Last updated on 2021-07-19 13:54:06 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.9 | 34.42 | 433.75 | 468.17 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.9 | 27.67 | 312.25 | 339.92 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.9 | 557.08 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.9 | 547.33 | OK | |||
| r-devel-windows-x86_64 | 1.9 | 29.00 | 300.00 | 329.00 | OK | |
| r-devel-windows-x86_64-gcc10-UCRT | 1.9 | OK | ||||
| r-patched-linux-x86_64 | 1.9 | 33.95 | 400.51 | 434.46 | OK | |
| r-patched-solaris-x86 | 1.9 | 502.10 | ERROR | |||
| r-release-linux-x86_64 | 1.9 | 28.65 | 400.33 | 428.98 | OK | |
| r-release-macos-arm64 | 1.3 | NOTE | ||||
| r-release-macos-x86_64 | 1.9 | ERROR | ||||
| r-release-windows-ix86+x86_64 | 1.9 | 76.00 | 395.00 | 471.00 | OK | |
| r-oldrel-macos-x86_64 | 1.9 | ERROR | ||||
| r-oldrel-windows-ix86+x86_64 | 1.9 | 84.00 | 407.00 | 491.00 | OK |
Version: 1.9
Check: examples
Result: ERROR
Running examples in ‘ecochange-Ex.R’ failed
The error most likely occurred in:
> ### Name: gaugeIndicator
> ### Title: Gauge Indicator
> ### Aliases: gaugeIndicator
>
> ### ** Examples
>
> ## Warnings from GDAL/PROJ are suppressed.
>
> ## RasterBrick of structural Essential Biodiversity Variables
> ## covering the extent of a location in the northern Amazon basin
> ## (Colombia) is imported:
> path. <- system.file('amazon.grd',package = 'ecochange')
> amazon <- suppressWarnings(brick(path.))
>
> ## Changes in layers of tree-canopy cover (TC) in the 'amazon'
> ## brick are computed:
> suppressWarnings(
+ def <- echanges(amazon, eco = 'TC',
+ change = 'lossyear',
+ eco_range = c(1,80),
+ get_unaffected = TRUE,
+ binary_output = FALSE,
+ mc.cores = 2)
+ )
[1] "'eco' has length > 1: matching names of 'eco' with values in 'change_vals'"
sh: gdal_calc.py: not found
Error in .local(.Object, ...) :
sh: gdal_calc.py: not found
Error in .local(.Object, ...) :
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘raster’ for signature ‘"try-error"’
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.9
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘ecochange_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ecochange
Loading required package: raster
Loading required package: sp
Loading required package: rgeos
rgeos version: 0.5-5, (SVN revision 640)
GEOS runtime version: 3.6.4-CAPI-1.10.4
Linking to sp version: 1.4-5
Polygon checking: TRUE
Loading required package: ggplot2
Loading required package: sf
Linking to GEOS 3.6.4, GDAL 2.2.4, PROJ 5.2.0
Loading required package: gdalUtils
Attaching package: 'gdalUtils'
The following object is masked from 'package:sf':
gdal_rasterize
Package 'ecochange' version 1.9
Type 'citation("ecochange")' for citing this R package in publications.
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
Path to GDAL shared files: /usr/local/share/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
Path to PROJ shared files: (autodetected)
Linking to sp version:1.4-5
Loading required package: parallel
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:R.methodsS3':
throw
The following object is masked from 'package:rgdal':
getDescription
The following objects are masked from 'package:raster':
extend, trim
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, load, save
R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following objects are masked from 'package:raster':
extract, resample
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings
Loading required package: rvest
Loading required package: xml2
Loading required package: tidyverse
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called 'tidyverse'
Loading required package: landscapemetrics
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:rgeos':
intersect, setdiff, union
The following objects are masked from 'package:raster':
intersect, select, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: httr
Loading required package: getPass
Loading required package: gdalUtilities
Attaching package: 'gdalUtilities'
The following objects are masked from 'package:gdalUtils':
gdal_grid, gdal_rasterize, gdal_translate, gdalbuildvrt, gdaldem,
gdalinfo, gdalwarp, nearblack, ogr2ogr
The following object is masked from 'package:sf':
gdal_rasterize
Loading required package: viridis
Loading required package: viridisLite
Loading required package: rasterVis
Loading required package: terra
terra version 1.3.4
Attaching package: 'terra'
The following object is masked from 'package:dplyr':
src
The following objects are masked from 'package:R.utils':
draw, wrap
The following object is masked from 'package:rgdal':
project
Loading required package: lattice
Loading required package: latticeExtra
Attaching package: 'latticeExtra'
The following object is masked from 'package:ggplot2':
layer
Loading required package: rlang
Attaching package: 'rlang'
The following object is masked from 'package:xml2':
as_list
The following object is masked from 'package:R.utils':
env
The following objects are masked from 'package:R.oo':
abort, ll
Loading required package: rasterDT
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:rlang':
:=
The following objects are masked from 'package:terra':
copy, shift
The following objects are masked from 'package:dplyr':
between, first, last
The following object is masked from 'package:raster':
shift
trying URL 'https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_COL_2_sp.rds'
Content type 'text/html; charset=iso-8859-1' length 1159816 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
rsp2ebv package:ecochange R Documentation
_<08>R_<08>e_<08>m_<08>o_<08>t_<08>e _<08>S_<08>e_<08>n_<08>s_<08>i_<08>n_<08>g _<08>P_<08>r_<08>o_<08>d_<08>u_<08>c_<08>t _<08>t_<08>o _<08>E_<08>B_<08>V
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
This function processes regions of interest (polygon geometry or
'GADM' unit) to integrate dissimilar remote sensing products (RSP)
into Essential biodiversity variables.
_<08>U_<08>s_<08>a_<08>g_<08>e:
rsp2ebv(roi = NULL, ...,
lyrs = NULL, path,
sr, ofr = c(30, 30),
mc.cores = round(detectCores() *
0.6, 0))
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
roi: 'SpatialPolygonsDataFrame'; or 'character'; or 'NULL'. Region
of interest. This can be whether 1) a polygon geometry; or 2)
the name of a 'GADM' unit (see 'getGADM'); or 3) a 'NULL'
value. Default 'NULL' makes the function to print a list of
'GADM' units.
...: If 'roi' is a 'GADM' unit then additional arguments in
'getGADM' can be specified here.
lyrs: 'character'. Remote sensing products, If 'NULL' then a list
of products is printed, see 'listGP'. Default 'NULL'.
path: 'character'. Path name indicating where the variables are
stored. If it is missing then a folder named as ''ecochange''
located in a current temporary directory is used.
sr: 'character'. 'PROJ.4' description of the target coordinate
reference system. If missing then the target layers are
projected to metric system 'UTM'.
ofr: 'numeric'. 'c(xres,yres)'. Output file resolution (in target
georeferenced units). Default 'c(30,30)' m2.
mc.cores: 'numeric'. The number of cores. Default uses around 60
percent of the cores.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
This function implements ''gdalUtils'' so it assumes the user has
a working GDAL on their system. From the documentation: "If the
''gdalUtils_gdalPath'' option has been set (usually by
''gdal_setInstallation''), the GDAL found in that 'path' will be
used. If nothing is found, ''gdal_setInstallation'' will be
executed to attempt to find a working GDAL that has the right
drivers as specified with the ''of'' (output format) parameter",
see example below.
_<08>V_<08>a_<08>l_<08>u_<08>e:
'RasterStack' of essential biodiversity variables (UTM crs), or
character lists suggesting GADM units/Global Products that can be
used to download 'rsp' (see 'NULL' defaults in arguments ''roi''
and ''lyrs'').
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Wilson Lara Henao <wilarhen@temple.edu> [aut, cre], Victor
Gutierrez-Velez [aut], Ivan Gonzales [aut]
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Jetz, W., McGeoch, M. A., Guralnick, R., Ferrier, S., Beck, J.,
Costello, M. J., ... & Meyer, C. (2019). Essential biodiversity
variables for mapping and monitoring species populations. Nature
Ecology & Evolution, 3(4), 539-551.
O'Connor, B., Secades, C., Penner, J., Sonnenschein, R., Skidmore,
A., Burgess, N. D., & Hutton, J. M. (2015). Earth observation as a
tool for tracking progress towards the Aichi Biodiversity Targets.
Remote sensing in ecology and conservation, 1(1), 19-28.
Skidmore, A. K., & Pettorelli, N. (2015). Agree on biodiversity
metrics to track from space: Ecologists and space agencies must
forge a global monitoring strategy. Nature, 523(7561), 403-406.
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
## First, we'll check to make sure there is a valid GDAL
## installation (from 'gdalUtils):
gdalUtils::gdal_setInstallation()
valid_install <- !is.null(getOption("gdalUtils_gdalPath"))
## Warnings from GDAL/PROJ are suppressed.
## A Global Surface Water layer ('seasonality') covering the extent of a
## Colombian municipality Cartagena del Chairá is formated into an
## spatial \code{EBV}:
load(system.file('cchaira_roi.RData',package = 'ecochange'))
suppressWarnings(
rsp_cchaira <- getrsp(roi = cchaira_roi,
lyrs = 'seasonality', mc.cores = 2, path = tempdir())
)
file.exists(rsp_cchaira) ##TRUE
suppressWarnings(
season_cchaira <- rsp2ebv(roi = cchaira_roi,
lyrs = 'seasonality', path = tempdir())
)
suppressWarnings(
plotebv(season_cchaira)
)
sh: gdal_calc.py: not found
sh: gdal_calc.py: not found
Quitting from lines 80-83 (ecochange_vignette.Rmd)
Error: processing vignette 'ecochange_vignette.Rmd' failed with diagnostics:
unable to find an inherited method for function 'raster' for signature '"try-error"'
--- failed re-building ‘ecochange_vignette.Rmd’
SUMMARY: processing the following file failed:
‘ecochange_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.3
Check: LazyData
Result: NOTE
'LazyData' is specified without a 'data' directory
Flavor: r-release-macos-arm64
Version: 1.9
Check: examples
Result: ERROR
Running examples in ‘ecochange-Ex.R’ failed
The error most likely occurred in:
> ### Name: gaugeIndicator
> ### Title: Gauge Indicator
> ### Aliases: gaugeIndicator
>
> ### ** Examples
>
> ## Warnings from GDAL/PROJ are suppressed.
>
> ## RasterBrick of structural Essential Biodiversity Variables
> ## covering the extent of a location in the northern Amazon basin
> ## (Colombia) is imported:
> path. <- system.file('amazon.grd',package = 'ecochange')
> amazon <- suppressWarnings(brick(path.))
>
> ## Changes in layers of tree-canopy cover (TC) in the 'amazon'
> ## brick are computed:
> suppressWarnings(
+ def <- echanges(amazon, eco = 'TC',
+ change = 'lossyear',
+ eco_range = c(1,80),
+ get_unaffected = TRUE,
+ binary_output = FALSE,
+ mc.cores = 2)
+ )
[1] "'eco' has length > 1: matching names of 'eco' with values in 'change_vals'"
sh: gdal_calc.py: command not found
sh: gdal_calc.py: command not found
Error in .local(.Object, ...) :
Error in .local(.Object, ...) :
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘raster’ for signature ‘"try-error"’
Execution halted
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.9
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘ecochange_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ecochange
Loading required package: raster
Loading required package: sp
Loading required package: rgeos
rgeos version: 0.5-5, (SVN revision 640)
GEOS runtime version: 3.8.1-CAPI-1.13.3
Linking to sp version: 1.4-5
Polygon checking: TRUE
Loading required package: ggplot2
Loading required package: sf
Linking to GEOS 3.8.1, GDAL 3.2.1, PROJ 7.2.1
Loading required package: gdalUtils
Attaching package: 'gdalUtils'
The following object is masked from 'package:sf':
gdal_rasterize
Package 'ecochange' version 1.9
Type 'citation("ecochange")' for citing this R package in publications.
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.1/rgdal/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.1/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.1/rgdal/proj
Loading required package: parallel
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following object is masked from 'package:R.methodsS3':
throw
The following object is masked from 'package:rgdal':
getDescription
The following objects are masked from 'package:raster':
extend, trim
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, load, save
R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
Attaching package: 'R.utils'
The following objects are masked from 'package:raster':
extract, resample
The following object is masked from 'package:utils':
timestamp
The following objects are masked from 'package:base':
cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings
Loading required package: rvest
Loading required package: xml2
Loading required package: tidyverse
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ tibble 3.1.2 ✔ dplyr 1.0.7
✔ tidyr 1.1.3 ✔ stringr 1.4.0
✔ readr 1.4.0 ✔ forcats 0.5.1
✔ purrr 0.3.4
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ tidyr::extract() masks R.utils::extract(), raster::extract()
✖ dplyr::filter() masks stats::filter()
✖ readr::guess_encoding() masks rvest::guess_encoding()
✖ dplyr::lag() masks stats::lag()
✖ dplyr::select() masks raster::select()
Loading required package: landscapemetrics
Loading required package: httr
Loading required package: getPass
Loading required package: gdalUtilities
Attaching package: 'gdalUtilities'
The following objects are masked from 'package:gdalUtils':
gdal_grid, gdal_rasterize, gdal_translate, gdalbuildvrt, gdaldem,
gdalinfo, gdalwarp, nearblack, ogr2ogr
The following object is masked from 'package:sf':
gdal_rasterize
Loading required package: viridis
Loading required package: viridisLite
Loading required package: rasterVis
Loading required package: terra
terra version 1.3.4
Attaching package: 'terra'
The following object is masked from 'package:dplyr':
src
The following objects are masked from 'package:R.utils':
draw, wrap
The following object is masked from 'package:rgdal':
project
Loading required package: lattice
Loading required package: latticeExtra
Attaching package: 'latticeExtra'
The following object is masked from 'package:ggplot2':
layer
Loading required package: rlang
Attaching package: 'rlang'
The following objects are masked from 'package:purrr':
%@%, as_function, flatten, flatten_chr, flatten_dbl, flatten_int,
flatten_lgl, flatten_raw, invoke, list_along, modify, prepend,
splice
The following object is masked from 'package:xml2':
as_list
The following object is masked from 'package:R.utils':
env
The following objects are masked from 'package:R.oo':
abort, ll
Loading required package: rasterDT
Loading required package: data.table
Attaching package: 'data.table'
The following object is masked from 'package:rlang':
:=
The following objects are masked from 'package:terra':
copy, shift
The following objects are masked from 'package:dplyr':
between, first, last
The following object is masked from 'package:purrr':
transpose
The following object is masked from 'package:raster':
shift
trying URL 'https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_COL_2_sp.rds'
Content type 'text/html; charset=iso-8859-1' length 1159816 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
rsp2ebv package:ecochange R Documentation
_<08>R_<08>e_<08>m_<08>o_<08>t_<08>e _<08>S_<08>e_<08>n_<08>s_<08>i_<08>n_<08>g _<08>P_<08>r_<08>o_<08>d_<08>u_<08>c_<08>t _<08>t_<08>o _<08>E_<08>B_<08>V
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
This function processes regions of interest (polygon geometry or
'GADM' unit) to integrate dissimilar remote sensing products (RSP)
into Essential biodiversity variables.
_<08>U_<08>s_<08>a_<08>g_<08>e:
rsp2ebv(roi = NULL, ...,
lyrs = NULL, path,
sr, ofr = c(30, 30),
mc.cores = round(detectCores() *
0.6, 0))
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
roi: 'SpatialPolygonsDataFrame'; or 'character'; or 'NULL'. Region
of interest. This can be whether 1) a polygon geometry; or 2)
the name of a 'GADM' unit (see 'getGADM'); or 3) a 'NULL'
value. Default 'NULL' makes the function to print a list of
'GADM' units.
...: If 'roi' is a 'GADM' unit then additional arguments in
'getGADM' can be specified here.
lyrs: 'character'. Remote sensing products, If 'NULL' then a list
of products is printed, see 'listGP'. Default 'NULL'.
path: 'character'. Path name indicating where the variables are
stored. If it is missing then a folder named as ''ecochange''
located in a current temporary directory is used.
sr: 'character'. 'PROJ.4' description of the target coordinate
reference system. If missing then the target layers are
projected to metric system 'UTM'.
ofr: 'numeric'. 'c(xres,yres)'. Output file resolution (in target
georeferenced units). Default 'c(30,30)' m2.
mc.cores: 'numeric'. The number of cores. Default uses around 60
percent of the cores.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
This function implements ''gdalUtils'' so it assumes the user has
a working GDAL on their system. From the documentation: "If the
''gdalUtils_gdalPath'' option has been set (usually by
''gdal_setInstallation''), the GDAL found in that 'path' will be
used. If nothing is found, ''gdal_setInstallation'' will be
executed to attempt to find a working GDAL that has the right
drivers as specified with the ''of'' (output format) parameter",
see example below.
_<08>V_<08>a_<08>l_<08>u_<08>e:
'RasterStack' of essential biodiversity variables (UTM crs), or
character lists suggesting GADM units/Global Products that can be
used to download 'rsp' (see 'NULL' defaults in arguments ''roi''
and ''lyrs'').
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Wilson Lara Henao <wilarhen@temple.edu> [aut, cre], Victor
Gutierrez-Velez [aut], Ivan Gonzales [aut]
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Jetz, W., McGeoch, M. A., Guralnick, R., Ferrier, S., Beck, J.,
Costello, M. J., ... & Meyer, C. (2019). Essential biodiversity
variables for mapping and monitoring species populations. Nature
Ecology & Evolution, 3(4), 539-551.
O'Connor, B., Secades, C., Penner, J., Sonnenschein, R., Skidmore,
A., Burgess, N. D., & Hutton, J. M. (2015). Earth observation as a
tool for tracking progress towards the Aichi Biodiversity Targets.
Remote sensing in ecology and conservation, 1(1), 19-28.
Skidmore, A. K., & Pettorelli, N. (2015). Agree on biodiversity
metrics to track from space: Ecologists and space agencies must
forge a global monitoring strategy. Nature, 523(7561), 403-406.
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
## First, we'll check to make sure there is a valid GDAL
## installation (from 'gdalUtils):
gdalUtils::gdal_setInstallation()
valid_install <- !is.null(getOption("gdalUtils_gdalPath"))
## Warnings from GDAL/PROJ are suppressed.
## A Global Surface Water layer ('seasonality') covering the extent of a
## Colombian municipality Cartagena del Chairá is formated into an
## spatial \code{EBV}:
load(system.file('cchaira_roi.RData',package = 'ecochange'))
suppressWarnings(
rsp_cchaira <- getrsp(roi = cchaira_roi,
lyrs = 'seasonality', mc.cores = 2, path = tempdir())
)
file.exists(rsp_cchaira) ##TRUE
suppressWarnings(
season_cchaira <- rsp2ebv(roi = cchaira_roi,
lyrs = 'seasonality', path = tempdir())
)
suppressWarnings(
plotebv(season_cchaira)
)
sh: gdal_calc.py: command not found
sh: gdal_calc.py: command not found
Quitting from lines 80-83 (ecochange_vignette.Rmd)
Error: processing vignette 'ecochange_vignette.Rmd' failed with diagnostics:
unable to find an inherited method for function 'raster' for signature '"try-error"'
--- failed re-building ‘ecochange_vignette.Rmd’
SUMMARY: processing the following file failed:
‘ecochange_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.9
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘ecochange_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ecochange
Loading required package: raster
Loading required package: sp
Loading required package: rgeos
rgeos version: 0.5-5, (SVN revision 640)
GEOS runtime version: 3.8.1-CAPI-1.13.3
Linking to sp version: 1.4-2
Polygon checking: TRUE
Loading required package: ggplot2
Loading required package: sf
Linking to GEOS 3.8.1, GDAL 3.2.1, PROJ 7.2.1
Loading required package: gdalUtils
Attaching package: 'gdalUtils'
The following object is masked from 'package:sf':
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Package 'ecochange' version 1.9
Type 'citation("ecochange")' for citing this R package in publications.
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/rgdal/gdal
GDAL binary built with GEOS: TRUE
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was /Volumes/Builds/packages/high-sierra-x86_64/Rlib/4.0/rgdal/proj
Loading required package: parallel
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R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
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Attaching package: 'R.oo'
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Attaching package: 'R.utils'
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── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
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── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
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gdalinfo, gdalwarp, nearblack, ogr2ogr
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trying URL 'https://biogeo.ucdavis.edu/data/gadm3.6/Rsp/gadm36_COL_2_sp.rds'
Content type 'text/html; charset=iso-8859-1' length 1159816 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
rsp2ebv package:ecochange R Documentation
_<08>R_<08>e_<08>m_<08>o_<08>t_<08>e _<08>S_<08>e_<08>n_<08>s_<08>i_<08>n_<08>g _<08>P_<08>r_<08>o_<08>d_<08>u_<08>c_<08>t _<08>t_<08>o _<08>E_<08>B_<08>V
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
This function processes regions of interest (polygon geometry or
'GADM' unit) to integrate dissimilar remote sensing products (RSP)
into Essential biodiversity variables.
_<08>U_<08>s_<08>a_<08>g_<08>e:
rsp2ebv(roi = NULL, ...,
lyrs = NULL, path,
sr, ofr = c(30, 30),
mc.cores = round(detectCores() *
0.6, 0))
_<08>A_<08>r_<08>g_<08>u_<08>m_<08>e_<08>n_<08>t_<08>s:
roi: 'SpatialPolygonsDataFrame'; or 'character'; or 'NULL'. Region
of interest. This can be whether 1) a polygon geometry; or 2)
the name of a 'GADM' unit (see 'getGADM'); or 3) a 'NULL'
value. Default 'NULL' makes the function to print a list of
'GADM' units.
...: If 'roi' is a 'GADM' unit then additional arguments in
'getGADM' can be specified here.
lyrs: 'character'. Remote sensing products, If 'NULL' then a list
of products is printed, see 'listGP'. Default 'NULL'.
path: 'character'. Path name indicating where the variables are
stored. If it is missing then a folder named as ''ecochange''
located in a current temporary directory is used.
sr: 'character'. 'PROJ.4' description of the target coordinate
reference system. If missing then the target layers are
projected to metric system 'UTM'.
ofr: 'numeric'. 'c(xres,yres)'. Output file resolution (in target
georeferenced units). Default 'c(30,30)' m2.
mc.cores: 'numeric'. The number of cores. Default uses around 60
percent of the cores.
_<08>D_<08>e_<08>t_<08>a_<08>i_<08>l_<08>s:
This function implements ''gdalUtils'' so it assumes the user has
a working GDAL on their system. From the documentation: "If the
''gdalUtils_gdalPath'' option has been set (usually by
''gdal_setInstallation''), the GDAL found in that 'path' will be
used. If nothing is found, ''gdal_setInstallation'' will be
executed to attempt to find a working GDAL that has the right
drivers as specified with the ''of'' (output format) parameter",
see example below.
_<08>V_<08>a_<08>l_<08>u_<08>e:
'RasterStack' of essential biodiversity variables (UTM crs), or
character lists suggesting GADM units/Global Products that can be
used to download 'rsp' (see 'NULL' defaults in arguments ''roi''
and ''lyrs'').
_<08>A_<08>u_<08>t_<08>h_<08>o_<08>r(_<08>s):
Wilson Lara Henao <wilarhen@temple.edu> [aut, cre], Victor
Gutierrez-Velez [aut], Ivan Gonzales [aut]
_<08>R_<08>e_<08>f_<08>e_<08>r_<08>e_<08>n_<08>c_<08>e_<08>s:
Jetz, W., McGeoch, M. A., Guralnick, R., Ferrier, S., Beck, J.,
Costello, M. J., ... & Meyer, C. (2019). Essential biodiversity
variables for mapping and monitoring species populations. Nature
Ecology & Evolution, 3(4), 539-551.
O'Connor, B., Secades, C., Penner, J., Sonnenschein, R., Skidmore,
A., Burgess, N. D., & Hutton, J. M. (2015). Earth observation as a
tool for tracking progress towards the Aichi Biodiversity Targets.
Remote sensing in ecology and conservation, 1(1), 19-28.
Skidmore, A. K., & Pettorelli, N. (2015). Agree on biodiversity
metrics to track from space: Ecologists and space agencies must
forge a global monitoring strategy. Nature, 523(7561), 403-406.
_<08>E_<08>x_<08>a_<08>m_<08>p_<08>l_<08>e_<08>s:
## First, we'll check to make sure there is a valid GDAL
## installation (from 'gdalUtils):
gdalUtils::gdal_setInstallation()
valid_install <- !is.null(getOption("gdalUtils_gdalPath"))
## Warnings from GDAL/PROJ are suppressed.
## A Global Surface Water layer ('seasonality') covering the extent of a
## Colombian municipality Cartagena del Chairá is formated into an
## spatial \code{EBV}:
load(system.file('cchaira_roi.RData',package = 'ecochange'))
suppressWarnings(
rsp_cchaira <- getrsp(roi = cchaira_roi,
lyrs = 'seasonality', mc.cores = 2, path = tempdir())
)
file.exists(rsp_cchaira) ##TRUE
suppressWarnings(
season_cchaira <- rsp2ebv(roi = cchaira_roi,
lyrs = 'seasonality', path = tempdir())
)
suppressWarnings(
plotebv(season_cchaira)
)
sh: gdal_calc.py: command not found
sh: gdal_calc.py: command not found
Quitting from lines 80-83 (ecochange_vignette.Rmd)
Error: processing vignette 'ecochange_vignette.Rmd' failed with diagnostics:
unable to find an inherited method for function 'raster' for signature '"try-error"'
--- failed re-building ‘ecochange_vignette.Rmd’
SUMMARY: processing the following file failed:
‘ecochange_vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64