Error(s) in re-building vignettes:
  ...
--- re-building ‘climate.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘climate.Rmd’

--- re-building ‘lidar.Rmd’ using rmarkdown
starting worker pid=1765910 on localhost:11109 at 18:01:29.866
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment

                                                                                
Quitting from lidar.Rmd:86-109 [unnamed-chunk-9]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `serverSocket()`:
! creation of server socket failed: port 11109 cannot be opened
---
Backtrace:
    ▆
 1. └─rcontroll::stack(...)
 2.   └─parallel::makeCluster(cores, outfile = "")
 3.     └─parallel::makePSOCKcluster(names = spec, ...)
 4.       └─base::serverSocket(port = port)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'lidar.Rmd' failed with diagnostics:
creation of server socket failed: port 11109 cannot be opened
--- failed re-building ‘lidar.Rmd’

--- re-building ‘troll.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘troll.Rmd’

--- re-building ‘workflow.Rmd’ using rmarkdown
starting worker pid=1840533 on localhost:11046 at 18:02:17.075
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment

Reading in file: /tmp/RtmpkytMKe/rcontroll/test/test_input_global.txt
rows: 100 cols: 100 HEIGHT: 70
Number of dcells: 16
Lin number of dcells: 4

Covariance matrix N,P,LMA could not be decomposed. Using uncorrelated variation of trait values instead
Easy MPI rank: 0
On proc #0 seed: 1

Reading in file: /tmp/RtmpkytMKe/rcontroll/test/test_input_species.txt
Successfully initialised 45 species from file.
Successfully read in species file.

Reading in file: /tmp/RtmpkytMKe/rcontroll/test/test_input_daily.txt
Read in: 24 timesteps per day, covering 12 hours of the day.
Successfully read in daytime variation file

Reading in file: /tmp/RtmpkytMKe/rcontroll/test/test_input_climate.txt
Read in climate data for 12 iterations per year.
Successfully read the climate file

Intraspecific variation initialisation: 
Max and min allometry deviation, lognormal (height): 1 | 1
Max and min allometry deviation, lognormal (crown radius): 1 | 1
Max and min trait deviation, lognormal (N): 1 | 1
Max and min trait deviation, lognormal (P): 1 | 1
Max and min trait deviation, lognormal (LMA): 1 | 1
Max and min allometry deviation, normal (crown depth): 1 | 1
Max and min trait deviation, normal (wsg): 0 | 0
Max and min trait deviation, lognormal (dmax): 1 | 1

Built-in maximal temperature: 50
Calculated LookUp table for LAImax. Min LAImax is: 4.14551 | max LAImax is: 4.89746 avg LAImax is: 4.56366
SBORD: 2800
row start: 0 | row end: 100 | sites_abc: 10000
klight is: 0.63
CO2 concentration is: 400
Number of species: 45

Activated Module: BASICTREEFALL
Activated Module: OUTPUT_extended
Simulation starts with 0 trees.
Writing snapshot of forest to file.
10000 Seedrain: 50000
Trees_mature: 0 Nbseedsadded: 47316 effective: 47316 nbspeciesaffected: 45
0	Trees (1/ha): 9924.00 | 0.00 | 0.00 *** nbdead (%): 0.04 | -nan | -nan *** AGB (t/ha): 1.00 GPP (MgC/ha/yr) 11.55 NPP 6.26 litterfall (Mg/ha/yr) 1.71
1	Trees (1/ha): 9927.00 | 0.00 | 0.00 *** nbdead (%): 0.01 | -nan | -nan *** AGB (t/ha): 1.00 GPP (MgC/ha/yr) 11.67 NPP 6.27 litterfall (Mg/ha/yr) 1.72
2	Trees (1/ha): 9926.00 | 0.00 | 0.00 *** nbdead (%): 0.02 | -nan | -nan *** AGB (t/ha): 1.00 GPP (MgC/ha/yr) 12.43 NPP 6.71 litterfall (Mg/ha/yr) 1.74
3	Trees (1/ha): 9924.00 | 0.00 | 0.00 *** nbdead (%): 0.04 | -nan | -nan *** AGB (t/ha): 1.00 GPP (MgC/ha/yr) 13.26 NPP 7.15 litterfall (Mg/ha/yr) 1.78
4	Trees (1/ha): 9925.00 | 0.00 | 0.00 *** nbdead (%): 0.03 | -nan | -nan *** AGB (t/ha): 2.00 GPP (MgC/ha/yr) 13.74 NPP 7.34 litterfall (Mg/ha/yr) 1.84
5	Trees (1/ha): 9925.00 | 0.00 | 0.00 *** nbdead (%): 0.03 | -nan | -nan *** AGB (t/ha): 2.00 GPP (MgC/ha/yr) 14.60 NPP 7.86 litterfall (Mg/ha/yr) 1.90
6	Trees (1/ha): 9927.00 | 0.00 | 0.00 *** nbdead (%): 0.01 | -nan | -nan *** AGB (t/ha): 2.00 GPP (MgC/ha/yr) 15.76 NPP 8.51 litterfall (Mg/ha/yr) 1.97
7	Trees (1/ha): 9927.00 | 0.00 | 0.00 *** nbdead (%): 0.01 | -nan | -nan *** AGB (t/ha): 3.00 GPP (MgC/ha/yr) 17.54 NPP 9.49 litterfall (Mg/ha/yr) 2.06
8	Trees (1/ha): 9922.00 | 0.00 | 0.00 *** nbdead (%): 0.06 | -nan | -nan *** AGB (t/ha): 3.00 GPP (MgC/ha/yr) 19.30 NPP 10.39 litterfall (Mg/ha/yr) 2.16
9	Trees (1/ha): 9926.00 | 0.00 | 0.00 *** nbdead (%): 0.02 | -nan | -nan *** AGB (t/ha): 3.00 GPP (MgC/ha/yr) 20.73 NPP 11.04 litterfall (Mg/ha/yr) 2.28
10	Trees (1/ha): 9922.00 | 0.00 | 0.00 *** nbdead (%): 0.06 | -nan | -nan *** AGB (t/ha): 4.00 GPP (MgC/ha/yr) 21.34 NPP 11.29 litterfall (Mg/ha/yr) 2.41
11	Trees (1/ha): 9925.00 | 0.00 | 0.00 *** nbdead (%): 0.03 | -nan | -nan *** AGB (t/ha): 4.00 GPP (MgC/ha/yr) 19.76 NPP 10.19 litterfall (Mg/ha/yr) 2.56
Simulation ends with 9925 trees.
Writing snapshot of forest to file.


Number of processors : 1
Average computation time : 0.22 seconds.
End of simulation.
starting worker pid=1885896 on localhost:11046 at 18:02:43.790
starting worker pid=1885893 on localhost:11046 at 18:02:43.830
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment
starting worker pid=1973200 on localhost:11046 at 18:03:25.633
Loading required package: rcontroll

Attaching package: ‘rcontroll’

The following object is masked from ‘package:utils’:

    stack

loaded rcontroll and set parent environment
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘lidar.Rmd’

Error: Vignette re-building failed.
Execution halted