v0.5.0.9000 -> v0.6.1: `read_opus()` fails

Question

v0.5.0.9000 -> v0.6.1: `read_opus()` fails

Closed this issue a year ago · 6 comments

I do not write issues often, so if I omitted something or the format is bad, sorry about that.

I usually pipe and map the opus_read function like this. I had to do an update today and reinstall the package. Apparently there were some changes that now lead to this error.

opus_lst <- list.dirs("C:/Users/iostovary/2023_Phenology_and_everything", full.names = TRUE) %>%

map(~read_opus(dsn = .x, parallel = TRUE, data_only = FALSE)) %>%
bind_rows() %>%
select(-matches("add_sample_id"))
Error in map():
ℹ In index: 1.
Caused by error in UseMethod():
! nicht anwendbare Methode für 'calc_parameter_chunk_size' auf Objekt der Klasse "parameter" angewendet
Backtrace:

... %>% select(-matches("add_sample_id"))
purrr::map(., ~read_opus(dsn = .x, parallel = TRUE, data_only = FALSE))
purrr:::map_("list", .x, .f, ..., .progress = .progress)
.f(.x[[i]], ...)
opusreader2::read_opus(dsn = .x, parallel = TRUE, data_only = FALSE)
...
future:::value.list(fs)
future:::resolve.list(...)
future (local) signalConditionsASAP(obj, resignal = FALSE, pos = ii)
future:::signalConditions(...)
base::stop(condition)

I also tried reading a single folder and a single file, both failed with the same error. I did it with the last three R versions (4.3.2, 4.3.1., 4.2.3) and RStudio 2023.09.1 Build 494

I reinstalled the tag opusreader2_v0.5.0.9000 and it works again. Just wanted to let you know.

Answer 1 · 2023-12-23T17:50:52.000Z

a little tip just for formatting code here, you can use this

# uncomment below
# ```r
# your R code
# ```

sessionInfo()
# or 
sessioninfo::session_info()

are really helpful for diangnostics.

For reproducible examples, I reprex is useful. Because reverse engineering is quite tricky, we really need OPUS files posted for full reproducibility.

Answer 2 · 2023-12-23T18:20:22.000Z

can confirm your issue, we have test running on files. I think I have messed up something. We had devtools::check() on GitHub actions before, but I updated the CI and apparently forgot to add.

Here is my local output on the test files to confirm.

> library(opusreader2)
> devtools::test()
ℹ Testing opusreader2
✔ | F W  S  OK | Context
✔ |          6 | create_dataset                                                                                
✔ |          4 | parse_header                                                                                  
✖ | 1        0 | read_opus                                                                                     
───────────────────────────────────────────────────────────────────────────────────────────────────────────────
Error (test-read_opus.R:2:3): all test files are parsed without warning
Error in `UseMethod("calc_parameter_chunk_size")`: no applicable method for 'calc_parameter_chunk_size' applied to an object of class "parameter"
Backtrace:
     ▆
  1. ├─testthat::expect_no_warning(read_opus(dsn = "../../inst/extdata/test_data")) at test-read_opus.R:2:3
  2. │ └─testthat:::expect_no_(...)
  3. │   └─testthat:::quasi_capture(enquo(object), NULL, capture)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─rlang::try_fetch(...)
  6. │     │   └─base::withCallingHandlers(...)
  7. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  8. └─opusreader2::read_opus(dsn = "../../inst/extdata/test_data")
  9.   └─opusreader2:::opus_lapply(dsn, data_only) at opusreader2/R/read_opus.R:152:5
 10.     └─base::lapply(...) at opusreader2/R/read_opus.R:237:3
 11.       └─opusreader2 (local) FUN(X[[i]], ...)
 12.         └─opusreader2::read_opus_single(x, data_only) at opusreader2/R/read_opus.R:240:7
 13.           └─opusreader2:::parse_opus(raw, data_only) at opusreader2/R/read_opus.R:213:3
 14.             └─base::lapply(dataset_list, calc_parameter_chunk_size) at opusreader2/R/parse_opus.R:148:5
 15.               └─opusreader2 (local) FUN(X[[i]], ...)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────

══ Results ════════════════════════════════════════════════════════════════════════════════════════════════════
── Failed tests ───────────────────────────────────────────────────────────────────────────────────────────────
Error (test-read_opus.R:2:3): all test files are parsed without warning
Error in `UseMethod("calc_parameter_chunk_size")`: no applicable method for 'calc_parameter_chunk_size' applied to an object of class "parameter"
Backtrace:
     ▆
  1. ├─testthat::expect_no_warning(read_opus(dsn = "../../inst/extdata/test_data")) at test-read_opus.R:2:3
  2. │ └─testthat:::expect_no_(...)
  3. │   └─testthat:::quasi_capture(enquo(object), NULL, capture)
  4. │     ├─testthat (local) .capture(...)
  5. │     │ └─rlang::try_fetch(...)
  6. │     │   └─base::withCallingHandlers(...)
  7. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  8. └─opusreader2::read_opus(dsn = "../../inst/extdata/test_data")
  9.   └─opusreader2:::opus_lapply(dsn, data_only) at opusreader2/R/read_opus.R:152:5
 10.     └─base::lapply(...) at opusreader2/R/read_opus.R:237:3
 11.       └─opusreader2 (local) FUN(X[[i]], ...)
 12.         └─opusreader2::read_opus_single(x, data_only) at opusreader2/R/read_opus.R:240:7
 13.           └─opusreader2:::parse_opus(raw, data_only) at opusreader2/R/read_opus.R:213:3
 14.             └─base::lapply(dataset_list, calc_parameter_chunk_size) at opusreader2/R/parse_opus.R:148:5
 15.               └─opusreader2 (local) FUN(X[[i]], ...)

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 10 ]
> sessioninfo::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.2 (2023-10-31)
 os       macOS Sonoma 14.2.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Zurich
 date     2023-12-23
 rstudio  2023.09.1+494 Desert Sunflower (desktop)
 pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────
 ! package     * version date (UTC) lib source
   brio          1.1.4   2023-12-10 [1] CRAN (R 4.3.1)
   cachem        1.0.8   2023-05-01 [1] CRAN (R 4.3.0)
   callr         3.7.3   2022-11-02 [1] CRAN (R 4.3.0)
   cli           3.6.2   2023-12-11 [1] CRAN (R 4.3.1)
   curl          5.2.0   2023-12-08 [1] CRAN (R 4.3.1)
   desc          1.4.3   2023-12-10 [1] CRAN (R 4.3.1)
   devtools      2.4.5   2022-10-11 [1] CRAN (R 4.3.0)
   digest        0.6.33  2023-07-07 [1] CRAN (R 4.3.0)
   ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.3.0)
   evaluate      0.23    2023-11-01 [1] CRAN (R 4.3.1)
   fansi         1.0.6   2023-12-08 [1] CRAN (R 4.3.1)
   fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
   fs            1.6.3   2023-07-20 [1] CRAN (R 4.3.0)
   glue          1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
   htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.3.1)
   htmlwidgets   1.6.4   2023-12-06 [1] CRAN (R 4.3.1)
   httpuv        1.6.13  2023-12-06 [1] CRAN (R 4.3.1)
   knitr         1.45    2023-10-30 [1] CRAN (R 4.3.1)
   later         1.3.2   2023-12-06 [1] CRAN (R 4.3.1)
   lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.3.1)
   magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
   memoise       2.0.1   2021-11-26 [1] CRAN (R 4.3.0)
   mime          0.12    2021-09-28 [1] CRAN (R 4.3.0)
   miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
 P opusreader2 * 0.6.1   2023-12-23 [?] Github (spectral-cockpit/opusreader2@87a6d41)
   pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
   pkgbuild      1.4.3   2023-12-10 [1] CRAN (R 4.3.1)
   pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
   pkgload       1.3.3   2023-09-22 [1] CRAN (R 4.3.1)
   processx      3.8.3   2023-12-10 [1] CRAN (R 4.3.1)
   profvis       0.3.8   2023-05-02 [1] CRAN (R 4.3.0)
   promises      1.2.1   2023-08-10 [1] CRAN (R 4.3.0)
   ps            1.7.5   2023-04-18 [1] CRAN (R 4.3.0)
   purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.0)
   R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
   Rcpp          1.0.11  2023-07-06 [1] CRAN (R 4.3.0)
   remotes     * 2.4.2.1 2023-07-18 [1] CRAN (R 4.3.0)
   rlang         1.1.2   2023-11-04 [1] CRAN (R 4.3.1)
   rmarkdown     2.25    2023-09-18 [1] CRAN (R 4.3.1)
   rprojroot     2.0.4   2023-11-05 [1] CRAN (R 4.3.1)
   rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.3.0)
   sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
   shiny         1.8.0   2023-11-17 [1] CRAN (R 4.3.1)
   stringi       1.8.3   2023-12-11 [1] CRAN (R 4.3.1)
   stringr       1.5.1   2023-11-14 [1] CRAN (R 4.3.1)
   testthat    * 3.2.1   2023-12-02 [1] CRAN (R 4.3.1)
   tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
   urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.3.0)
   usethis       2.2.2   2023-07-06 [1] CRAN (R 4.3.0)
   utf8          1.2.4   2023-10-22 [1] CRAN (R 4.3.1)
   vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.3.1)
   waldo         0.5.2   2023-11-02 [1] CRAN (R 4.3.1)
   withr         2.5.2   2023-10-30 [1] CRAN (R 4.3.1)
   xfun          0.41    2023-11-01 [1] CRAN (R 4.3.1)
   xtable        1.8-4   2019-04-21 [1] CRAN (R 4.3.0)
   yaml          2.3.8   2023-12-11 [1] CRAN (R 4.3.1)

 [1] /Users/philipp/Library/R/arm64/4.3/library
 [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

 P ── Loaded and on-disk path mismatch.

─────────────────────────────────────────────────────────────────────────────────────────────────────────────

Answer 3 · 2023-12-23T22:12:11.000Z

Hi @iostovary

Thanks a lot for opening getting back to us with this issue. The issue what caused by a recent commit. Unfortunately, this was an annoying mistake on my side because of bad release practice (lesson learnt). We actually have the tests in place that would have picked what you report, since v0.6.1.

To fix, I did a patch release v0.6.2. I have some further explanations what was the root cause and how I hot-fixed it in the NEWS update of today's version bumping.

I ran the tests on the files I have, they pass. Would be great if you can reinstall the newest patch, and close this if it works.

Thanks for your understanding.

Cheers,
Philipp

Answer 4 · 2024-01-08T08:44:05.000Z

Hi Philipp, Happy new year and thanks a lot for taking care of this so fast. I’m curious to see if it works now. I will test the latest release tomorrow and will get back to you whether it worked. Cheers, Isabella Von: Philipp Baumann ***@***.***> Gesendet: Samstag, 23. Dezember 2023 23:12 An: spectral-cockpit/opusreader2 ***@***.***> Cc: Ostovary Isabella ***@***.***>; Mention ***@***.***> Betreff: Re: [spectral-cockpit/opusreader2] v0.5.0.9000 -> v0.6.1: `read_opus()` fails (Issue #101) Hi @iostovary<https://github.com/iostovary> Thanks a lot for opening getting back to us with this issue. The issue what caused by a recent commit. Unfortunately, this was an annoying mistake on my side because of bad release practice (lesson learnt). We actually have the tests in place that would have picked what you report, since v0.6.1. To fix, I did a patch release v0.6.2. I have some further explanations what was the root cause and how I hot-fixed it in the NEWS update<https://github.com/spectral-cockpit/opusreader2/blob/main/NEWS.md> of today's version bumping. I ran the tests on the files I have, they pass. Would be great if you can reinstall the newest patch, and close this if it works. Thanks for your understanding. Cheers, Philipp — Reply to this email directly, view it on GitHub<#101 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AYIH7OO7VNTUXLSGUDHGUQ3YK5JMNAVCNFSM6AAAAABA3NBKOGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRYGM3TQOJRGQ>. You are receiving this because you were mentioned.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#101 (comment)", "url": "#101 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

Answer 5 · 2024-01-08T13:28:43.000Z

Hi Isabella,

Thanks, hope you also had a good start in 2024. Good testing tomorrow.

Cheers,
Philipp

Answer 6 · 2024-01-11T10:32:08.000Z

Dear Philipp, I have updated the opusreader2 to the newest version and mapping read_opus now works again. I’ve closed the issue. Thanks again for fixing it so fast! Cheers, Isabella Von: Philipp Baumann ***@***.***> Gesendet: Montag, 8. Januar 2024 14:29 An: spectral-cockpit/opusreader2 ***@***.***> Cc: Ostovary Isabella ***@***.***>; Mention ***@***.***> Betreff: Re: [spectral-cockpit/opusreader2] v0.5.0.9000 -> v0.6.1: `read_opus()` fails (Issue #101) Hi Isabella, Thanks, hope you also had a good start in 2024. Good testing tomorrow. Cheers, Philipp — Reply to this email directly, view it on GitHub<#101 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AYIH7OJIJCWTUJZDQ24HHSTYNPYBNAVCNFSM6AAAAABA3NBKOGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBRGAYDQMRXGI>. You are receiving this because you were mentioned.Message ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#101 (comment)", "url": "#101 (comment)", "name": "View Issue" }, "description": "View this Issue on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]