[R-SIG-Mac] Error message reading files in R Commander
Fox, John
j|ox @end|ng |rom mcm@@ter@c@
Tue Nov 26 02:21:33 CET 2019
Dear José,
As a general matter and an ideal, users should *never* see errors in the Rcmdr code -- the Rcmdr should ideally intercept all errors.
I'm now able to reproduce the error you reported. I believe that I've fixed it in the development version 2.7-0 of the Rcmdr package on R-Forge. I should test the fix some more, but if it holds up, I'll also apply it to Rcmdr 2.6-2 when and if that's submitted to CRAN.
If you want to try Rcmdr 2.7-0, you can download the source tree for the package from R-Forge via svn and build and install it yourself.
Also see some comments below:
> On Nov 25, 2019, at 2:25 PM, Jose G Conde Santiago <jose.conde1 using upr.edu> wrote:
>
> Dear John.
>
> My apologies, and thanks for your patience. This is what I did today:
>
> 1. I read the data set using the R Commander menu “Data” -> “Load dataset”. When I am working with an R workspace, I load the workspace with the “Data” -> “Load dataset” menu, and then read the specific data set in the work space with the “Data set” button.
Once again, the "Data set" button doesn't read a data set, it just makes a data frame in your R workspace the active data set in the Rcmdr. It also closes and reopens the data set viewer for the data set if such a window is open. The source of the error was that the Rcmdr didn't detect that you had closed the viewer window for the data set.
>
> 2. Viewed the data set using R Commander’s “View data set button”.
>
> 3. Closed the “View data set” window.
>
> 4. Try to read the same data set using R Commander’s “Data set” button.
Please see my preceding remark.
>
> Then I get the error message.
>
> After I found the problem with my files,
These aren't files but data frames residing in memory.
I apologize if these distinctions seem pedantic, but the failure to make them made it hard for me to understand your original report of the problem.
Thank you for the bug report.
John
> I tested with a few data sets from the packages in R available thorough the “Data” -> “Data in packages” menu and had the same results. The files are: CO2, airquality and ChickWeight included in the “datasets” package, and ethanol from the “lattice” package.
>
> José
>
> José G. Conde, MD, MPH
> Catedrático
> Escuela de Medicina
> Recinto de Ciencias Médicas
> Universidad de Puerto Rico
>
> Tel (787) 763-9401 Fax (787) 758-5206
>
> Correo electrónico: jose.conde1 using upr.edu
>
>> On Nov 25, 2019, at 11:42 AM, Fox, John <jfox using mcmaster.ca> wrote:
>>
>> Dear José,
>>
>>> On Nov 25, 2019, at 10:17 AM, Jose G Conde Santiago <jose.conde1 using upr.edu> wrote:
>>>
>>> Dear John,
>>>
>>> To keep the session as simple as possible, this time I did not configure R Commander to send the output to the R console.
>>>
>>> This is what I did.
>>>
>>> 1. Load the file/workspace using R Commander.
>>
>> What does this mean? What is a "file/workspace"? How did you "load" it with the R Commander? Can you share the "file/workspace" so that I can replicate what you did?
>>
>>>
>>> 2. Read the data set using R Commander’s “Data set” button.
>>
>> As I said in my earlier response, the R Commander's "Data set" button doesn't "read" a data set -- it chooses from among data frames currently in the user's R workspace.
>>
>>>
>>> 3. View the data set using R Commander’s “View data set button”.
>>>
>>> 4. Close the “View data set” window.
>>>
>>> 5. Try to read the same data set using R Commander’s “Data set” button.
>>>
>>> This is the error message I got today. It was displayed in the R Console, not in the R Commander output window .
>>>
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>> [tcl] bad window path name ".3".
>>>
>>>
>>>
>>> Additional information:
>>>
>>> I tried to “Refresh the active data set” from the “Data” -> “Active Data set” menu, and got the same error message, but with a different number at the end.
>>>
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>> [tcl] bad window path name ".6".
>>>
>>>
>>> I saved the file with a different name, but when I tried to read the file with the new name I got a similar error message.
>>
>> Do you really mean a *file* -- that is stored on your computer's file system -- or a data frame in the R workspace?
>>
>> In either case, if you can share the file or data frame, creating a reproducible example, I'd be much more likely to be able to figure out what's happening.
>>
>> Best,
>> John
>>
>>>
>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>> [tcl] bad window path name ".6".
>>>
>>>
>>> Thanks for your time.
>>>
>>> José
>>>
>>>
>>> José G. Conde, MD, MPH
>>> Catedrático
>>> Escuela de Medicina
>>> Recinto de Ciencias Médicas
>>> Universidad de Puerto Rico
>>>
>>> Tel (787) 763-9401 Fax (787) 758-5206
>>>
>>> Correo electrónico: jose.conde1 using upr.edu
>>>
>>>> On Nov 23, 2019, at 2:44 PM, Fox, John <jfox using mcmaster.ca> wrote:
>>>>
>>>> Dear José,
>>>>
>>>> Please keep the discussion on the r-sig-mac list rather than replying only to me, so that other potentially interested individuals can follow it. I'm therefore cc'ing this response to the list.
>>>>
>>>>> On Nov 22, 2019, at 9:43 PM, Jose G Conde Santiago <jose.conde1 using upr.edu> wrote:
>>>>>
>>>>> Thanks for your prompt reply, John.
>>>>>
>>>>> I clicked on the "Data set" button to read an R dataset. Then I clicked on the "View data set" button to view it, and closed the view window. I tried to read the same file again, and that is where I get the error message.
>>>>
>>>> That's different from what I understood. When you use the "Data set" button in the Rcmdr toolbar you can choose among data sets that have *already* been read into the workspace, assuming that there are more than one.
>>>>
>>>> I still can't duplicate the problem that you report. I can repeatedly select a data set using the button, and each time it becomes the active data set and the data viewer window is refreshed.
>>>>
>>>>> I had the same issue when I tested with R Commander and R, without RStudio.
>>>>
>>>> Yes, I saw that and I can't duplicate the problem in either context.
>>>>
>>>> Best,
>>>> John
>>>>
>>>>>
>>>>> I will check again on Monday with the file you used.
>>>>>
>>>>> Best,
>>>>>
>>>>> José
>>>>>
>>>>> On Fri, Nov 22, 2019, 6:04 PM Fox, John <jfox using mcmaster.ca> wrote:
>>>>> Dear Jose,
>>>>>
>>>>> I'm afraid that I can't duplicate this problem. I tried with the current CRAN version of the Rcmdr under RStudio, reading a text file repeatedly into the same data set. My session info is
>>>>>
>>>>> --------- snip ---------
>>>>>
>>>>>> sessionInfo()
>>>>> R version 3.6.1 (2019-07-05)
>>>>> Platform: x86_64-apple-darwin15.6.0 (64-bit)
>>>>> Running under: macOS Catalina 10.15.1
>>>>>
>>>>> 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_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
>>>>>
>>>>> attached base packages:
>>>>> [1] splines stats graphics grDevices utils datasets methods
>>>>> [8] base
>>>>>
>>>>> other attached packages:
>>>>> [1] Rcmdr_2.6-1 effects_4.1-4 RcmdrMisc_2.5-1 sandwich_2.5-1
>>>>> [5] car_3.0-5 carData_3.0-3
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] Formula_1.2-3 assertthat_0.2.1 latticeExtra_0.6-28
>>>>> [4] cellranger_1.1.0 pillar_1.4.2 backports_1.1.5
>>>>> [7] lattice_0.20-38 glue_1.3.1 digest_0.6.22
>>>>> [10] RColorBrewer_1.1-2 checkmate_1.9.4 minqa_1.2.4
>>>>> [13] colorspace_1.4-1 htmltools_0.4.0 Matrix_1.2-17
>>>>> [16] survey_3.36 pkgconfig_2.0.3 haven_2.2.0
>>>>> [19] purrr_0.3.3 scales_1.0.0 openxlsx_4.1.3
>>>>> [22] rio_0.5.16 lme4_1.1-21 htmlTable_1.13.2
>>>>> [25] tibble_2.1.3 relimp_1.0-5 ggplot2_3.2.1
>>>>> [28] nnet_7.3-12 lazyeval_0.2.2 survival_3.1-7
>>>>> [31] magrittr_1.5 crayon_1.3.4 readxl_1.3.1
>>>>> [34] nlme_3.1-142 MASS_7.3-51.4 forcats_0.4.0
>>>>> [37] foreign_0.8-72 class_7.3-15 tools_3.6.1
>>>>> [40] data.table_1.12.6 hms_0.5.2 mitools_2.4
>>>>> [43] tcltk2_1.2-11 stringr_1.4.0 munsell_0.5.0
>>>>> [46] cluster_2.1.0 zip_2.0.4 compiler_3.6.1
>>>>> [49] e1071_1.7-2 rlang_0.4.1 grid_3.6.1
>>>>> [52] nloptr_1.2.1 rstudioapi_0.10 htmlwidgets_1.5.1
>>>>> [55] tcltk_3.6.1 base64enc_0.1-3 boot_1.3-23
>>>>> [58] gtable_0.3.0 abind_1.4-5 DBI_1.0.0
>>>>> [61] curl_4.2 R6_2.4.0 gridExtra_2.3
>>>>> [64] zoo_1.8-6 knitr_1.25 dplyr_0.8.3
>>>>> [67] zeallot_0.1.0 nortest_1.0-4 Hmisc_4.3-0
>>>>> [70] stringi_1.4.3 Rcpp_1.0.3 vctrs_0.2.0
>>>>> [73] rpart_4.1-15 acepack_1.4.1 tidyselect_0.2.5
>>>>> [76] xfun_0.10
>>>>>
>>>>> --------- snip ---------
>>>>>
>>>>> The output that the Rcmdr generates each time in the RStudio console is
>>>>>
>>>>> Rcmdr> Duncan <-
>>>>> Rcmdr+ read.table("/Users/johnfox/Documents/Courses/2017-2018/ICPSR/Lectures/Duncan.txt",
>>>>> Rcmdr+ header=TRUE, sep="", na.strings="NA", dec=".", strip.white=TRUE)
>>>>> RcmdrMsg: [3] NOTE: The dataset Duncan has 45 rows and 4 columns.
>>>>>
>>>>> Of course, there's a warning each time that Duncan will be overwritten, and the dataset in the viewer is automatically refreshed. That is, AFAICS everything works as it should.
>>>>>
>>>>> You can find the data file I used at <https://socialsciences.mcmaster.ca/jfox/Books/RCommander/Duncan.txt>.
>>>>>
>>>>> Can you elaborate what you did and ideally create a reproducible example of the problem?
>>>>>
>>>>> Best,
>>>>> John
>>>>>
>>>>> -----------------------------
>>>>> John Fox, Professor Emeritus
>>>>> McMaster University
>>>>> Hamilton, Ontario, Canada
>>>>> Web: http::/socserv.mcmaster.ca/jfox
>>>>>
>>>>>> On Nov 22, 2019, at 2:23 PM, Jose G Conde Santiago via R-SIG-Mac <r-sig-mac using r-project.org> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I am using R Commander in combination with RStudio. I configured RStudio to display the output on the RStudio console.
>>>>>>
>>>>>> If I open a file in R Commander, then view the data file in R Commander and then try to read the same file again using R Commander, the following error message is displayed in the console and I cannot read the file with R Commander:
>>>>>>
>>>>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>>>>> [tcl] bad window path name “.29”.
>>>>>>
>>>>>> The message is always the same, except that the number at the end changes. Here are a few more examples:
>>>>>>
>>>>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>>>>> [tcl] bad window path name ".35".
>>>>>>
>>>>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>>>>> [tcl] bad window path name ".51".
>>>>>>
>>>>>>> Error in structure(.External(.C_dotTcl, ...), class = "tclObj") :
>>>>>>> [tcl] bad window path name ".56".
>>>>>>
>>>>>>
>>>>>> Initially, I thought there could be a problem between R Commander and RStudio, but I got the same error message under the same conditions when I tested using R Commander with R alone (without RStudio).
>>>>>>
>>>>>> The files seem to be fine, since I can access them directly with R or with RStudio.
>>>>>>
>>>>>> My computer is an iMac (27-inch, late 2012)
>>>>>> MacOS High Sierra version 10.13.6.
>>>>>> R version 3.6.1
>>>>>> RStudio version 1.2.5001
>>>>>> R Commander version 2.6-0
>>>>>> XQuartz 2.7.11
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> José
>>>>>>
>>>>>> José G. Conde, MD, MPH
>>>>>> Professor, School of Medicine
>>>>>> Medical Sciences Campus
>>>>>> University of Puerto Rico
>>>>>>
>>>>>> Tel (787) 763-9401 Fax (787) 758-5206
>>>>>>
>>>>>> Email: jose.conde1 using upr.edu
>>>>>>
>>>>>> _______________________________________________
>>>>>> R-SIG-Mac mailing list
>>>>>> R-SIG-Mac using r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>
>>>>
>>>
>>
>
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