Intigeo_Mode_1 tag
     Data found to be logtransformed
     tag saved data every 300 seconds, and is assumed to measure data every 60 seconds, and write down max
    
     checking dawn 1
     checking dawn 2
     checking dawn 3
     checking dawn 4
     checking dawn 5
     checking dawn 6
     checking dawn 7
     checking dawn 8
     checking dawn 9
     checking dawn 10
     checking dawn 11
     checking dawn 12
     checking dawn 13
     checking dusk 1
     checking dusk 2
     checking dusk 3
     checking dusk 4
     checking dusk 5
     checking dusk 6
     checking dusk 7
     checking dusk 8
     checking dusk 9
     checking dusk 10
     checking dusk 11
     checking dusk 12
     checking dusk 13
     checking dusk 14
     checking dusk 15
     calibration method used: parametric.slope
     likelihood correction turned off as no correction found in the calibration
     estimating dusks
     doing 1
     doing 11
     estimating dawns
     doing 1
     doing 11
     processing results
     smart filter is OFF
    
    
     ##########################
     Time.Period 1 of 27
     generating new particlesESS is 1000
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 2 of 27
     generating new particlesESS is 480.2373 - resampling 1
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 3 of 27
     generating new particlesESS is 343.8343 - resampling 2
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 4 of 27
     generating new particlesESS is 734.5274 - resampling 3
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 5 of 27
     generating new particlesESS is 831.3218 - resampling 4
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 6 of 27
     generating new particlesESS is 795.3091 - resampling 5
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 7 of 27
     generating new particlesESS is 889.551 - resampling 6
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 8 of 27
     generating new particlesESS is 838.2381 - resampling 7
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 9 of 27
     generating new particlesESS is 905.9616 - resampling 8
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 10 of 27
     generating new particlesESS is 925.617 - resampling 9
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 11 of 27
     generating new particlesESS is 881.6191 - resampling 10
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 12 of 27
     generating new particlesESS is 894.1541 - resampling 11
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 13 of 27
     generating new particlesESS is 510.7076 - resampling 12
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 14 of 27
     generating new particlesESS is 853.2843 - resampling 13
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 15 of 27
     generating new particlesESS is 931.1268 - resampling 14
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 16 of 27
     generating new particlesESS is 876.3087 - resampling 15
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 17 of 27
     generating new particlesESS is 898.4655 - resampling 16
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 18 of 27
     generating new particlesESS is 910.0714 - resampling 17
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 19 of 27
     generating new particlesESS is 922.0196 - resampling 18
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 20 of 27
     generating new particlesESS is 911.2558 - resampling 19
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 21 of 27
     generating new particlesESS is 840.8175 - resampling 20
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 22 of 27
     generating new particlesESS is 892.7195 - resampling 21
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 23 of 27
     generating new particlesESS is 935.036 - resampling 22
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 24 of 27
     generating new particlesESS is 925.7606 - resampling 23
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 25 of 27
     generating new particlesESS is 810.762 - resampling 24
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 26 of 27
     generating new particlesESS is 966.0224 - resampling 25
     unique P in point leaving stack 1
     creating stack
    
    
     ##########################
     Time.Period 27 of 27
     generating new particlesESS is 693.0606 - resampling 26
     unique P in point leaving stack 1
     creating stack
     adding last points form the stack to the resutls
     +----------------------------------+
     | estimated negative Log Likelihood is -11.61001
     +----------------------------------+
     estimating results object
     estimating quantiles for positions
     adding 95% credibility intervals to medians
     estimating distances
     estimating directions
     estimating mean directions and kappas
     estimating kappas
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
     DONE!
     bird likely did not move, exiting without result
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 29 SKIPPED: 0 FAILED: 1
     1. Error: plot_util_distr_works (@test_data_result_summary_and_plotting.R#57)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-linux-x86_64