[R-SIG-Mac] Error message reading files in R Commander
Jose G Conde Santiago
jo@e@conde1 @end|ng |rom upr@edu
Tue Nov 26 13:57:07 CET 2019
Thanks a lot, John.
José
On Mon, Nov 25, 2019, 9:21 PM Fox, John <jfox using mcmaster.ca> wrote:
> 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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