Error in normalizer_GUI() #34

hzhu48187 · 2020-03-21T07:05:10Z

Hello,

I'm new to Premessa, and I've been trying to use the normalizer_GUI() to do bead normalization but running into repeated issues with this error:

I've triple checked that the fcs files I'm feeding in have the same number of channels and channel names, but I keep getting this error no matter which fcs files I feed in (even two fcs files from the same experiment).

Would you have any insight on this? This also seems to happen regardless of if I choose "Fluidigm" or "beta beads" as an option. Thank you so much!

pfgherardini · 2020-04-06T15:49:18Z

Can you please open a new R session an post the result of running the following commands:

library(shiny)
library(premessa)
sessionInfo()

MLTWhite · 2020-05-15T05:33:31Z

I have the same question. I opened a new comment because I have two questions. Thank you!

angel611 · 2020-10-06T11:21:13Z

I need help, I am having the same error when i run premessa_GUI.i have tried to put xcode but its still not working.
Any help?
Listening on http://127.0.0.1:6994
Warning: Error in [: incorrect number of dimensions
90: compute_bead_slopes
89: correct_data_channels
88: FUN
87: lapply
86: premessa::normalize_folder
73: observeEventHandler [/Library/Frameworks/R.framework/Versions/3.5/Resources/library/premessa/normalizer_shinyGUI/server.R#266]
2: shiny::runApp
1: premessa::normalizer_GUI

my session info is
sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.15.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] premessa_0.2.6 shiny_1.5.0

loaded via a namespace (and not attached):
[1] reticulate_1.13 remotes_2.2.0 lattice_0.20-38 pcaPP_1.9-73
[5] testthat_2.3.2 usethis_1.6.3 htmltools_0.5.0 stats4_3.5.3
[9] yaml_2.2.1 flowCore_1.48.1 rlang_0.4.7 pkgbuild_1.1.0
[13] later_1.1.0.1 glue_1.4.2 withr_2.3.0 BiocGenerics_0.28.0
[17] rhandsontable_0.3.7 sessioninfo_1.1.1 matrixStats_0.56.0 robustbase_0.93-5
[21] umap_0.2.5.0 htmlwidgets_1.5.1 devtools_2.3.2 mvtnorm_1.1-0
[25] memoise_1.1.0 Biobase_2.42.0 callr_3.4.4 fastmap_1.0.1
[29] httpuv_1.5.4 ps_1.3.4 parallel_3.5.3 fansi_0.4.1
[33] DEoptimR_1.0-8 Rcpp_1.0.5 corpcor_1.6.9 xtable_1.8-4
[37] openssl_1.4.1 backports_1.1.10 promises_1.1.1 desc_1.2.0
[41] pkgload_1.1.0 graph_1.60.0 jsonlite_1.7.1 mime_0.9
[45] fs_1.5.0 RSpectra_0.16-0 askpass_1.1 digest_0.6.25
[49] processx_3.4.4 grid_3.5.3 rprojroot_1.3-2 cli_2.0.2
[53] tools_3.5.3 magrittr_1.5 crayon_1.3.4 rrcov_1.5-2
[57] MASS_7.3-51.1 ellipsis_0.3.1 Matrix_1.2-15 prettyunits_1.1.1
[61] assertthat_0.2.1 rstudioapi_0.11 R6_2.4.1 compiler_3.5.3

pfgherardini · 2020-10-07T18:17:39Z

Can you please share in a Box/Dropbox/Googl Drive folder a couple of FCS files that fail? I need them to be able to reproduce the error and investigate.

angel611 · 2020-10-08T12:44:11Z

CYTOF DATA <https://drive.google.com/drive/folders/1rnE7emoZrQZIW1gpg_ASScMqZ0arjBMg> Kindly ,here is the data

…

On Wed, 7 Oct 2020 at 21:17, Pier Federico Gherardini < ***@***.***> wrote: Can you please share in a Box/Dropbox/Googl Drive folder a couple of FCS files that fail? I need them to be able to reproduce the error and investigate. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APLOONJTTZJCDBOP446A5GTSJSWFJANCNFSM4LQ2F2AQ> .

pfgherardini · 2020-10-08T19:42:31Z

The link is not accessible. Can you please make it publicly accessible?

Thanks

pfgherardini · 2020-10-13T18:02:14Z

Pinging you again @angel611 and @hzhu48187 . I am happy to look into this issue but i need data to reproduce it

angel611 · 2020-10-21T09:55:05Z

This is the link to the data https://drive.google.com/drive/folders/1rnE7emoZrQZIW1gpg_ASScMqZ0arjBMg?usp=sharing

…

On Tue, 13 Oct 2020 at 21:02, Pier Federico Gherardini < ***@***.***> wrote: Pinging you again @angel611 <https://github.com/angel611> and @hzhu48187 <https://github.com/hzhu48187> . I am happy to look into this issue but i need data to reproduce it — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#34 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APLOONOGXL5QI5RZFLA63X3SKSI3RANCNFSM4LQ2F2AQ> .

angel611 · 2020-10-21T09:57:02Z

https://drive.google.com/drive/folders/1rnE7emoZrQZIW1gpg_ASScMqZ0arjBMg

ZdSonwa · 2020-11-24T12:38:53Z

Has this issue been resolved? I am experiencing a similar problem where the run freezes with this message

Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
Some data values of 'Ir193Di' channel exceed its $PnR value 4096 and will be truncated!
To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
Warning in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
Some data values of 'Time' channel exceed its $PnR value 997 and will be truncated!
To avoid truncation, either fix $PnR before generating FCS or set 'truncate_max_range = FALSE'
Warning: Error in [: incorrect number of dimensions
90: compute_bead_slopes
89: correct_data_channels
88: FUN
87: lapply
86: premessa::normalize_folder
73: observeEventHandler [C:\Users\Zd. Sonwa\Documents\R\win-library\4.0\premessa\normalizer_shinyGUI/server.R#266]
2: shiny::runApp
1: normalizer_GUI

pfgherardini · 2020-11-25T00:00:57Z

I used the files @angel611 above provided for testing and I could not reproduce. Can you please try upgrading to the latest version of the flowCore package? On my system with the following sessionInfo() the files normalize correctly

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] flowCore_1.52.1 shiny_1.5.0     premessa_0.2.6 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          compiler_3.6.3      pillar_1.4.6        later_1.1.0.1       plyr_1.8.6          tools_3.6.3        
 [7] digest_0.6.25       jsonlite_1.7.1      lifecycle_0.2.0     tibble_3.0.4        gtable_0.3.0        pkgconfig_2.0.3    
[13] rlang_0.4.8         cli_2.0.2           rstudioapi_0.11     parallel_3.6.3      fastmap_1.0.1       dplyr_1.0.2        
[19] withr_2.2.0         generics_0.0.2      vctrs_0.3.4         tidyselect_1.1.0    stats4_3.6.3        grid_3.6.3         
[25] reshape_0.8.8       glue_1.4.2          Biobase_2.46.0      R6_2.4.1            fansi_0.4.1         sessioninfo_1.1.1  
[31] farver_2.0.3        purrr_0.3.4         ggplot2_3.3.2       magrittr_1.5        scales_1.1.1        promises_1.1.1     
[37] matrixStats_0.56.0  htmltools_0.5.0     ellipsis_0.3.1      BiocGenerics_0.32.0 assertthat_0.2.1    mime_0.9           
[43] xtable_1.8-4        colorspace_1.4-1    httpuv_1.5.4        labeling_0.3        munsell_0.5.0       crayon_1.3.4

@ZdSonwa do you have some other files I can test? I only need one that's failing

ZdSonwa · 2020-11-25T13:27:11Z

Here is a subset of the data I used which gave me that error.
https://drive.google.com/drive/folders/19K4KifCkya2rW8pUxDY-KxCtObxdGshi?usp=sharing

ZdSonwa · 2020-11-25T13:31:06Z

This is the version I'm using
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
Biobase 2.48.0 2020-04-27 [1] Bioconductor
BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
cytolib 2.0.3 2020-06-09 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
flowCore * 2.0.1 2020-06-09 [1] Bioconductor
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
premessa * 0.2.6 2020-09-15 [1] Github (467d641)

ZdSonwa · 2020-11-25T13:31:08Z

This is the version I'm using
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
Biobase 2.48.0 2020-04-27 [1] Bioconductor
BiocGenerics 0.34.0 2020-04-27 [1] Bioconductor
callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.0)
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0)
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
cytolib 2.0.3 2020-06-09 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.0)
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
flowCore * 2.0.1 2020-06-09 [1] Bioconductor
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
matrixStats 0.57.0 2020-09-25 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.0)
premessa * 0.2.6 2020-09-15 [1] Github (467d641)

pfgherardini · 2020-11-25T17:36:45Z

I have tried everything I could think of to reproduce this bug, but I couldn't. @ZdSonwa can you send me an email at
[AT] parkerici [DOT] org, so that we can schedule a zoom meeting and look at this together?

ZdSonwa · 2020-11-26T18:02:25Z

@pfgherardini the email doesn't seem complete, or do you mean your user name before@

pfgherardini · 2020-11-30T16:23:35Z

Yes that's what i meant [AT] parkerici [DOT] org

Ferfera2610 · 2021-02-02T22:34:20Z

Hello,
I get the same error and I am also a Mac user. I was wondering if this bug comes for Mac users rather than windows users or it is for something else.
Here is my session info:
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] shiny_1.6.0 premessa_0.2.6 devtools_2.3.2 usethis_2.0.0 BiocManager_1.30.10

loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 jquerylib_0.1.3 bslib_0.2.4 compiler_3.6.2 later_1.1.0.1 prettyunits_1.1.1
[7] remotes_2.2.0 tools_3.6.2 testthat_3.0.1 digest_0.6.27 pkgbuild_1.2.0 pkgload_1.1.0
[13] jsonlite_1.7.2 memoise_2.0.0 lifecycle_0.2.0 rlang_0.4.10 cli_2.3.0 rstudioapi_0.13
[19] yaml_2.2.1 parallel_3.6.2 curl_4.3 xfun_0.20 fastmap_1.1.0 knitr_1.31
[25] withr_2.4.1 htmlwidgets_1.5.3 sass_0.3.1 desc_1.2.0 fs_1.5.0 stats4_3.6.2
[31] rprojroot_2.0.2 Biobase_2.44.0 glue_1.4.2 R6_2.5.0 processx_3.4.5 sessioninfo_1.1.1
[37] callr_3.5.1 purrr_0.3.4 magrittr_2.0.1 matrixStats_0.58.0 BiocGenerics_0.30.0 ps_1.5.0
[43] promises_1.1.1 ellipsis_0.3.1 htmltools_0.5.1.1 assertthat_0.2.1 rhandsontable_0.3.7 flowCore_1.50.0
[49] mime_0.9 xtable_1.8-4 httpuv_1.5.5 cachem_1.0.1 crayon_1.4.0

Thanks!
Faezeh

pfgherardini · 2021-02-03T18:30:03Z

I think I had already tried to reproduce on Mac but I couldn't. However I am happy to try again. @Ferfera2610 can you share some data with me that displays the problem?

Thanks

Federico

Ferfera2610 · 2021-02-03T20:51:47Z

Hello again,
Here is the data. It is public available dataset that I am trying to regenerate their results. If it is not Mac issue, I would like to use it on my own dataset afterward.
Thanks!
Faezeh
combined.fcs.zip

Ferfera2610 · 2021-02-09T20:11:54Z

I think I had already tried to reproduce on Mac but I couldn't. However I am happy to try again. @Ferfera2610 can you share some data with me that displays the problem?

Thanks

Federico

Hello,
I tried my files on windows system and it worked properly. However, I cannot redo it anymore and now that I try it again (in windows) I receive this error:
Error in [: incorrect number of dimensions 2: shiny::runApp
1: normalizer_GUI
Do you know what might be the issue? I have deleted the normed folder that was created before too.
Thanks!
Faezeh

MLTWhite mentioned this issue May 15, 2020

Issues with Normalizer #37

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Error in normalizer_GUI() #34

Error in normalizer_GUI() #34

hzhu48187 commented Mar 21, 2020

pfgherardini commented Apr 6, 2020 •

edited

Loading

MLTWhite commented May 15, 2020

angel611 commented Oct 6, 2020

pfgherardini commented Oct 7, 2020

angel611 commented Oct 8, 2020 via email

pfgherardini commented Oct 8, 2020

pfgherardini commented Oct 13, 2020

angel611 commented Oct 21, 2020 via email

angel611 commented Oct 21, 2020

ZdSonwa commented Nov 24, 2020

pfgherardini commented Nov 25, 2020

ZdSonwa commented Nov 25, 2020

ZdSonwa commented Nov 25, 2020

ZdSonwa commented Nov 25, 2020

pfgherardini commented Nov 25, 2020

ZdSonwa commented Nov 26, 2020

pfgherardini commented Nov 30, 2020

Ferfera2610 commented Feb 2, 2021

pfgherardini commented Feb 3, 2021

Ferfera2610 commented Feb 3, 2021

Ferfera2610 commented Feb 9, 2021

Error in normalizer_GUI() #34

Error in normalizer_GUI() #34

Comments

hzhu48187 commented Mar 21, 2020

pfgherardini commented Apr 6, 2020 • edited Loading

MLTWhite commented May 15, 2020

angel611 commented Oct 6, 2020

pfgherardini commented Oct 7, 2020

angel611 commented Oct 8, 2020 via email

pfgherardini commented Oct 8, 2020

pfgherardini commented Oct 13, 2020

angel611 commented Oct 21, 2020 via email

angel611 commented Oct 21, 2020

ZdSonwa commented Nov 24, 2020

pfgherardini commented Nov 25, 2020

ZdSonwa commented Nov 25, 2020

ZdSonwa commented Nov 25, 2020

ZdSonwa commented Nov 25, 2020

pfgherardini commented Nov 25, 2020

ZdSonwa commented Nov 26, 2020

pfgherardini commented Nov 30, 2020

Ferfera2610 commented Feb 2, 2021

pfgherardini commented Feb 3, 2021

Ferfera2610 commented Feb 3, 2021

Ferfera2610 commented Feb 9, 2021

pfgherardini commented Apr 6, 2020 •

edited

Loading