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daniel1noble / metaDigitise

Digitising functions in R for extracting data and summary statistics from figures in primary research papers
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metaDigitise occasionally crashes on plot clicking #67

Open szymekdr opened 1 month ago

szymekdr commented 1 month ago

When in the "clicking" mode, the point-clicking process sometimes unexpectedly leads to a crash—the package exits the digitalisation process with an error message "the output element is empty" (sorry for not providing an exact error message; I will try to do it next time it happens; it is hard to predict).

When this happens, no data gets recorded in the caldat folder. Sometimes, the process happens several times on subsequent attempts to digitalise the points. Interestingly, it often seems to happen when trying to click the same areas of the plot—and can be (seemingly) prevented by skipping this area for the final moments of point clicking.

Thing to not: I'm using mD in VSCode, and not using httpgd plotting engine (so the plots appear in a native Python-based separate window).

Session info:

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS Big Sur ... 10.16
 system   x86_64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Warsaw
 date     2024-10-24
 pandoc   2.10 @ /Users/szymek/opt/anaconda3/bin/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package           * version    date (UTC) lib source
 ape               * 5.8        2024-04-11 [1] CRAN (R 4.4.0)
 askpass             1.2.0      2023-09-03 [1] CRAN (R 4.4.0)
 bayestestR          0.13.2     2024-02-12 [1] CRAN (R 4.4.0)
 bdsmatrix         * 1.3-7      2024-03-02 [1] CRAN (R 4.4.0)
 bit                 4.0.5      2022-11-15 [1] CRAN (R 4.4.0)
 bit64               4.0.5      2020-08-30 [1] CRAN (R 4.4.0)
 boot                1.3-30     2024-02-26 [1] CRAN (R 4.4.1)
 cachem              1.1.0      2024-05-16 [1] CRAN (R 4.4.0)
 cli                 3.6.3      2024-06-21 [1] CRAN (R 4.4.0)
 clusterGeneration   1.3.8      2023-08-16 [1] CRAN (R 4.4.0)
 coda                0.19-4.1   2024-01-31 [1] CRAN (R 4.4.0)
 codetools           0.2-20     2024-03-31 [1] CRAN (R 4.4.1)
 colorspace          2.1-0      2023-01-23 [1] CRAN (R 4.4.0)
 combinat            0.0-8      2012-10-29 [1] CRAN (R 4.4.0)
 coxme             * 2.2-22     2024-08-23 [1] CRAN (R 4.4.1)
 crayon              1.5.3      2024-06-20 [1] CRAN (R 4.4.0)
 data.table          1.15.4     2024-03-30 [1] CRAN (R 4.4.0)
 datawizard          0.12.1     2024-07-15 [1] CRAN (R 4.4.0)
 DEoptim             2.2-8      2022-11-11 [1] CRAN (R 4.4.0)
 devtools          * 2.4.5      2022-10-11 [1] CRAN (R 4.4.0)
 digest              0.6.36     2024-06-23 [1] CRAN (R 4.4.0)
 doParallel          1.0.17     2022-02-07 [1] CRAN (R 4.4.0)
 dplyr             * 1.1.4      2023-11-17 [1] CRAN (R 4.4.0)
 effectsize        * 0.8.9      2024-07-03 [1] CRAN (R 4.4.0)
 ellipsis            0.3.2      2021-04-29 [1] CRAN (R 4.4.0)
 emmeans           * 1.10.3     2024-07-01 [1] CRAN (R 4.4.0)
 estimability        1.5.1      2024-05-12 [1] CRAN (R 4.4.0)
 evaluate            0.24.0     2024-06-10 [1] CRAN (R 4.4.0)
 expm                0.999-9    2024-01-11 [1] CRAN (R 4.4.0)
 fansi               1.0.6      2023-12-08 [1] CRAN (R 4.4.0)
 fastmap             1.2.0      2024-05-15 [1] CRAN (R 4.4.0)
 fastmatch           1.1-4      2023-08-18 [1] CRAN (R 4.4.0)
 flextable         * 0.9.6      2024-05-05 [1] CRAN (R 4.4.0)
 fontBitstreamVera   0.1.1      2017-02-01 [1] CRAN (R 4.4.0)
 fontLiberation      0.1.0      2016-10-15 [1] CRAN (R 4.4.0)
 fontquiver          0.2.1      2017-02-01 [1] CRAN (R 4.4.0)
 forcats           * 1.0.0      2023-01-29 [1] CRAN (R 4.4.0)
 foreach             1.5.2      2022-02-02 [1] CRAN (R 4.4.0)
 fs                  1.6.4      2024-04-25 [1] CRAN (R 4.4.0)
 gdtools             0.4.0      2024-08-28 [1] CRAN (R 4.4.1)
 generics            0.1.3      2022-07-05 [1] CRAN (R 4.4.0)
 ggplot2           * 3.5.1      2024-04-23 [1] CRAN (R 4.4.0)
 glue                1.7.0      2024-01-09 [1] CRAN (R 4.4.0)
 gtable              0.3.5      2024-04-22 [1] CRAN (R 4.4.0)
 here              * 1.0.1      2020-12-13 [1] CRAN (R 4.4.0)
 hms                 1.1.3      2023-03-21 [1] CRAN (R 4.4.0)
 htmltools           0.5.8.1    2024-04-04 [1] CRAN (R 4.4.0)
 htmlwidgets         1.6.4      2023-12-06 [1] CRAN (R 4.4.0)
 httpuv              1.6.15     2024-03-26 [1] CRAN (R 4.4.0)
 igraph              2.0.3      2024-03-13 [1] CRAN (R 4.4.0)
 insight             0.20.2     2024-07-13 [1] CRAN (R 4.4.0)
 iterators           1.0.14     2022-02-05 [1] CRAN (R 4.4.0)
 jsonlite            1.8.8      2023-12-04 [1] CRAN (R 4.4.0)
 knitr               1.48       2024-07-07 [1] CRAN (R 4.4.0)
 later               1.3.2      2023-12-06 [1] CRAN (R 4.4.0)
 lattice             0.22-6     2024-03-20 [1] CRAN (R 4.4.1)
 lifecycle           1.0.4      2023-11-07 [1] CRAN (R 4.4.0)
 lme4              * 1.1-35.5   2024-07-03 [1] CRAN (R 4.4.0)
 lubridate         * 1.9.3      2023-09-27 [1] CRAN (R 4.4.0)
 magrittr            2.0.3      2022-03-30 [1] CRAN (R 4.4.0)
 maps              * 3.4.2      2023-12-15 [1] CRAN (R 4.4.0)
 MASS                7.3-60.2   2024-04-26 [1] CRAN (R 4.4.1)
 mathjaxr            1.6-0      2022-02-28 [1] CRAN (R 4.4.0)
 Matrix            * 1.7-0      2024-04-26 [1] CRAN (R 4.4.1)
 memoise             2.0.1      2021-11-26 [1] CRAN (R 4.4.0)
 metadat           * 1.2-0      2022-04-06 [1] CRAN (R 4.4.0)
 metaDigitise      * 1.0.1      2020-03-13 [1] CRAN (R 4.4.0)
 metafor           * 4.6-0      2024-03-28 [1] CRAN (R 4.4.0)
 mime                0.12       2021-09-28 [1] CRAN (R 4.4.0)
 miniUI              0.1.1.1    2018-05-18 [1] CRAN (R 4.4.0)
 minqa               1.2.7      2024-05-20 [1] CRAN (R 4.4.0)
 mnormt              2.1.1      2022-09-26 [1] CRAN (R 4.4.0)
 multcomp            1.4-25     2023-06-20 [1] CRAN (R 4.4.0)
 munsell             0.5.1      2024-04-01 [1] CRAN (R 4.4.0)
 mvtnorm             1.2-5      2024-05-21 [1] CRAN (R 4.4.0)
 nlme                3.1-164    2023-11-27 [1] CRAN (R 4.4.1)
 nloptr              2.1.1      2024-06-25 [1] CRAN (R 4.4.0)
 numDeriv          * 2016.8-1.1 2019-06-06 [1] CRAN (R 4.4.0)
 officer             0.6.7      2024-10-09 [1] CRAN (R 4.4.1)
 openssl             2.2.0      2024-05-16 [1] CRAN (R 4.4.0)
 optimParallel       1.0-2      2021-02-11 [1] CRAN (R 4.4.0)
 pacman              0.5.1      2019-03-11 [1] CRAN (R 4.4.0)
 parameters          0.22.0     2024-06-20 [1] CRAN (R 4.4.0)
 patchwork         * 1.2.0      2024-01-08 [1] CRAN (R 4.4.0)
 phangorn            2.11.1     2023-01-23 [1] CRAN (R 4.4.0)
 phytools          * 2.3-0      2024-06-13 [1] CRAN (R 4.4.0)
 pillar              1.9.0      2023-03-22 [1] CRAN (R 4.4.0)
 pkgbuild            1.4.4      2024-03-17 [1] CRAN (R 4.4.0)
 pkgconfig           2.0.3      2019-09-22 [1] CRAN (R 4.4.0)
 pkgload             1.4.0      2024-06-28 [1] CRAN (R 4.4.0)
 profvis             0.4.0      2024-09-20 [1] CRAN (R 4.4.1)
 promises            1.3.0      2024-04-05 [1] CRAN (R 4.4.0)
 purrr             * 1.0.2      2023-08-10 [1] CRAN (R 4.4.0)
 quadprog            1.5-8      2019-11-20 [1] CRAN (R 4.4.0)
 R.cache             0.16.0     2022-07-21 [1] CRAN (R 4.4.0)
 R.methodsS3         1.8.2      2022-06-13 [1] CRAN (R 4.4.0)
 R.oo                1.26.0     2024-01-24 [1] CRAN (R 4.4.0)
 R.rsp             * 0.46.0     2024-02-17 [1] CRAN (R 4.4.0)
 R.utils             2.12.3     2023-11-18 [1] CRAN (R 4.4.0)
 R6                  2.5.1      2021-08-19 [1] CRAN (R 4.4.0)
 ragg                1.3.3      2024-09-11 [1] CRAN (R 4.4.1)
 Rcpp                1.0.12     2024-01-09 [1] CRAN (R 4.4.0)
 readr             * 2.1.5      2024-01-10 [1] CRAN (R 4.4.0)
 remotes             2.5.0      2024-03-17 [1] CRAN (R 4.4.0)
 rlang               1.1.4      2024-06-04 [1] CRAN (R 4.4.0)
 rmarkdown           2.28       2024-08-17 [1] CRAN (R 4.4.1)
 rprojroot           2.0.4      2023-11-05 [1] CRAN (R 4.4.0)
 sandwich            3.1-0      2023-12-11 [1] CRAN (R 4.4.0)
 scales              1.3.0      2023-11-28 [1] CRAN (R 4.4.0)
 scatterplot3d       0.3-44     2023-05-05 [1] CRAN (R 4.4.0)
 sessioninfo         1.2.2      2021-12-06 [1] CRAN (R 4.4.0)
 shiny               1.9.1      2024-08-01 [1] CRAN (R 4.4.0)
 stringi             1.8.4      2024-05-06 [1] CRAN (R 4.4.0)
 stringr           * 1.5.1      2023-11-14 [1] CRAN (R 4.4.0)
 survival          * 3.6-4      2024-04-24 [1] CRAN (R 4.4.1)
 systemfonts         1.1.0      2024-05-15 [1] CRAN (R 4.4.0)
 textshaping         0.4.0      2024-05-24 [1] CRAN (R 4.4.0)
 TH.data             1.1-2      2023-04-17 [1] CRAN (R 4.4.0)
 tibble            * 3.2.1      2023-03-20 [1] CRAN (R 4.4.0)
 tidyr             * 1.3.1      2024-01-24 [1] CRAN (R 4.4.0)
 tidyselect          1.2.1      2024-03-11 [1] CRAN (R 4.4.0)
 tidyverse         * 2.0.0      2023-02-22 [1] CRAN (R 4.4.0)
 timechange          0.3.0      2024-01-18 [1] CRAN (R 4.4.0)
 tzdb                0.4.0      2023-05-12 [1] CRAN (R 4.4.0)
 urlchecker          1.0.1      2021-11-30 [1] CRAN (R 4.4.0)
 usethis           * 3.0.0      2024-07-29 [1] CRAN (R 4.4.0)
 utf8                1.2.4      2023-10-22 [1] CRAN (R 4.4.0)
 uuid                1.2-1      2024-07-29 [1] CRAN (R 4.4.0)
 vctrs               0.6.5      2023-12-01 [1] CRAN (R 4.4.0)
 vroom               1.6.5      2023-12-05 [1] CRAN (R 4.4.0)
 withr               3.0.0      2024-01-16 [1] CRAN (R 4.4.0)
 xfun                0.45       2024-06-16 [1] CRAN (R 4.4.0)
 xml2                1.3.6      2023-12-04 [1] CRAN (R 4.4.0)
 xtable              1.8-4      2019-04-21 [1] CRAN (R 4.4.0)
 zip                 2.3.1      2024-01-27 [1] CRAN (R 4.4.0)
 zoo                 1.8-12     2023-04-13 [1] CRAN (R 4.4.0)

 [1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library
joelpick commented 1 month ago

Thanks Szymek. I strongly suspect that is an issue with the plotting window, and not the metaDigitise code, in which case we can’t do much about it (apart from warn people). We can try and catch the error, but if the point extraction crashes, I don't think that there would be a way of saving the points - I will look into it!!

On 24 Oct 2024, at 08:07, Szymek Drobniak @.***> wrote:

When in the "clicking" mode, the point-clicking process sometimes unexpectedly leads to a crash—the package exits the digitalisation process with an error message "the output element is empty" (sorry for not providing an exact error message; I will try to do it next time it happens; it is hard to predict).

When this happens, no data gets recorded in the caldat folder. Sometimes, the process happens several times on subsequent attempts to digitalise the points. Interestingly, it often seems to happen when trying to click the same areas of the plot—and can be (seemingly) prevented by skipping this area for the final moments of point clicking.

Thing to not: I'm using mD in VSCode, and not using httpgd plotting engine (so the plots appear in a native Python-based separate window).

Session info:

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.4.1 (2024-06-14) os macOS Big Sur ... 10.16 system x86_64, darwin20 ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz Europe/Warsaw date 2024-10-24 pandoc 2.10 @ /Users/szymek/opt/anaconda3/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────── package version date (UTC) lib source ape 5.8 2024-04-11 [1] CRAN (R 4.4.0) askpass 1.2.0 2023-09-03 [1] CRAN (R 4.4.0) bayestestR 0.13.2 2024-02-12 [1] CRAN (R 4.4.0) bdsmatrix 1.3-7 2024-03-02 [1] CRAN (R 4.4.0) bit 4.0.5 2022-11-15 [1] CRAN (R 4.4.0) bit64 4.0.5 2020-08-30 [1] CRAN (R 4.4.0) boot 1.3-30 2024-02-26 [1] CRAN (R 4.4.1) cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0) cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0) clusterGeneration 1.3.8 2023-08-16 [1] CRAN (R 4.4.0) coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.4.0) codetools 0.2-20 2024-03-31 [1] CRAN (R 4.4.1) colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.4.0) combinat 0.0-8 2012-10-29 [1] CRAN (R 4.4.0) coxme 2.2-22 2024-08-23 [1] CRAN (R 4.4.1) crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0) data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0) datawizard 0.12.1 2024-07-15 [1] CRAN (R 4.4.0) DEoptim 2.2-8 2022-11-11 [1] CRAN (R 4.4.0) devtools 2.4.5 2022-10-11 [1] CRAN (R 4.4.0) digest 0.6.36 2024-06-23 [1] CRAN (R 4.4.0) doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.4.0) dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.4.0) effectsize 0.8.9 2024-07-03 [1] CRAN (R 4.4.0) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.4.0) emmeans 1.10.3 2024-07-01 [1] CRAN (R 4.4.0) estimability 1.5.1 2024-05-12 [1] CRAN (R 4.4.0) evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.0) expm 0.999-9 2024-01-11 [1] CRAN (R 4.4.0) fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0) fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0) fastmatch 1.1-4 2023-08-18 [1] CRAN (R 4.4.0) flextable 0.9.6 2024-05-05 [1] CRAN (R 4.4.0) fontBitstreamVera 0.1.1 2017-02-01 [1] CRAN (R 4.4.0) fontLiberation 0.1.0 2016-10-15 [1] CRAN (R 4.4.0) fontquiver 0.2.1 2017-02-01 [1] CRAN (R 4.4.0) forcats 1.0.0 2023-01-29 [1] CRAN (R 4.4.0) foreach 1.5.2 2022-02-02 [1] CRAN (R 4.4.0) fs 1.6.4 2024-04-25 [1] CRAN (R 4.4.0) gdtools 0.4.0 2024-08-28 [1] CRAN (R 4.4.1) generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) ggplot2 3.5.1 2024-04-23 [1] CRAN (R 4.4.0) glue 1.7.0 2024-01-09 [1] CRAN (R 4.4.0) gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0) here 1.0.1 2020-12-13 [1] CRAN (R 4.4.0) hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0) htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.4.0) igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0) insight 0.20.2 2024-07-13 [1] CRAN (R 4.4.0) iterators 1.0.14 2022-02-05 [1] CRAN (R 4.4.0) jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0) knitr 1.48 2024-07-07 [1] CRAN (R 4.4.0) later 1.3.2 2023-12-06 [1] CRAN (R 4.4.0) lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.1) lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) lme4 1.1-35.5 2024-07-03 [1] CRAN (R 4.4.0) lubridate 1.9.3 2023-09-27 [1] CRAN (R 4.4.0) magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) maps 3.4.2 2023-12-15 [1] CRAN (R 4.4.0) MASS 7.3-60.2 2024-04-26 [1] CRAN (R 4.4.1) mathjaxr 1.6-0 2022-02-28 [1] CRAN (R 4.4.0) Matrix 1.7-0 2024-04-26 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szymekdr commented 1 month ago

Tried catching it but of course (Murphy's Law...) when I decided to do it, it stopped crashing. Started again when I forgot about it after a dozen or so plots... I'll check if i see same behaviour in RStudio - thanks anyway!