Last updated on 2019-12-05 10:48:37 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.1 | 4.02 | 33.40 | 37.42 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.1 | 3.56 | 26.76 | 30.32 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.1 | 44.03 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.1 | 46.65 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.1 | 9.00 | 67.00 | 76.00 | ERROR | |
| r-devel-windows-ix86+x86_64-gcc8 | 1.0.1 | 9.00 | 47.00 | 56.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.1 | 3.41 | 31.18 | 34.59 | ERROR | |
| r-patched-solaris-x86 | 1.0.1 | 59.10 | ERROR | |||
| r-release-linux-x86_64 | 1.0.1 | 3.43 | 32.42 | 35.85 | ERROR | |
| r-release-windows-ix86+x86_64 | 1.0.1 | 7.00 | 48.00 | 55.00 | ERROR | |
| r-release-osx-x86_64 | 1.0.1 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.1 | 6.00 | 46.00 | 52.00 | ERROR | |
| r-oldrel-osx-x86_64 | 1.0.1 | OK |
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in 'forestr-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calc_tls_mean_leaf_ht
> ### Title: Process single PCL transects.
> ### Aliases: calc_tls_mean_leaf_ht
> ### Keywords: processing tls
>
> ### ** Examples
>
>
> # with designated file
> ## Not run: process_pcl("pcl_data.csv", marker.spacing = 10, user_height = 1.05, max.vai = 8)
>
>
> # with data frame
> process_pcl(osbs, marker.spacing = 10, user_height = 1.05, max.vai = 8)
Transect Length
[1] 40
Table of sky hits
FALSE TRUE
3048 7458
RAW LiDAR metrics -- WARNING
Mean Return Height (m) of raw data
[1] 10.76431
Standard Deviation of raw Canopy Height returns-- meanStd in old code
[1] 3.569992
Max Measured Canopy Height (m)
[1] 14.827
Scan Density
[1] 262.65
OPENNESS AND COVER METRICS
Sky Fraction (%)
[1] 71.02181
Cover Fraction (%)
[1] 28.97819
Rumple
[1] 2.125
Mean Gap Fraction ---as error check should be same as porosity
[1] 0.928125
now we replace the 0's with 1's so when we take the ln they = 0
Clumping Index
[1] 0.9823258
Transect Length (m)
[1] 40
HEIGHT METRICS
Mean Leaf Height (H) - plot mean of column mean leaf height
[1] 4.205116
Height2 (H[2]) - standard deviation of column mean leaf height
[1] 5.614907
Mean Leaf Height variance (H[var]) - variance of column mean leaf height
[1] 31.52718
Root Mean Square Mean Leaf Height (H[rms]) - the root mean square or quadratic mean of column mean leaf height for the transect
[1] 6.958592
Max canopy height (m)
[1] 14.827
Mean Outer Canopy Height (m) or MOCH
[1] 4.4666
AREA AND DENSITY METRICS
Mean VAI - mean VAI for entire transect
[1] 1.506926
Mean Height of VAI[max] - modeEl
[1] 3.975
Mode 2- The standard deviation of VAImax or MaxEl
[1] 5.35646
Maximum VAI for entire transect -- max el!
[1] 5.75966
Mean Peak VAI for entire transect
[1] 0.9317552
CANOPY AND OPENNESS METRICS (cont.)
Deep Gaps
[1] 24
Deep Gap Fraction (0-1)
[1] 0.6
ARRANGEMENT METRICS
Canopy porosity
[1] 0.928125
Square of leaf height variance (stdStd from old script)
[1] 0.4566521
Mean Standard deviation of leaf heights -- meanStd
[1] 0.2439959
Canopy Rugosity
[1] 0.6301731
Surface Rugosity--TopRugosity
[1] 5.861305
Effective Number of Layers:
[1] 11.02083
[1] "_output"
[1] "./output/"
No. of NA values in hit matrix
[1] 594
Error in stats::approxfun(x_in, lab_in[, 1]) :
need at least two non-NA values to interpolate
Calls: process_pcl ... seq_gradient_pal -> gradient_n_pal -> colour_ramp -> <Anonymous>
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'pcl-vignette.Rmd' using rmarkdown
Quitting from lines 43-49 (pcl-vignette.Rmd)
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building 'pcl-vignette.Rmd'
SUMMARY: processing the following file failed:
'pcl-vignette.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.1
Check: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
'output'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.1
Check: examples
Result: ERROR
Running examples in ‘forestr-Ex.R’ failed
The error most likely occurred in:
> ### Name: calc_tls_mean_leaf_ht
> ### Title: Process single PCL transects.
> ### Aliases: calc_tls_mean_leaf_ht
> ### Keywords: processing tls
>
> ### ** Examples
>
>
> # with designated file
> ## Not run: process_pcl("pcl_data.csv", marker.spacing = 10, user_height = 1.05, max.vai = 8)
>
>
> # with data frame
> process_pcl(osbs, marker.spacing = 10, user_height = 1.05, max.vai = 8)
Transect Length
[1] 40
Table of sky hits
FALSE TRUE
3048 7458
RAW LiDAR metrics -- WARNING
Mean Return Height (m) of raw data
[1] 10.76431
Standard Deviation of raw Canopy Height returns-- meanStd in old code
[1] 3.569992
Max Measured Canopy Height (m)
[1] 14.827
Scan Density
[1] 262.65
OPENNESS AND COVER METRICS
Sky Fraction (%)
[1] 71.02181
Cover Fraction (%)
[1] 28.97819
Rumple
[1] 2.125
Mean Gap Fraction ---as error check should be same as porosity
[1] 0.928125
now we replace the 0's with 1's so when we take the ln they = 0
Clumping Index
[1] 0.9823258
Transect Length (m)
[1] 40
HEIGHT METRICS
Mean Leaf Height (H) - plot mean of column mean leaf height
[1] 4.205116
Height2 (H[2]) - standard deviation of column mean leaf height
[1] 5.614907
Mean Leaf Height variance (H[var]) - variance of column mean leaf height
[1] 31.52718
Root Mean Square Mean Leaf Height (H[rms]) - the root mean square or quadratic mean of column mean leaf height for the transect
[1] 6.958592
Max canopy height (m)
[1] 14.827
Mean Outer Canopy Height (m) or MOCH
[1] 4.4666
AREA AND DENSITY METRICS
Mean VAI - mean VAI for entire transect
[1] 1.506926
Mean Height of VAI[max] - modeEl
[1] 3.975
Mode 2- The standard deviation of VAImax or MaxEl
[1] 5.35646
Maximum VAI for entire transect -- max el!
[1] 5.75966
Mean Peak VAI for entire transect
[1] 0.9317552
CANOPY AND OPENNESS METRICS (cont.)
Deep Gaps
[1] 24
Deep Gap Fraction (0-1)
[1] 0.6
ARRANGEMENT METRICS
Canopy porosity
[1] 0.928125
Square of leaf height variance (stdStd from old script)
[1] 0.4566521
Mean Standard deviation of leaf heights -- meanStd
[1] 0.2439959
Canopy Rugosity
[1] 0.6301731
Surface Rugosity--TopRugosity
[1] 5.861305
Effective Number of Layers:
[1] 11.02083
[1] "_output"
[1] "./output/"
No. of NA values in hit matrix
[1] 594
Error in stats::approxfun(x_in, lab_in[, 1]) :
need at least two non-NA values to interpolate
Calls: process_pcl ... seq_gradient_pal -> gradient_n_pal -> colour_ramp -> <Anonymous>
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘pcl-vignette.Rmd’ using rmarkdown
Quitting from lines 43-49 (pcl-vignette.Rmd)
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘pcl-vignette.Rmd’
SUMMARY: processing the following file failed:
‘pcl-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64
Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘pcl-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-49 (pcl-vignette.Rmd)
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘pcl-vignette.Rmd’
SUMMARY: processing the following file failed:
‘pcl-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
Error in re-building vignettes:
...
Quitting from lines 43-49 (pcl-vignette.Rmd)
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64