Bioequivalence and Bioavailability Forum • Problem with bear 2.9.1

Balu
☆

India,
2024-08-30 07:42
(41 d 15:03 ago)

Posting: # 24170
Views: 1,282

Problem with bear 2.9.1 [🇷 for BE/BA]

Dear Sir,

I'm recently using R software in clinical studies by calculating the pharmacokinetic and statistical analysis using BEAR Toolkit version 2.9.1.

I'm facing the below mentioned error when i run the replicate cross-over designs.

Error Description:
[image]

Regards,
Baljai.

Edit: Category and subject line changed; see also this post #1 and #2.
Not interested in replies by female members? The forum is not a gentlemens‘ club! [Helmut]

Original subject line: Problem with BEAR Toolkit 2.9.1 version when PK & BE analysis for Replicate crossover desings

Helmut
★★★

Vienna, Austria,
2024-08-30 10:14
(41 d 12:30 ago)

@ Balu
Posting: # 24171
Views: 1,129

Problem with bear 2.9.1

Post reply

Hi Balu,

welcome to the forum!

❝ Dear Sir,

Incidentally I host XY indeed. :-D

❝ I'm recently using R software in clinical studies by calculating the pharmacokinetic and statistical analysis using BEAR Toolkit version 2.9.1.

bear is a package for [image]

. Do you come from the realm of Certara? Phoenix has Toolkits.

❝ I'm facing the below mentioned error when i run the replicate cross-over designs.

Not quite. You successfully attached it after typing library(bear) because you saw …

[image]

… and got this error already at start, i.e., after typing go(). Did you follow the installation instructions exactly? I have no problems on Windows 7 and 11 (see this post).

[image]

Furthermore, I haven’t seen this ASCII-graph for ages (only with previous versions). I don’t see it running in R 4.1.3 (2022-03-10) and 4.4.1 (2024-06-14)… Therefore, I suspect that something went wrong with your installation.

I suggest to deinstall it: In the R-GUI type remove.packages("bear"). Download it again and follow the installation instructions (particularly run the script preinst.r from SourceForge).

If that doesn’t resolve your problem, I’m afraid you have to wait till Yung-jin passes by. Perhaps you can contact him directly (email in his profile). Alternatively, after library(bear) type help(p = bear) and click on the first link DESCRIPTION file to get his contact.

I strongly suggest to always update to the latest version of R (current as of today is 4.4.1). For the procedure see this article. Sooner or later with version 4.1.3 you will face a situation where a package is no more supported. Furthermore, bugs are fixed in later versions, functions might be deprecated or even removed, and new ones introduced.
For the procedure to use library(bear) with newer versions of R see this post.
Please upload screenshots as (8-bit = 256 colors) PNGs. JPEGs are blurred and full of compression artifacts, esp. after downscaling.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

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Balu ☆ India, 2024-08-31 08:28 (40 d 14:16 ago) @ Helmut Posting: # 24172 Views: 970	Problem with bear 2.9.1 Post reply
	Dear Helmut, I will try as per your suggestions but again same error will display. kindly solve the error. Regards, Balu.

Helmut
★★★

Vienna, Austria,
2024-08-31 10:27
(40 d 12:17 ago)

@ Balu
Posting: # 24173
Views: 968

Did you try?

Post reply

Hi Babu,

❝ I will try as per your suggestions but again same error will display.

Future tense? Do you have a crystal ball or did you already?

❝ kindly solve the error.

If you buy me a round-trip ticket to India, I can try it. My daily rates on request. Have you contacted Yung-jin in the meantime?

A remote diagnosis is difficult. In the R-GUI type sessionInfo(). Mine:

sessionInfo() after library(bear):

R version 4.4.1 (2024-06-14 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22000) Matrix products: default locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 time zone: Europe/Vienna tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] bear_2.9.1 loaded via a namespace (and not attached): [1] sandwich_3.1-0 utf8_1.2.4 generics_0.1.3 randomizeBE_0.3-6 coin_1.4-3 [6] gtools_3.9.5 stringi_1.8.4 lattice_0.22-6 magrittr_2.0.3 grid_4.4.0 [11] mvtnorm_1.3-0 plyr_1.8.9 Matrix_1.7-0 reshape_0.8.9 DBI_1.2.3 [16] survival_3.7-0 multcomp_1.4-26 fansi_1.0.6 scales_1.3.0 TH.data_1.1-2 [21] codetools_0.2-20 modeltools_0.2-23 gWidgets_0.0-54.2 cli_3.6.3 mitools_2.4 [26] rlang_1.1.4 munsell_0.5.1 splines_4.4.0 plotrix_3.8-4 tools_4.4.0 [31] parallel_4.4.0 reshape2_1.4.4 dplyr_1.1.4 colorspace_2.1-1 ggplot2_3.5.1 [36] vctrs_0.6.5 R6_2.5.1 png_0.1-8 zoo_1.8-12 matrixStats_1.3.0 [41] stats4_4.4.0 lifecycle_1.0.4 stringr_1.5.1 MASS_7.3-61 libcoin_1.0-10 [46] pkgconfig_2.0.3 pillar_1.9.0 gtable_0.3.5 glue_1.7.0 Rcpp_1.0.13 [51] tibble_3.2.1 tidyselect_1.2.1 nlme_3.1-166 survey_4.4-2 gdata_3.0.0 [56] compiler_4.4.0 ICSNP_1.1-2 ICS_1.4-1

Why so many? bear imports the entire library gWidgets and certain functions of the libraries coin, gdata, ggplot2, grid, ICSNP, nlme, plotrix, plyr, png, randomizeBE, reshape, and reshape2. Each of them imports from other libraries themselves.
For example nlme → lattice → grid, grDevices, and stats.

Post your results please (text – not a screenshot). Otherwise, we are fishing in the dark.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

Balu
☆

India,
2024-09-04 12:38
(36 d 10:06 ago)

@ Helmut
Posting: # 24180
Views: 813

Did you try?

Post reply

Dear Helmut,

I am facing the error working with partial replicate design in BEAR 2.9.1 version

please find the below mentioned error

> library(bear)





  bear (BE/BA for R) v2.9.1

  Please type 'go()' to run.



> go()

> go()









 .b                             v2.9.1    

 88                                       

 888oooo    .ooooo.   eoooo.   oooood8b   

 d88    88 d8(   )8b       )8b  888  8)   

 888    88 888ooo88b o8o89888   888       

 888    88 888       88(   88   888       

   o8ooo8   88bod8P   doooo8b  d888b      



Error in LL[, 2] : subscript out of bounds

Regards,
Balu.

Edit: Text BBcoded (see there). [Helmut]

Helmut
★★★

Vienna, Austria,
2024-09-04 13:43
(36 d 09:02 ago)

@ Balu
Posting: # 24182
Views: 817

Perseverance…

Post reply

Hi Babu,

❝ I am facing the error working with partial replicate design in BEAR 2.9.1 version

You wrote that already. The design of the study is irrelevant.

Why didn’t you answer my questions and post what I asked for above? Repeating what you showed in the screenshot of your first post is neither interesting nor useful.
Why did you type go() twice?

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes

Balu ☆ India, 2024-09-04 13:48 (36 d 08:56 ago) @ Helmut Posting: # 24183 Views: 802	Perseverance… Post reply
	Dear Helmut, As per your suggestions all above mentioned process was done. But again same Error came. Regards, Balu.

Helmut
★★★

Vienna, Austria,
2024-09-04 16:12
(36 d 06:33 ago)

@ Balu
Posting: # 24184
Views: 795

Getting tired 😴

Post reply

Hi Balu,

❝ As per your suggestions all above mentioned process was done. But again same Error came.

You are testing my patience. I. Did. Not. Ask. For. That.
Read my post again. And again. _{And again.} Once you understood it, come back.

—
Dif-tor heh smusma 🖖🏼 Довге життя Україна!
Helmut Schütz

The quality of responses received is directly proportional to the quality of the question asked. 🚮
Science Quotes