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filelock error when working with drake plan #1280
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This is an instance of #1232. If you remove |
Thanks for the response, but I had actually never ran I tried your suggestions of deleting This seems to be independent of |
I now ran |
|
I can't really reproduce this issue. But I have seemingly narrowed it down to possibly a permissions issue. The original directory is located within a mounted volume on my Mac (network drive at my institute), and not the internal storage on my Mac. For some reason when I copied the whole directory over to my local machine it worked...so could it be a permissions issue? Within the network drive, the project is in a folder that I have full read/write permissions so I can't imagine why I would be limited in any way. I really am at a loss for why this doesn't work when the directory is opened from its normal location. |
Session InfoR version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] ggtext_0.1.0 gghighlight_0.3.0 ggforce_0.3.1
[4] assertthat_0.2.1 progress_1.2.2 here_0.1
[7] fs_1.4.1 glue_1.4.1 rhdf5_2.32.0
[10] keras_2.3.0.0 reticulate_1.16 lubridate_1.7.9
[13] vroom_1.2.1 readxl_1.3.1 openxlsx_4.1.5
[16] yardstick_0.0.6 workflows_0.1.1 tune_0.1.0
[19] rsample_0.0.7 recipes_0.1.12 parsnip_0.1.1
[22] infer_0.5.2 dials_0.0.7 scales_1.1.1
[25] broom_0.5.6 tidymodels_0.1.0 forcats_0.5.0
[28] stringr_1.4.0 dplyr_1.0.0 purrr_0.3.4
[31] readr_1.3.1 tidyr_1.1.0 tibble_3.0.1
[34] ggplot2_3.3.2 tidyverse_1.3.0 drake_7.12.2
[37] dotenv_1.0.2 conflicted_1.0.4 testthat_2.3.2
[40] devtools_2.3.0 usethis_1.6.1
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 lme4_1.1-23
[3] htmlwidgets_1.5.1 grid_4.0.0
[5] pROC_1.16.2 munsell_0.5.0
[7] base64url_1.4 codetools_0.2-16
[9] statmod_1.4.34 DT_0.13
[11] future_1.17.0 miniUI_0.1.1.1
[13] withr_2.2.0 colorspace_1.4-1
[15] filelock_1.0.2 knitr_1.28
[17] prompt_1.0.0 rstudioapi_0.11
[19] stats4_4.0.0 tensorflow_2.2.0
[21] bayesplot_1.7.2 listenv_0.8.0
[23] rstan_2.19.3 polyclip_1.10-0
[25] farver_2.0.3 bit64_0.9-7
[27] DiceDesign_1.8-1 txtq_0.2.0
[29] rprojroot_1.3-2 vctrs_0.3.1
[31] generics_0.0.2 ipred_0.9-9
[33] xfun_0.15 R6_2.4.1
[35] markdown_1.1 rstanarm_2.19.3
[37] lhs_1.0.2 promises_1.1.1
[39] nnet_7.3-14 gtable_0.3.0
[41] globals_0.12.5 processx_3.4.2
[43] timeDate_3043.102 rlang_0.4.6
[45] clisymbols_1.2.0 zeallot_0.1.0
[47] splines_4.0.0 inline_0.3.15
[49] reshape2_1.4.4 modelr_0.1.8
[51] tidytext_0.2.4 threejs_0.3.3
[53] crosstalk_1.1.0.1 backports_1.1.8
[55] httpuv_1.5.4 rsconnect_0.8.16
[57] tokenizers_0.2.1 gridtext_0.1.1
[59] tools_4.0.0 lava_1.6.7
[61] ellipsis_0.3.1 sessioninfo_1.1.1
[63] ggridges_0.5.2 Rcpp_1.0.4.6
[65] plyr_1.8.6 base64enc_0.1-3
[67] ps_1.3.3 prettyunits_1.1.1
[69] rpart_4.1-15 zoo_1.8-8
[71] haven_2.3.1 furrr_0.1.0
[73] magrittr_1.5 colourpicker_1.0
[75] reprex_0.3.0 GPfit_1.0-8
[77] SnowballC_0.7.0 whisker_0.4
[79] packrat_0.5.0 storr_1.2.1
[81] matrixStats_0.56.0 pkgload_1.1.0
[83] tidyposterior_0.0.3 hms_0.5.3
[85] shinyjs_1.1 mime_0.9
[87] xtable_1.8-4 tidypredict_0.4.5
[89] shinystan_2.5.0 tfruns_1.4
[91] gridExtra_2.3 rstantools_2.1.0
[93] compiler_4.0.0 crayon_1.3.4
[95] minqa_1.2.4 StanHeaders_2.21.0-5
[97] htmltools_0.5.0 later_1.1.0.1
[99] RcppParallel_5.0.1 DBI_1.1.0
[101] tweenr_1.0.1 dbplyr_1.4.4
[103] MASS_7.3-51.6 boot_1.3-25
[105] Matrix_1.2-18 cli_2.0.2
[107] parallel_4.0.0 gower_0.2.1
[109] igraph_1.2.5 pkgconfig_2.0.3
[111] xml2_1.3.2 foreach_1.5.0
[113] dygraphs_1.1.1.6 prodlim_2019.11.13
[115] rvest_0.3.5 janeaustenr_0.1.5
[117] callr_3.4.3 digest_0.6.25
[119] cellranger_1.1.0 shiny_1.4.0.2
[121] gtools_3.8.2 nloptr_1.2.2.1
[123] lifecycle_0.2.0 nlme_3.1-148
[125] jsonlite_1.6.1 Rhdf5lib_1.10.0
[127] desc_1.2.0 fansi_0.4.1
[129] pillar_1.4.4 lattice_0.20-41
[131] loo_2.2.0 fastmap_1.0.1
[133] httr_1.4.1 pkgbuild_1.0.8
[135] survival_3.2-3 xts_0.12-0
[137] remotes_2.1.1 zip_2.0.4
[139] shinythemes_1.1.2 iterators_1.0.12
[141] bit_1.1-15.2 class_7.3-17
[143] stringi_1.4.6 blob_1.2.1
[145] memoise_1.1.0 |
Thanks. And next time you see the error, would you post a traceback too? |
## Load packages ----
source("_packages.R")
## Source R files ----
purrr::walk(fs::dir_ls("./R", glob = "*.R"), source)
vis_drake_graph(plan) 19: filelock::unlock(lock)
18: private$txtq_exclusive({
file_create(private$db_file)
if (!file.exists(private$head_file)) {
private$txtq_set_head(0)
}
if (!file.exists(private$total_file)) {
private$txtq_set_total(0)
}
})
17: private$txtq_establish(path)
16: .subset2(public_bind_env, "initialize")(...)
15: R6_txtq$new(path = path)
14: txtq::txtq(history_path)
13: history_queue(history_path)
12: recover_default_history(path)
11: methods::initRefFields(.Object, classDef, selfEnv, list(...))
10: initialize(value, ...)
9: initialize(value, ...)
8: methods::new(def, ...)
7: refclass_decorated_storr$new(storr = storr, driver = storr$driver,
default_namespace = storr$default_namespace, envir = storr$envir,
hash_algorithm = hash_algorithm, digest = digest, history = recover_default_history(path),
ht_encode_path = ht_new(), ht_decode_path = ht_new(), ht_encode_namespaced = ht_new(),
ht_decode_namespaced = ht_new(), ht_hash = ht_new(), ht_keys = ht_keys(digest),
path = path, path_return = file.path(path, "drake", "return"),
path_tmp = file.path(path, "drake", "tmp"))
6: decorate_storr(storr::storr_rds(path = path))
5: drake_fetch_rds(path = path)
4: this_cache_(path = path)
3: drake::drake_cache()
2: drake_config2(...)
1: vis_drake_graph(plan) |
Okay, that really helps. Does |
txtq::txtq(".drake/drake/history")
|
I will upload the history folder, one sec. |
I think this is what you wanted. This is a zip of |
Thanks for that. Odd, but I cannot reproduce the error with
|
Also worth checking |
library(filelock)
lock <- lock(".drake/drake/history/lock")
unlock(lock)
Regarding permission: fs::file_access(".drake/drake/history/lock", c("read", "write", "execute"))
|
I think we have narrowed down the issue as much as we can here. I think the next thing to do is ask Gabor about it on the By the way, thank you so much for helping us get to the bottom of this issue. I have heard other reports of this happening (which sometimes could be avoided by suppressing history) but it is super tough to reproduce on my end. |
No problem, I'll post the issue over on Not a problem; happy to help any way I can. Thanks a lot for your help. I am fairly new to |
You know what? After reading the discussions of file systems at r-lib/filelock#26, I think I need to revisit wlandau/txtq#18. |
NB the fix requires |
@pydupont confirmed the patch works, so I am closing. Please let me know if it persists for you. |
@wlandau I also confirm everything seems to be working perfectly after installing the dev versions of |
Hi,
Seemingly out of nowhere I keep getting the following error when I try to run any function that acts on my drake plan (e.g. visualization):
I had a working plan, then this error started showing up. I worked backwards to slowly try to figure out what the issue was by removing functions and targets in the plan. Even clearing the entire global environment, resetting R, and creating an empty plan doesn't work...
I honestly have no idea why this started happening. I have even tried deleting the
.drake
directory, resetting R, and trying again but it still happens. Any idea what this error means? How to fix it?The text was updated successfully, but these errors were encountered: