Last updated on 2020-06-15 08:53:24 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 4.82 | 55.26 | 60.08 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 4.19 | 42.20 | 46.39 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 77.41 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 72.34 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 1.0.0 | 19.00 | 70.00 | 89.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.0 | 4.86 | 53.25 | 58.11 | ERROR | |
| r-patched-solaris-x86 | 1.0.0 | 104.60 | ERROR | |||
| r-release-linux-x86_64 | 1.0.0 | 4.63 | 57.09 | 61.72 | ERROR | |
| r-release-osx-x86_64 | 1.0.0 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 1.0.0 | 22.00 | 65.00 | 87.00 | ERROR | |
| r-oldrel-osx-x86_64 | 1.0.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 1.0.0 | 15.00 | 97.00 | 112.00 | ERROR |
Version: 1.0.0
Check: whether the namespace can be loaded with stated dependencies
Result: WARN
Warning: S4 exports specified in 'NAMESPACE' but not defined in package 'photosynthesis'
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, r-devel-windows-ix86+x86_64
Version: 1.0.0
Check: examples
Result: ERROR
Running examples in 'photosynthesis-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: photosynthesis
> ### Title: Simulate C3 photosynthesis
> ### Aliases: photosynthesis photo
>
> ### ** Examples
>
> # Single parameter set with 'photo'
>
> bake_par <- make_bakepar()
> constants <- make_constants(use_tealeaves = FALSE)
> enviro_par <- make_enviropar(use_tealeaves = FALSE)
> leaf_par <- make_leafpar(use_tealeaves = FALSE)
> photo(leaf_par, enviro_par, bake_par, constants,
+ use_tealeaves = FALSE)
Solving for C_chl ... done
C_chl value convergence g_tc
1 24.52925 [Pa] -1.09648e-06 0 1.668765 [umol/Pa/m^2/s]
A g_mc25 g_sc g_uc
1 27.48581 [umol/m^2/s] 4 [umol/Pa/m^2/s] 4 [umol/Pa/m^2/s] 0.1 [umol/Pa/m^2/s]
gamma_star25 J_max25 K_C25 K_O25 k_mc k_sc k_uc
1 3.743 [Pa] 200 [umol/m^2/s] 27.238 [Pa] 16.582 [kPa] 1 [1] 1 [1] 1 [1]
leafsize phi_J R_d25 T_leaf theta_J V_cmax25
1 0.1 [m] 0.331 [1] 2 [umol/m^2/s] 298.15 [K] 0.825 [1] 150 [umol/m^2/s]
V_tpu25 g_mc gamma_star J_max K_C K_O R_d V_cmax V_tpu C_air
1 200 [umol/m^2/s] 4 3.743 200 27.238 16.582 2 150 200 41 [Pa]
O P PPFD RH wind
1 21.27565 [kPa] 101.3246 [kPa] 1500 [umol/m^2/s] 0.5 [1] 2 [m/s]
>
> # Multiple parameter sets with 'photosynthesis'
>
> leaf_par <- make_leafpar(
+ replace = list(
+ T_leaf = set_units(c(293.14, 298.15), "K")
+ ), use_tealeaves = FALSE
+ )
> photosynthesis(leaf_par, enviro_par, bake_par, constants,
+ use_tealeaves = FALSE)
Solving for photosynthetic rate from 2 parameter sets ...New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Error in UseMethod("units<-") :
no applicable method for 'units<-' applied to an object of class "NULL"
Calls: photosynthesis ... withVisible -> <Anonymous> -> eval -> eval -> units<-
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: 1.0.0
Check: package vignettes
Result: NOTE
Package vignette with placeholder title 'Vignette Title':
'photosynthesis-introduction.Rmd'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'photosynthesis-introduction.Rmd' using rmarkdown
Attaching package: 'dplyr'
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: units
udunits system database from /usr/share/xml/udunits
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd)
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building 'photosynthesis-introduction.Rmd'
SUMMARY: processing the following file failed:
'photosynthesis-introduction.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: 1.0.0
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘tidyr’
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: 1.0.0
Check: examples
Result: ERROR
Running examples in ‘photosynthesis-Ex.R’ failed
The error most likely occurred in:
> ### Name: photosynthesis
> ### Title: Simulate C3 photosynthesis
> ### Aliases: photosynthesis photo
>
> ### ** Examples
>
> # Single parameter set with 'photo'
>
> bake_par <- make_bakepar()
> constants <- make_constants(use_tealeaves = FALSE)
> enviro_par <- make_enviropar(use_tealeaves = FALSE)
> leaf_par <- make_leafpar(use_tealeaves = FALSE)
> photo(leaf_par, enviro_par, bake_par, constants,
+ use_tealeaves = FALSE)
Solving for C_chl ... done
C_chl value convergence g_tc
1 24.52925 [Pa] -1.09648e-06 0 1.668765 [umol/Pa/m^2/s]
A g_mc25 g_sc g_uc
1 27.48581 [umol/m^2/s] 4 [umol/Pa/m^2/s] 4 [umol/Pa/m^2/s] 0.1 [umol/Pa/m^2/s]
gamma_star25 J_max25 K_C25 K_O25 k_mc k_sc k_uc
1 3.743 [Pa] 200 [umol/m^2/s] 27.238 [Pa] 16.582 [kPa] 1 [1] 1 [1] 1 [1]
leafsize phi_J R_d25 T_leaf theta_J V_cmax25
1 0.1 [m] 0.331 [1] 2 [umol/m^2/s] 298.15 [K] 0.825 [1] 150 [umol/m^2/s]
V_tpu25 g_mc gamma_star J_max K_C K_O R_d V_cmax V_tpu C_air
1 200 [umol/m^2/s] 4 3.743 200 27.238 16.582 2 150 200 41 [Pa]
O P PPFD RH wind
1 21.27565 [kPa] 101.3246 [kPa] 1500 [umol/m^2/s] 0.5 [1] 2 [m/s]
>
> # Multiple parameter sets with 'photosynthesis'
>
> leaf_par <- make_leafpar(
+ replace = list(
+ T_leaf = set_units(c(293.14, 298.15), "K")
+ ), use_tealeaves = FALSE
+ )
> photosynthesis(leaf_par, enviro_par, bake_par, constants,
+ use_tealeaves = FALSE)
Solving for photosynthetic rate from 2 parameter sets ...New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Error in UseMethod("units<-") :
no applicable method for 'units<-' applied to an object of class "NULL"
Calls: photosynthesis ... withVisible -> <Anonymous> -> eval -> eval -> units<-
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘photosynthesis-introduction.Rmd’ using rmarkdown
Attaching package: 'dplyr'
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: units
udunits system database from /usr/share/udunits
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd)
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building ‘photosynthesis-introduction.Rmd’
SUMMARY: processing the following file failed:
‘photosynthesis-introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'photosynthesis-introduction.Rmd' using rmarkdown
Attaching package: 'dplyr'
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: units
udunits system database from D:/temp/Rtmpkx8jtZ/RLIBS_2361412227d4b/units/share/udunits
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd)
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building 'photosynthesis-introduction.Rmd'
SUMMARY: processing the following file failed:
'photosynthesis-introduction.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘photosynthesis-introduction.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.
Attaching package: 'dplyr'
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: units
udunits system database from /usr/local/share/udunits
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd)
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building ‘photosynthesis-introduction.Rmd’
SUMMARY: processing the following file failed:
‘photosynthesis-introduction.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'photosynthesis-introduction.Rmd' using rmarkdown
Attaching package: 'dplyr'
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: units
udunits system database from D:/temp/Rtmp8k7Gc1/RLIBS_b59460b4402f/units/share/udunits
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd)
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building 'photosynthesis-introduction.Rmd'
SUMMARY: processing the following file failed:
'photosynthesis-introduction.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-windows-ix86+x86_64
Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building 'photosynthesis-introduction.Rmd' using rmarkdown
Attaching package: 'dplyr'
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: units
udunits system database from D:/temp/RtmpUtTVMk/RLIBS_21964194260ed/units/share/udunits
Attaching package: 'purrr'
The following object is masked from 'package:magrittr':
set_names
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
New names:
* g_mc25 -> g_mc25...6
* g_sc -> g_sc...7
* g_uc -> g_uc...8
* gamma_star25 -> gamma_star25...9
* J_max25 -> J_max25...10
* ...
Quitting from lines 100-129 (photosynthesis-introduction.Rmd)
Error: processing vignette 'photosynthesis-introduction.Rmd' failed with diagnostics:
no applicable method for 'units<-' applied to an object of class "NULL"
--- failed re-building 'photosynthesis-introduction.Rmd'
SUMMARY: processing the following file failed:
'photosynthesis-introduction.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64