• using R Under development (unstable) (2025-09-17 r88852)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-4) 15.2.0     GNU Fortran (Debian 15.2.0-4) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘rcontroll/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘rcontroll’ version ‘0.1.2’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [1s/2s] OK
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘rcontroll’ can be installed ... OK See the install log for details.
• used C++ compiler: ‘g++-15 (Debian 15.2.0-4) 15.2.0’
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
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• checking index information ... OK
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• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
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• checking whether startup messages can be suppressed ... [6s/7s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
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• checking for unstated dependencies in examples ... OK
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• checking use of PKG_*FLAGS in Makefiles ... OK
• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
• checking pragmas in C/C++ headers and code ... OK
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• checking compiled code ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [8s/10s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [44s/181s] ERROR 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
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR