[BUGZILLA #14910] Black pop-up window produced by TCL-TK in windows

MichaelChirico commented 4 years ago

Created attachment 1293 [details] black popup windows produced by TCL-TK in windows

I am the maintainer of oneChannleGUI, a graphical interface of Bioconductor. I have recently observed a critical behaviour in TCL TK windows under windows 7 When the interface call a popup window the window is visualized as a black window (see attached pdf). The only possibility to access to the information inside the window is maximizing the popup windows from the windows bar menu. The problem is present only in windows7 since we extensively tested both linux and mac OS version of the package without observing any problem. It seems like the grafic window and the functional contents inside it are not presented on the screen in the same locations.

cheers Raffaele

sessionInfo()

R version 2.15.0 (2012-03-30) Platform: x86_64-pc-mingw32/x64 (64-bit)

locale: [1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252 LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C LC_TIME=Italian_Italy.1252

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

other attached packages: [1] oneChannelGUI_1.22.0 Rsamtools_1.8.0 Biostrings_2.24.1 GenomicRanges_1.8.3 IRanges_1.14.2 tkWidgets_1.34.0 DynDoc_1.34.0 widgetTools_1.34.0
[9] affylmGUI_1.30.0 affyio_1.24.0 affy_1.34.0 limma_3.12.0 Biobase_2.16.0 BiocGenerics_0.2.0

loaded via a namespace (and not attached): [1] BiocInstaller_1.4.3 bitops_1.0-4.1 preprocessCore_1.18.0 stats4_2.15.0 zlibbioc_1.2.0

METADATA

Bug author - raffaele.calogero
Creation time - 2012-05-08 12:33:00 UTC
Bugzilla link
Status - CLOSED CONTRIBUTED PACKAGE
Alias - None
Component - Windows GUI / Window specific
Version - R 2.15.0
Hardware - x86_64/x64/amd64 (64-bit) Other
Importance - P5 major
Assignee - R-core
URL -
Modification time - 2012-12-18 11:51 UTC

MichaelChirico commented 4 years ago

Please provide self-contained code to duplicate the bug. If possible, extract the code that displays the window from the packages, so only base packages need to be installed. (If that's not possible, it could well be that one of those other packages contains the bug, not R.)

METADATA

Comment author - Duncan Murdoch
Timestamp - 2012-05-08 14:42:07 UTC

MichaelChirico commented 4 years ago

(In reply to comment #1)

Please provide self-contained code to duplicate the bug.  If possible,
extract
the code that displays the window from the packages, so only base packages
need
to be installed.  (If that's not possible, it could well be that one of those
other packages contains the bug, not R.)

The problem applys, as far as I know, to the use of two GUI of Bioconductor, affylmGUI and oneChannelGUI. oneChannelGUI, is inheriting the vast majority of the graphical environment of affylmGUI. AffylmGUI can be installed with the following code: source("http://bioconductor.org/biocLite.R") biocLite("affylmGUI")

After loading the library: library(affylmGUI) if you issue multiple times the command that generates the frame for folder definition: SetWD()

SetWD
function () { WD <- chooseDir() if (!nchar(WD)) { tkfocus(.affylmGUIglobals$ttMain) return("") } Try(setwd(WD)) tkfocus(.affylmGUIglobals$ttMain) return(WD) }

In an erratic way you get the black window, I described. The following is a little statistics I generated running mutilple times SetWD() black windows appears after: 3 normal windows 3 normal windows 10 normal windows 6 normal windows Exit from R and repeating: 3 normal windows 3 normal windows 11 normal windows 5 normal windows Exit from R and repeating: 3 normal windows 2 normal windows 13 normal windows 1 normal windows

The problem however, is not limited to SetWD() but to any of the windows generated by the GUI The error is only present in windows 7 installation and it never appears in linux or Mac OS

METADATA

Comment author - raffaele.calogero
Timestamp - 2012-05-08 16:10:42 UTC

MichaelChirico commented 4 years ago

On 08/05/2012 11:10 AM, r-bugs@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>-project.org wrote:

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14910

--- Comment #2 from raffaele.calogero@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> 2012-05-08 11:10:42 EDT ---
(In reply to comment #1)
>  Please provide self-contained code to duplicate the bug.  If possible,
extract
>  the code that displays the window from the packages, so only base packages
need
>  to be installed.  (If that's not possible, it could well be that one of
those
>  other packages contains the bug, not R.)
The problem applys, as far as I know, to the use of two GUI of Bioconductor,
affylmGUI and oneChannelGUI. oneChannelGUI, is inheriting the vast majority
of
the graphical environment of affylmGUI.

What makes you think this is a problem in R, rather than in affylmGUI or one of the packages it uses?

Duncan Murdoch

AffylmGUI can be installed with the following code:
source("http://bioconductor.org/biocLite.R")
biocLite("affylmGUI")

After loading the library:
library(affylmGUI)
if you issue multiple times the command that generates the frame for folder
definition:
SetWD()

SetWD
function ()
{
WD<- chooseDir()
if (!nchar(WD)) {
tkfocus(.affylmGUIglobals$ttMain)
return("")
}
Try(setwd(WD))
tkfocus(.affylmGUIglobals$ttMain)
return(WD)
}

In an erratic way you get the black window, I described.
The following is a little statistics I generated running mutilple times
SetWD()
black windows appears after:
3 normal windows
3 normal windows
10 normal windows
6 normal windows
Exit from R and repeating:
3 normal windows
3 normal windows
11 normal windows
5 normal windows
Exit from R and repeating:
3 normal windows
2 normal windows
13 normal windows
1 normal windows

The problem however, is not limited to SetWD() but to any of the windows
generated by the GUI
The error is only present in windows 7 installation and it never appears in
linux or Mac OS

METADATA

Comment author - Duncan Murdoch
Timestamp - 2012-05-08 20:18:27 UTC

MichaelChirico commented 4 years ago

Referring to comment #3 Yes I think is a problem of R because if you run affylmGUI under Mac OS or linux I never observe the black window problem. Since I am running many introductory courses on microarray/RNA-seq data analysis using the affylmGUI/oneChannelGUI interfaces I had to move from windows to linux installation to avoid the black window problem, which never appear running affylmGUI or oneChannelGUI on linux based machines. Cheers Raffaele

P.S: concernig MAC OS I ma developing oneChannelGUI on may mac and runing 100 times the code in comment 2 I never got the black window.

####################### Mac OS Lion:

sessionInfo()

Searching for user-defined affylmGUI commands in /Library/Frameworks/R.framework/Versions/2.15/Resources/library/affylmGUI/etc ...

sessionInfo()

R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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] tcltk stats graphics grDevices utils datasets methods base

other attached packages: [1] affylmGUI_1.30.0 affyio_1.24.0 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 [6] limma_3.12.0

loaded via a namespace (and not attached): [1] BiocInstaller_1.4.4 preprocessCore_1.18.0 zlibbioc_1.2.0

######################## Suse Enterprise 11: sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit)

locale: [1] LC_CTYPE=en_US.ISO-8859-1 LC_NUMERIC=C
[3] LC_TIME=en_US.ISO-8859-1 LC_COLLATE=en_US.ISO-8859-1
[5] LC_MONETARY=en_US.ISO-8859-1 LC_MESSAGES=en_US.ISO-8859-1
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.ISO-8859-1 LC_IDENTIFICATION=C

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

other attached packages: [1] affylmGUI_1.30.0 affyio_1.24.0 affy_1.34.0 Biobase_2.16.0
[5] BiocGenerics_0.2.0 limma_3.12.0

loaded via a namespace (and not attached): [1] BiocInstaller_1.4.4 preprocessCore_1.18.0 zlibbioc_1.2.0

METADATA

Comment author - raffaele.calogero
Timestamp - 2012-05-09 07:06:50 UTC

MichaelChirico commented 4 years ago

On 12-05-09 2:06 AM, r-bugs@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>-project.org wrote:

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14910

--- Comment #3 from Duncan Murdoch<murdoch@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>>  2012-05-08 15:18:27
EDT ---
On 08/05/2012 11:10 AM, r-bugs@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>-project.org wrote:
> https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14910
>
> --- Comment #2 from raffaele.calogero@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> 2012-05-08 11:10:42 EDT ---
> (In reply to comment #1)
>>   Please provide self-contained code to duplicate the bug.  If possible,
>>   extract
>>   the code that displays the window from the packages, so only base
>>   packages need
>>   to be installed.  (If that's not possible, it could well be that one of
>>   those
>>   other packages contains the bug, not R.)
> The problem applys, as far as I know, to the use of two GUI of Bioconductor,
> affylmGUI and oneChannelGUI. oneChannelGUI, is inheriting the vast majority
> of
> the graphical environment of affylmGUI.

What makes you think this is a problem in R, rather than in affylmGUI or
one of the packages it uses?

Duncan Murdoch
--- Comment #4 from raffaele.calogero@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::> 2012-05-09 02:06:50 EDT ---
Referring to comment #3
Yes I think is a problem of R because if you run affylmGUI under Mac OS or
linux I never observe the black window problem.

I don't see how that is relevant. Please show me how to reproduce the problem without any of the contributed packages, or report the problem to their maintainers.

Duncan Murdoch

Since I am running many introductory courses on microarray/RNA-seq data
analysis using the affylmGUI/oneChannelGUI interfaces I had to move from
windows to linux installation to avoid the black window problem, which never
appear running affylmGUI or oneChannelGUI on linux based machines.

Cheers
Raffaele

P.S: concernig MAC OS I ma developing oneChannelGUI on may mac and runing 100
times the code in comment 2 I never got the black window.

METADATA

Comment author - Duncan Murdoch
Timestamp - 2012-05-09 16:49:16 UTC

MichaelChirico commented 4 years ago

I contacted the affylmGUI maintainer to help me to produce a code that allow to simulate the problem we have observed. I will be back to you shortly Cheers Raffaele

METADATA

Comment author - raffaele.calogero
Timestamp - 2012-05-11 15:00:04 UTC

MichaelChirico commented 4 years ago

This problem can also be observed with the 'debug' package under Windows, but I've never seen it under GNU/Linux. The behavior is documented under the 'Display Bugs:' section of the 'help("debug-package", package = "debug")' page.

METADATA

Comment author - Henric Winell
Timestamp - 2012-05-17 13:46:40 UTC

MichaelChirico commented 4 years ago

Same problem with Rcmdr on Windows 7 (64bit) / R 2.15.0 (32 and 64bit) and ActiveTCL 8.4 and 8.5.

METADATA

Comment author - werner
Timestamp - 2012-05-18 13:22:40 UTC

MichaelChirico commented 4 years ago

On 18.05.2012 14:22, r-bugs@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>-project.org wrote:

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14910

werner<werner.wackernagel@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>>  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
CC|                            |werner.wackernagel@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>
|                            |az.at

--- Comment #8 from werner<werner.wackernagel@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>>  2012-05-18
08:22:40 EDT ---
Same problem with Rcmdr on Windows 7 (64bit) / R 2.15.0 (32 and 64bit) and
ActiveTCL 8.4 and 8.5.

This does not help to reproduce the bug for us, as Duncan said earlier: "Please show me how to reproduce the problem without any of the contributed packages, or report the problem to their maintainers."

Best, Uwe Ligges

METADATA

Comment author - Uwe Ligges
Timestamp - 2012-05-18 18:11:57 UTC

MichaelChirico commented 4 years ago

On 12-05-18 8:22 AM, r-bugs@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>-project.org wrote:

https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14910

werner<werner.wackernagel@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>>  changed:

What    |Removed                     |Added
----------------------------------------------------------------------------
CC|                            |werner.wackernagel@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>
|                            |az.at

--- Comment #8 from werner<werner.wackernagel@<::CENSORED -- SEE ORIGINAL ON BUGZILLA::>>  2012-05-18
08:22:40 EDT ---
Same problem with Rcmdr on Windows 7 (64bit) / R 2.15.0 (32 and 64bit) and
ActiveTCL 8.4 and 8.5.

I'll repeat this a third time:

So far I have no set of instructions for making this reproducible using base packages. I won't work on it without that.

Duncan Murdoch

METADATA

Comment author - Duncan Murdoch
Timestamp - 2012-05-18 19:37:13 UTC

MichaelChirico commented 4 years ago

As no demo code using base packages has been produced, I'll assume this bug is due to one of the contributed packages involved.

METADATA

Comment author - Duncan Murdoch
Timestamp - 2012-06-02 18:21:24 UTC

MichaelChirico commented 4 years ago

(V odpovědi na komentář #11)

As no demo code using base packages has been produced, I'll assume this bug
is
due to one of the contributed packages involved.

I have found the demonstrate code of this bug. Situation: fresh instalation 2.15.2 on Win 7 (64bit) only basic packages

sessionInfo()

R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit)

locale: [1] LC_COLLATE=Czech_Czech Republic.1250 LC_CTYPE=Czech_Czech Republic.1250
[3] LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C
[5] LC_TIME=Czech_Czech Republic.1250

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

loaded via a namespace (and not attached): [1] tools_2.15.2

execute

demo(tkttest)

After few attempts (sometimes 3-6x) the black window is apeared. No matter 32-bit, 64-bit or R2.15.x. I have tried it on Win XP with R2.15 and the window only freeze the black color is missing. The old version R2.13.x is OK.

Cheers Lubomir

METADATA

Comment author - Lubomir Pavliska
Timestamp - 2012-12-18 11:51:27 UTC

MichaelChirico / r-bugs