Merge seg files bug - Githubissues

JpGuegan commented 2 years ago

With the new version of PhenoptrReport (3.1), the merge_cell_seg_file function stops on files with no detected cells (empty cell seg file with just the column names) and we have to stop the command because it lasts forever. However, when we processed the same batch of files with an older version (v2.4), the script runs smoothly and a merge_cell_seg_file is created. How to solve this?

AB-Kent commented 2 years ago

That's odd, the merge function has changed very little since version 0.2.4. Can you share a set of files that fail? (Email a link to files.) Also please show the output of the command devtools::session_info()

JpGuegan commented 2 years ago

Here is a link to some files https://explicyte.transfernow.net/dl/20211208q7dRXnGK

and below is the session info

Session info ------------------------------------------------------------------------------------------------------------------------------------------------------ hash: woman cook: medium-dark skin tone, snowboarder, flag: St. Kitts & Nevis

setting value version R version 4.1.1 (2021-08-10) os Windows Server x64 (build 17763) system x86_64, mingw32 ui RStudio language (EN) collate English_United States.1252 ctype English_United States.1252 tz Europe/Paris date 2021-12-08 rstudio 2021.09.0+351 Ghost Orchid (desktop) pandoc NA
Packages ----------------------------------------------------------------------------------------------------------------------------------------------------------- package * version date (UTC) lib source abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.1) assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) backports 1.3.0 2021-10-27 [1] CRAN (R 4.1.1) broom 0.7.10 2021-10-31 [1] CRAN (R 4.1.1) cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1) callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1) car 3.0-12 2021-11-06 [1] CRAN (R 4.1.1) carData 3.0-4 2020-05-22 [1] CRAN (R 4.1.1) cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1) colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.1) crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1) DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.1) desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.1) devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.1) digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.1) dplyr 1.0.7 2021-06-18 [1] CRAN (R 4.1.1) DT 0.19 2021-09-02 [1] CRAN (R 4.1.1) ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.1) ExplicyteTools 0.1.0 2021-12-02 [1] local fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.1) fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.1) fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0) generics 0.1.1 2021-10-25 [1] CRAN (R 4.1.1) ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.1.1) ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.1.1) ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.1) glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1) htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.1.1) janitor 2.1.0 2021-01-05 [1] CRAN (R 4.1.1) knitr 1.36 2021-09-29 [1] CRAN (R 4.1.1) lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1) lubridate 1.8.0 2021-10-07 [1] CRAN (R 4.1.1) magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0) memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.1) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1) pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) pkgload 1.2.3 2021-10-13 [1] CRAN (R 4.1.1) plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.1) ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.1) purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1) Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.1) remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.1) reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.0) rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.1) rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0) rstatix 0.7.0 2021-02-13 [1] CRAN (R 4.1.1) scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0) sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.1) snakecase 0.11.0 2019-05-25 [1] CRAN (R 4.1.1) stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.1) stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.1) tibble 3.1.5 2021-09-30 [1] CRAN (R 4.1.1) tidyr 1.1.4 2021-09-27 [1] CRAN (R 4.1.1) tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.1) usethis 2.1.3 2021-10-27 [1] CRAN (R 4.1.1) utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1) vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.1) withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.1) xfun 0.27 2021-10-18 [1] CRAN (R 4.1.1)

[1] C:/Users/JPGUEGAN/Documents/R/win-library/4.1 [2] C:/Program Files/R/R-4.1.1/library

AB-Kent commented 2 years ago

Hmm, I'm able to merge that data without problem. My system is very similar to yours, though Windows 10 vs Windows Server.

Is there anything else you can tell me about the failure? What versions of readr and vroom do you have, they are not in the list above.

JpGuegan commented 2 years ago

Ok, that's weird because I have tested it on two different computers (Windows10 & server). Here are the versions of readr (v2.0.2) and vroom (1.5.5).

AB-Kent commented 2 years ago

Please update both readr and vroom to the latest versions; you seem to have run into this readr bug: https://github.com/tidyverse/readr/issues/1297

JpGuegan commented 2 years ago

Thanks! The updates fixed the problem. Sorry for the inconvenience!

akoyabio / phenoptrReports

Merge seg files bug #55