Bioequivalence and Bioavailability Forum • Error using Bear when clicking "Start data analysis"

gpinkham
☆

US,
2015-09-29 00:03
(3496 d 15:17 ago)

Posting: # 15483
Views: 11,750

Error using Bear when clicking "Start data analysis" [🇷 for BE/BA]

I started getting this error all of a sudden (see below). it happens every time I click "start data analysis" now. at first I was using Bear inside R Studio and thought maybe something went wrong with the studio.. my first attempt in R Console worked.. (but I mis typed the file name and tried again).. second attempt failed again at "start data analysis".. Any suggestions? delete install and start again?

here is the complete R console.. the error happens when selecting "Start data analysis"

R version 3.2.2 (2015-08-14) -- "Fire Safety"

Copyright (C) 2015 The R Foundation for Statistical Computing

Platform: x86_64-pc-linux-gnu (64-bit)



R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.



  Natural language support but running in an English locale



R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.



Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.



> library(bear)

Loading required package: reshape

Loading required package: nlme

Loading required package: gdata

gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.



gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.



Attaching package: ‘gdata’



The following object is masked from ‘package:stats’:



    nobs



The following object is masked from ‘package:utils’:



    object.size





....................................

                          

   bear (BE/BA for R) 

   v2.6.8

   under license of GPL-2|GPL-3

                                                                   

   Please type 'go()' to run; or

   'about.bear()' to read more.               



....................................

> go()



 If the next step goes crahsed, please make sure the working directory

 has writing permission. Use setwd() to set your working directory.





 -----------------  Current settings ----------------



                Methods               Setting

                 ------                ------

          study design?        parallel study

            dosing type           single-dose

      lambda_z estimate   Two-Times-Tmax(TTT)

        trapezoidal AUC    linear-up/log-down

   BE criterion (LL, %)                    80

             dose (mg)?                   200

 drug plasma conc. unit                 ng/mL

        label of x-axis Time after dosing(hr)

        label of y-axis    drugX plasma conc.



 ----------------------------------------------------



 *** All output files will be placed in the folder of

 /home/gpinkham/Documents ***.





*** You have selected the following -> (new)





*** You have selected the following ->

  Single-dosed, 





Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 

  [tcl] grab failed: window not viewable.

yjlee168
★★★

Kaohsiung, Taiwan,
2015-09-29 00:34
(3496 d 14:47 ago)

@ gpinkham
Posting: # 15484
Views: 10,029

Error using Bear when clicking "Start data analysis"

Post reply

Hi gpinkham,

I never see this error before. I suggest that you may check your working directory to see if there is any weird file left. It sounds like that you stop running after you mis type the file name and you tried to force it to stop running or because of errors. If there is any weird file (such as .***) in your working directory and you are pretty sure these weird files should not be there, then you can delete them. Try to run R console and bear again.

❝ ... my first attempt in R Console worked.. (but I mis typed the file name and tried again).. second attempt failed again at "start data analysis".. Any suggestions? delete install and start again?

❝

❝ Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") :

❝ [tcl] grab failed: window not viewable.[/code]

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

gpinkham
☆

US,
2015-09-29 00:44
(3496 d 14:37 ago)

@ yjlee168
Posting: # 15485
Views: 10,398

Error using Bear when clicking "Start data analysis"

Post reply

❝ […] I suggest that you may check your working directory to see if there is any weird file left. It sounds like that you stop running after you mis type the file name and you tried to force it to stop running or because of errors. If there is any weird file (such as .***) in your working directory and you are pretty sure these weird files should not be there, then you can delete them. Try to run R console and bear again.

that did the trick.. deleted all possible R/Bear files in the working directory and it worked... of course I got this error that I saw in a previous post.. I'll dig and see what could be going on..

Error in NAToUnknown.default(x = ke, unknown = 0) : 

  'x' already has value “0”

Edit: Full quote removed. Please delete everything from the text of the original poster which is not necessary in understanding your answer; see also this post! [Helmut]

gpinkham
☆

US,
2015-09-29 00:48
(3496 d 14:32 ago)

@ gpinkham
Posting: # 15486
Views: 10,048

Error using Bear when clicking "Start data analysis"

Post reply

well I take it back,.., we're back to the tcl error.. deleted all files.. still getting the old error.. I'll keep digging and see if I can find out why., (new to R so my R debugging skills are non existent but I will give it a go).

thanks!

Edit: Full quote removed. Please delete everything from the text of the original poster which is not necessary in understanding your answer; see also this post! BTW, you can edit your posts for 24 hours. No need for a new one. [Helmut]

yjlee168
★★★

Kaohsiung, Taiwan,
2015-09-29 00:56
(3496 d 14:25 ago)

@ gpinkham
Posting: # 15487
Views: 10,056

Error using Bear when clicking "Start data analysis"

Post reply

Hi gpinkham,

Try another lambda_z estimation method such as ARS or manual selection. Also delete the subjects with many missing data points from your dataset.

❝ ❝ Error in NAToUnknown.default(x = ke, unknown = 0) :

❝ ❝ 'x' already has value “0”

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here

gpinkham
☆

US,
2015-09-29 01:15
(3496 d 14:06 ago)

@ yjlee168
Posting: # 15488
Views: 10,016

Error using Bear when clicking "Start data analysis"

Post reply

❝ Try another lambda_z estimation method such as ARS or manual selection. Also delete the subjects with many missing data points from your dataset.

as soon as I can get passed the error clicking "start data analysis" I'll try some different lamba_z settings.. (and clean up the data.. I know there are some missing.. didn't know that would cause an issue.. )

thanks again,
Gary

Edit: Full quote removed. Please delete everything from the text of the original poster which is not necessary in understanding your answer; see also this post! [Helmut]

gpinkham ☆ US, 2015-09-30 18:19 (3494 d 21:02 ago) @ gpinkham Posting: # 15505 Views: 9,841	Error using Bear when clicking "Start data analysis" Post reply
	ok just wanted to mention I think I figured out how to get passed the TCL error.. I noticed when I double click an option in the menu it fails.. if I click once and click the OK button it seems to be working.. for the record I'm running Ubuntu 14..

yjlee168
★★★

Kaohsiung, Taiwan,
2015-09-30 19:14
(3494 d 20:07 ago)

(edited on 2015-10-01 09:09)
@ gpinkham
Posting: # 15507
Views: 9,935

bear in ubuntu or linux pc or Mac OS X

Post reply

Hi gpinkham,

Great. Ubuntu is the keyword for me to be able to reproduce your error finally. Your findings may not be completely correct (or a mistake).

always do not click 'Quit' button at R Data Editor window (including data display/editing), but 'x' to close window in Linux, like Ubuntu. If you do so, it may not cause the error immediately. But after 2-3 times clicks of menu option, the error occurs, including any double-click of menu item. In MS Windows, there is no such 'Quit' button at all. Mac OS X is the same as Linux. I will try to add a warning for this in next release.
after the error, you still can restart bear. However, there will be two menu windows appearing in your desktop. The real one is overlapped by an empty one. Just drag away the empty window to see the real one and close the empty one by clicking 'x'.
as long as you do not click 'Quit', any double-click in menu option should not cause any error.
Some other differences in Linux or Mac OS X from Windows OS are: (i) if you want to enter anything in R data editor window, you have to press 'Enter' once to make it happen after entry. Otherwise, the content will be ignored or remains unchanged. This is not necessary in Windows OS. (ii) the function of file.choose() cannot pop-up the dialogue for choosing file as Windows OS or Mac OS X in GUI mode does. Instead, the entire file name must be entered in R console. Except these, Linux is a perfect OS to run R/bear.

❝ ... I noticed when I double click an option in the menu it fails.. if I click once and click the OK button it seems to be working.. for the record I'm running Ubuntu 14.

—
All the best,
-- Yung-jin Lee
bear v2.9.2:- created by Hsin-ya Lee & Yung-jin Lee
Kaohsiung, Taiwan https://www.pkpd168.com/bear
Download link (updated) -> here