Last updated on 2024-04-18 11:50:55 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.2 | 15.23 | 393.37 | 408.60 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2.2 | 10.64 | 280.29 | 290.93 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2.2 | 489.84 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.2 | 608.00 | OK | |||
| r-prerel-macos-arm64 | 0.2.2 | 171.00 | ERROR | |||
| r-prerel-macos-x86_64 | 0.2.2 | 472.00 | OK | |||
| r-prerel-windows-x86_64 | 0.2.2 | 12.00 | 226.00 | 238.00 | OK | |
| r-patched-linux-x86_64 | 0.2.2 | 12.92 | 363.03 | 375.95 | OK | |
| r-release-linux-x86_64 | 0.2.2 | 12.32 | 368.41 | 380.73 | OK | |
| r-release-macos-arm64 | 0.2.2 | 171.00 | ERROR | |||
| r-release-macos-x86_64 | 0.2.2 | 450.00 | OK | |||
| r-release-windows-x86_64 | 0.2.2 | 15.00 | 296.00 | 311.00 | OK | |
| r-oldrel-macos-arm64 | 0.2.2 | 168.00 | ERROR | |||
| r-oldrel-windows-x86_64 | 0.2.2 | 16.00 | 301.00 | 317.00 | OK |
Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘vignette1.Rmd’ using rmarkdown
BTsubset_meta package:BioTIMEr R Documentation
_<08>B_<08>i_<08>o_<08>T_<08>I_<08>M_<08>E _<08>s_<08>u_<08>b_<08>s_<08>e_<08>t _<08>m_<08>e_<08>t_<08>a_<08>d_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
A subset of the metadata from BioTIME
_<08>U_<08>s_<08>a_<08>g_<08>e:
BTsubset_meta
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
## `BTsubset_meta` A data frame with 12 rows and 25 columns:
STUDY_ID BioTIME study unique identifier
REALM Realm of study location, i.e. Marine
CLIMATE Climate of study location, i.e. Temperate
HABITAT Habitat of study location, i.e. Rivers
PROTECTED_AREA binary variable indicating if the study is within a
protected area
BIOME_MAP Biome of study location (taken from the WWF biomes, i.e.
Temperate broadleaf and mixed forests
TAXA High level taxonomic identity of study species, i.e. Fish
ORGANISMS More detailed information on taxonomy, i.e. woody plants
TITLE Title of study as identified in original source
AB_BIO A, B or AB to designate abundance only, biomass only or
both
DATA_POINTS Number of unique data points in study, e.g. 10 data
points spanning 15 years = 10
START_YEAR first year of study
END_YEAR last year of study
CENT_LAT Central latitude taken from the convex hull around all
study coordinates
CENT_LONG Central longitude taken from the convex hull around all
study coordinates
NUMBER_OF_SPECIES Number of distinct species in study
NUMBER_OF_SAMPLES Number of distinct samples in study
NUMBER_LAT_LONG Number of distinct geographic coordinates in study
TOTAL Total number of records in study
GRAIN_SQ_KM Grain size in km2, i.e. size of forest plots
AREA_SQ_KM total area of study in km2
DATE_STUDY_ADDED Date that the study was added to the database
ABUNDANCE_TYPE Type of abundance, i.e. count
BIOMASS_TYPE Type of biomass, i.e. weight
SAMPLE_DESC concatenation of descriptors comprising the unique
sampling event
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
<https://biotime.st-andrews.ac.uk/download.php>
BTsubset_data package:BioTIMEr R Documentation
_<08>B_<08>i_<08>o_<08>T_<08>I_<08>M_<08>E _<08>s_<08>u_<08>b_<08>s_<08>e_<08>t
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
A subset of data from BioTIME temporal surveys.
_<08>U_<08>s_<08>a_<08>g_<08>e:
BTsubset_data
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
## `BTsubset_data` A data frame with 81,084 rows and 17 columns:
ID_ALL_RAW_DATA Unique BioTIME identifier for record
ABUNDANCE Double representing the abundance for the record (see
metadata for details of ABUNDANCE_TYPE
BIOMASS Double representing the biomass for the record (see
metadata for details of BIOMASS_TYPE
ID_SPECIES Unique identifier linking to the species table
SAMPLE_DESC Concatenation of variables comprising unique sampling
event
PLOT Name or identifier of plot field, only used for fixed plots
such as forest quadrats
LATITUDE Latitude of record
LONGITUDE Longitude of record
DEPTH Depth or elevation of record if available
DAY Numerical day of record
MONTH Numerical value of month for record, i.e. January=1
YEAR Year of record
STUDY_ID BioTIME study unique identifier
newID Validated species identifier key
valid_name Highest taxonomic resolution of individual, preferred
is genus and species
resolution Level of resolution, i.e. 'species' represented by
genus and species
taxon Higher level taxonomic grouping, i.e. Fish
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
<https://biotime.st-andrews.ac.uk/download.php>
Vignettes with name or keyword or title matching 'BioTIMEr' using fuzzy
matching:
BioTIMEr::vignette1 Introduction to BioTIMEr
Type 'vignette(PKG::FOO)' to inspect entries 'PKG::FOO'.
Help files with alias or concept or title matching 'BioTIMEr' using
fuzzy matching:
BioTIMEr::BTsubset_data
BioTIME subset
BioTIMEr::BTsubset_meta
BioTIME subset metadata
BioTIMEr::BioTIMEr-package
BioTIMEr: Tools to Use and Explore the
'BioTIME' Database
Aliases: BioTIMEr, BioTIMEr-package
BioTIMEr::getLinearRegressions
Get Linear Regressions BioTIME
BioTIMEr::gridding gridding BioTIME data
BioTIMEr::plotSlopes Plot slopes BioTIME
Aliases: themeBioTIME
BioTIMEr::rarefysamples
Rarefy BioTIME data Applies sample-based
rarefaction to standardise the number of
samples per year within a cell-level time
series.
BioTIMEr::resampling Rarefy BioTIME data to an equal number of
samples per year
BioTIMEr::scale_color_biotime
Scale construction for ggplot use
Aliases: scale_color_biotime, scale_colour_biotime,
scale_fill_biotime
Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.
Quitting from lines 471-490 [trends8] (vignette1.Rmd)
Error: processing vignette 'vignette1.Rmd' failed with diagnostics:
Faceting variables must have at least one value.
--- failed re-building ‘vignette1.Rmd’
SUMMARY: processing the following file failed:
‘vignette1.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-prerel-macos-arm64
Version: 0.2.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘vignette1.Rmd’ using rmarkdown
BTsubset_meta package:BioTIMEr R Documentation
_<08>B_<08>i_<08>o_<08>T_<08>I_<08>M_<08>E _<08>s_<08>u_<08>b_<08>s_<08>e_<08>t _<08>m_<08>e_<08>t_<08>a_<08>d_<08>a_<08>t_<08>a
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
A subset of the metadata from BioTIME
_<08>U_<08>s_<08>a_<08>g_<08>e:
BTsubset_meta
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
## `BTsubset_meta` A data frame with 12 rows and 25 columns:
STUDY_ID BioTIME study unique identifier
REALM Realm of study location, i.e. Marine
CLIMATE Climate of study location, i.e. Temperate
HABITAT Habitat of study location, i.e. Rivers
PROTECTED_AREA binary variable indicating if the study is within a
protected area
BIOME_MAP Biome of study location (taken from the WWF biomes, i.e.
Temperate broadleaf and mixed forests
TAXA High level taxonomic identity of study species, i.e. Fish
ORGANISMS More detailed information on taxonomy, i.e. woody plants
TITLE Title of study as identified in original source
AB_BIO A, B or AB to designate abundance only, biomass only or
both
DATA_POINTS Number of unique data points in study, e.g. 10 data
points spanning 15 years = 10
START_YEAR first year of study
END_YEAR last year of study
CENT_LAT Central latitude taken from the convex hull around all
study coordinates
CENT_LONG Central longitude taken from the convex hull around all
study coordinates
NUMBER_OF_SPECIES Number of distinct species in study
NUMBER_OF_SAMPLES Number of distinct samples in study
NUMBER_LAT_LONG Number of distinct geographic coordinates in study
TOTAL Total number of records in study
GRAIN_SQ_KM Grain size in km2, i.e. size of forest plots
AREA_SQ_KM total area of study in km2
DATE_STUDY_ADDED Date that the study was added to the database
ABUNDANCE_TYPE Type of abundance, i.e. count
BIOMASS_TYPE Type of biomass, i.e. weight
SAMPLE_DESC concatenation of descriptors comprising the unique
sampling event
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
<https://biotime.st-andrews.ac.uk/download.php>
BTsubset_data package:BioTIMEr R Documentation
_<08>B_<08>i_<08>o_<08>T_<08>I_<08>M_<08>E _<08>s_<08>u_<08>b_<08>s_<08>e_<08>t
_<08>D_<08>e_<08>s_<08>c_<08>r_<08>i_<08>p_<08>t_<08>i_<08>o_<08>n:
A subset of data from BioTIME temporal surveys.
_<08>U_<08>s_<08>a_<08>g_<08>e:
BTsubset_data
_<08>F_<08>o_<08>r_<08>m_<08>a_<08>t:
## `BTsubset_data` A data frame with 81,084 rows and 17 columns:
ID_ALL_RAW_DATA Unique BioTIME identifier for record
ABUNDANCE Double representing the abundance for the record (see
metadata for details of ABUNDANCE_TYPE
BIOMASS Double representing the biomass for the record (see
metadata for details of BIOMASS_TYPE
ID_SPECIES Unique identifier linking to the species table
SAMPLE_DESC Concatenation of variables comprising unique sampling
event
PLOT Name or identifier of plot field, only used for fixed plots
such as forest quadrats
LATITUDE Latitude of record
LONGITUDE Longitude of record
DEPTH Depth or elevation of record if available
DAY Numerical day of record
MONTH Numerical value of month for record, i.e. January=1
YEAR Year of record
STUDY_ID BioTIME study unique identifier
newID Validated species identifier key
valid_name Highest taxonomic resolution of individual, preferred
is genus and species
resolution Level of resolution, i.e. 'species' represented by
genus and species
taxon Higher level taxonomic grouping, i.e. Fish
_<08>S_<08>o_<08>u_<08>r_<08>c_<08>e:
<https://biotime.st-andrews.ac.uk/download.php>
Vignettes with name or keyword or title matching 'BioTIMEr' using fuzzy
matching:
BioTIMEr::vignette1 Introduction to BioTIMEr
Type 'vignette("FOO", package="PKG")' to inspect entries 'PKG::FOO'.
Help files with alias or concept or title matching 'BioTIMEr' using
fuzzy matching:
BioTIMEr::BTsubset_data
BioTIME subset
BioTIMEr::BTsubset_meta
BioTIME subset metadata
BioTIMEr::BioTIMEr BioTIMEr: Tools to Use and Explore the
'BioTIME' Database
Aliases: BioTIMEr, BioTIMEr-package
BioTIMEr::getLinearRegressions
Get Linear Regressions BioTIME
BioTIMEr::gridding gridding BioTIME data
BioTIMEr::plotSlopes Plot slopes BioTIME
Aliases: themeBioTIME
BioTIMEr::rarefysamples
Rarefy BioTIME data Applies sample-based
rarefaction to standardise the number of
samples per year within a cell-level time
series.
BioTIMEr::resampling Rarefy BioTIME data to an equal number of
samples per year
BioTIMEr::scale_color_biotime
Scale construction for ggplot use
Aliases: scale_color_biotime, scale_colour_biotime,
scale_fill_biotime
Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.
Quitting from lines 471-490 [trends8] (vignette1.Rmd)
Error: processing vignette 'vignette1.Rmd' failed with diagnostics:
Faceting variables must have at least one value.
--- failed re-building ‘vignette1.Rmd’
SUMMARY: processing the following file failed:
‘vignette1.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-release-macos-arm64, r-oldrel-macos-arm64