Dear all,
I have installed oneChannelGUi on a suse machine and when I try to
produce any type of graph I got this error:
error in
structure(.external("dotTcl",...,PACKAGE="tcltk"),class=tclObj):
use of NULL environmnet is defunct)
I attach info:
sessionInfo()
R version 2.6.2 (2008-02-08)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US
.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.
UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8
;LC_IDENTIFICATION=C
attached base packages:
[1] tcltk tools stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] hgu133plus2cdf_2.0.0 tkrplot_0.0-9 oneChannelGUI_1.4.4
[4] tkWidgets_1.16.0 DynDoc_1.16.0 widgetTools_1.14.0
[7] affylmGUI_1.12.0 affy_1.12.2 affyio_1.0.0
[10] limma_2.12.0 Biobase_1.16.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
--
---------------------------------------
Marco Fabbri
Istituto Clinico Humanitas
via Manzoni, 56
20089 Rozzano (Mi)
Tel. 028224 5130
Fax 028224 5101
Hi Marco,
I run oneChannelGUI on a SUN server with SUSE Enterprise
10.0. On monday I will check for your problem.
Could please tell me which graphical output will produce
errors?
oneChannelGUI inherits all the graphical functions of
affylmGUI and , to reduce the RAM consumption
oneChannelGUI specific graphical functions are directed on
the R interface and they are not controlled by tcl/tk.
To understand where the bug is located I need to
understand if it is a problem due to the inherited
affylmGUI graphics or oneChannelGUI specific.
Could you please try to load some 3'IVT affy .CEL files
using affylmGUI and let me know if you encounter the same
problem and on which kind of graphical output?
Cheers
Raffaele
Marco wrote:
>Dear all,
>I have installed oneChannelGUi on a suse machine and when
I try to
>produce any type of graph I got this error:
>
>error in
structure(.external("dotTcl",...,PACKAGE="tcltk"),class=tclObj):
>use of NULL environmnet is defunct)
>
>I attach info:
>
>sessionInfo()
>R version 2.6.2 (2008-02-08)
>i686-pc-linux-gnu
>
>locale:
>LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_U
S.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US
.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-
8;LC_IDENTIFICATION=C
>
>attached base packages:
>[1] tcltk tools stats graphics grDevices
utils datasets
>[8] methods base
>
>other attached packages:
>[1] hgu133plus2cdf_2.0.0 tkrplot_0.0-9
oneChannelGUI_1.4.4
>[4] tkWidgets_1.16.0 DynDoc_1.16.0
widgetTools_1.14.0
>[7] affylmGUI_1.12.0 affy_1.12.2 affyio_1.0.0
>[10] limma_2.12.0 Biobase_1.16.3
>
>loaded via a namespace (and not attached):
>[1] rcompgen_0.1-17
I run affylmGUI with plus2 chip and I got the same error when I try to
produce any type of plot.
I changed the plot option from "Tk R plot" to "R" without any
improvement.
Thank you
Marco
On 17/02/2008, raffaele.calogero at unito.it <raffaele.calogero at="" unito.it=""> wrote:
> Hi Marco,
> I run oneChannelGUI on a SUN server with SUSE Enterprise
> 10.0. On monday I will check for your problem.
> Could please tell me which graphical output will produce
> errors?
> oneChannelGUI inherits all the graphical functions of
> affylmGUI and , to reduce the RAM consumption
> oneChannelGUI specific graphical functions are directed on
> the R interface and they are not controlled by tcl/tk.
> To understand where the bug is located I need to
> understand if it is a problem due to the inherited
> affylmGUI graphics or oneChannelGUI specific.
> Could you please try to load some 3'IVT affy .CEL files
> using affylmGUI and let me know if you encounter the same
> problem and on which kind of graphical output?
> Cheers
> Raffaele
>
> Marco wrote:
> >Dear all,
> >I have installed oneChannelGUi on a suse machine and when
> I try to
> >produce any type of graph I got this error:
> >
> >error in
> structure(.external("dotTcl",...,PACKAGE="tcltk"),class=tclObj):
> >use of NULL environmnet is defunct)
> >
> >I attach info:
> >
> >sessionInfo()
> >R version 2.6.2 (2008-02-08)
> >i686-pc-linux-gnu
> >
> >locale:
> >LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en
_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_
US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT
F-8;LC_IDENTIFICATION=C
> >
> >attached base packages:
> >[1] tcltk tools stats graphics grDevices
> utils datasets
> >[8] methods base
> >
> >other attached packages:
> >[1] hgu133plus2cdf_2.0.0 tkrplot_0.0-9
> oneChannelGUI_1.4.4
> >[4] tkWidgets_1.16.0 DynDoc_1.16.0
> widgetTools_1.14.0
> >[7] affylmGUI_1.12.0 affy_1.12.2 affyio_1.0.0
> >[10] limma_2.12.0 Biobase_1.16.3
> >
> >loaded via a namespace (and not attached):
> >[1] rcompgen_0.1-17
>
>
>
--
---------------------------------------
Marco Fabbri
Istituto Clinico Humanitas
via Manzoni, 56
20089 Rozzano (Mi)
Tel. 028224 5130
Fax 028224 5101
I tested oneChannelGUI on my SUSE server and I do not get
any problem in producing TK plots.
It might be a problem of you TCL-TK library installation.
Check the thread:
http://article.gmane.org/gmane.science.biology.informatics.conductor/1
2496/match=re+bioc+devel+tcl+tk+pckage+bwidget
I hope it helps
Cheers
Raffaele
>
>
> ------------------ Messaggio originale -------------------
> Oggetto: Re: oneChannelGUI problem
> Da: "Marco Fabbri" <fabbri.marco at="" gmail.com="">
> Data: Mar, 19 Febbraio 2008, 10:59 am
> A: "raffaele.calogero at unito.it"
> <raffaele.calogero at="" unito.it="">
> Cc: bioconductor at stat.math.ethz.ch
> ----------------------------------------------------------
>
> I run affylmGUI with plus2 chip and I got the same error
> when I try to
> produce any type of plot.
> I changed the plot option from "Tk R plot" to "R" without
> any improvement.
>
> Thank you
>
> Marco
>
> On 17/02/2008, raffaele.calogero at unito.it
> <raffaele.calogero at="" unito.it=""> wrote:
>> Hi Marco,
>> I run oneChannelGUI on a SUN server with SUSE Enterprise
>> 10.0. On monday I will check for your problem.
>> Could please tell me which graphical output will produce
>> errors?
>> oneChannelGUI inherits all the graphical functions of
>> affylmGUI and , to reduce the RAM consumption
>> oneChannelGUI specific graphical functions are directed
>> on
>> the R interface and they are not controlled by tcl/tk.
>> To understand where the bug is located I need to
>> understand if it is a problem due to the inherited
>> affylmGUI graphics or oneChannelGUI specific.
>> Could you please try to load some 3'IVT affy .CEL files
>> using affylmGUI and let me know if you encounter the
>> same
>> problem and on which kind of graphical output?
>> Cheers
>> Raffaele
>>
>> Marco wrote:
>> >Dear all,
>> >I have installed oneChannelGUi on a suse machine and
>> when
>> I try to
>> >produce any type of graph I got this error:
>> >
>> >error in
>> structure(.external("dotTcl",...,PACKAGE="tcltk"),class=tclObj):
>> >use of NULL environmnet is defunct)
>> >
>> >I attach info:
>> >
>> >sessionInfo()
>> >R version 2.6.2 (2008-02-08)
>> >i686-pc-linux-gnu
>> >
>> >locale:
>> >LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e
n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en
_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U
TF-8;LC_IDENTIFICATION=C
>> >
>> >attached base packages:
>> >[1] tcltk tools stats graphics grDevices
>> utils datasets
>> >[8] methods base
>> >
>> >other attached packages:
>> >[1] hgu133plus2cdf_2.0.0 tkrplot_0.0-9
>> oneChannelGUI_1.4.4
>> >[4] tkWidgets_1.16.0 DynDoc_1.16.0
>> widgetTools_1.14.0
>> >[7] affylmGUI_1.12.0 affy_1.12.2
>> affyio_1.0.0
>> >[10] limma_2.12.0 Biobase_1.16.3
>> >
>> >loaded via a namespace (and not attached):
>> >[1] rcompgen_0.1-17
>>
>>
>>
>
>
> --
> ---------------------------------------
> Marco Fabbri
> Istituto Clinico Humanitas
> via Manzoni, 56
> 20089 Rozzano (Mi)
> Tel. 028224 5130
> Fax 028224 5101
>
>
