Suggestion: Option to not "closeAllConnections()"

[GPawi]

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:

clam/R/clam.R

Line 412 in 0851eab

closeAllConnections()

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

[Maarten14C]

Dear Gregor, Thank you for reporting this. I can't remember at the moment why I had put that closeAllConnections command in the code (it's also in my other packages rbacon and rplum). I don't use RStudio either so it doesn't have to do with that. I'll have a look at the code when I have time (hopefully soon) and then probably remove that closeAllConnections() command. Cheers, Maarten

On 13/04/2021 16:24, Gregor Pfalz wrote: *This message is from an external sender. Please take care when responding, clicking links or opening attachments.* Dear Maarten, I recently ran your package in a jupyter notebook with R kernel. My code was fairly simple with this dataset (PG1972.txt <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMaarten14C%2Fclam%2Ffiles%2F6304733%2FPG1972.txt&data=04%7C01%7Cmaarten.blaauw%40qub.ac.uk%7C9ae7c28838c64263ccdf08d8fe904e9f%7Ceaab77eab4a549e3a1e8d6dd23a1f286%7C0%7C0%7C637539243738850289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=urXjPgI7ZrUK8nF8j0BHqsTRvuX%2FlumH%2Fp8RHIjExDk%3D&reserved=0> - 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: https://github.com/Maarten14C/clam/blob/0851eaba7998288f960d38c1fbd1198d7abe7396/R/clam.R#L412 <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMaarten14C%2Fclam%2Fblob%2F0851eaba7998288f960d38c1fbd1198d7abe7396%2FR%2Fclam.R%23L412&data=04%7C01%7Cmaarten.blaauw%40qub.ac.uk%7C9ae7c28838c64263ccdf08d8fe904e9f%7Ceaab77eab4a549e3a1e8d6dd23a1f286%7C0%7C0%7C637539243738850289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2%2FRq4S8IeTNln%2BgxGi9%2BiZ9EbHgaU2TvKrZ%2BFK0BINo%3D&reserved=0> 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 <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMaarten14C%2Fclam%2Ffiles%2F6304773%2FScreenshot.2021-04-13.171414.pdf&data=04%7C01%7Cmaarten.blaauw%40qub.ac.uk%7C9ae7c28838c64263ccdf08d8fe904e9f%7Ceaab77eab4a549e3a1e8d6dd23a1f286%7C0%7C0%7C637539243738860284%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=IUfyS4fmnLoQon%2F%2FWXC3QXx5xZ253yJD1Afs32tfxO0%3D&reserved=0> 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 | — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FMaarten14C%2Fclam%2Fissues%2F1&data=04%7C01%7Cmaarten.blaauw%40qub.ac.uk%7C9ae7c28838c64263ccdf08d8fe904e9f%7Ceaab77eab4a549e3a1e8d6dd23a1f286%7C0%7C0%7C637539243738870276%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=MkbeqzGTKvdM99tcXjapn1kfDzc%2B7bfAnSG0vEG4QYw%3D&reserved=0>, or unsubscribe <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACZNBI3W5TUOZHRDNOYEBEDTIRO4NANCNFSM423SCIRQ&data=04%7C01%7Cmaarten.blaauw%40qub.ac.uk%7C9ae7c28838c64263ccdf08d8fe904e9f%7Ceaab77eab4a549e3a1e8d6dd23a1f286%7C0%7C0%7C637539243738870276%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=LdZlAePHxKjHJnRpfIwb5qEulMcOgLvEE%2Fj1Ezdz%2BfU%3D&reserved=0>.

-- | Dr Maarten Blaauw (Reader) | | Archaeology and Palaeoecology | School of Natural and Built Environment | Queen's University Belfast, UK | | www http://www.qub.ac.uk/chrono/blaauw | tel +44 (0)28 9097 3895

[Maarten14C]

Gregor,

I've updated the code - does it work as expected now?

Cheers,

Maarten

[GPawi]

Hi Maarten,

Thank you so much for the swift answer and quick fix!
Yes, now everything works as expected. I tested it with both jupyter notebook and RStudio.

Cheers,
Gregor