A package for 'classical' age-depth modelling of cores from deposits.
Dear Maarten,
I recently ran your package in a jupyter notebook with R kernel. My code was fairly simple with this dataset (PG1972.txt - had to convert the .csv to .txt to upload it to this issue):
setwd('D:/HEIBRiDS/Data/clam_runs')
library('clam')
clam(core='PG1972', coredir= 'D:/HEIBRiDS/Data/clam_runs', type = 1, its = 10000)
But it produced an error:
The run's files will be put in this folder: D:\HEIBRiDS\Data\clam_runs/PG1972
Calibrating dates... extrapolating beyond dated levels, dangerous!
Interpolating, sampling.....
Error in isOpen(con): invalid connection
I think this has to do with the following line:
Line 412 in 0851eab
I tested my theory by using the trace('clam', edit = TRUE) command and comment line 412 out. Now, I was able to receive an output: Screenshot 2021-04-13 171414.pdf
Would it be possible for you to implement an option to make the statement "closeAllConnections()" optional? It would be helpful for users, who don't use RStudio, as this seems to interfere with the connection from the kernel and the clam package.
All the best,
Gregor
P.S. here's my sessionInfo() for reproducibility:
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clam_2.3.7
loaded via a namespace (and not attached):
[1] fansi_0.4.2 digest_0.6.27 utf8_1.2.1 crayon_1.4.1
[5] IRdisplay_0.7.0 repr_1.1.0 lifecycle_1.0.0 jsonlite_1.7.2
[9] evaluate_0.14 pillar_1.5.1 rlang_0.4.10 uuid_0.1-4
[13] IntCal_0.1.3 ellipsis_0.3.1 IRkernel_1.1.1 tools_4.0.4
[17] compiler_4.0.4 base64enc_0.1-3 pbdZMQ_0.3-3.1 htmltools_0.5.0
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