help in attach function

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help in attach function

Changbin Du
Hi, r-community,

This morning, I MET the following problem several times when I try to attach
the data set.

When I closed the current console and reopen the R console, the problem
disappear. BUt with the time passed on, the problem occurs again.

Can anyone help me with this?

> attach(total)

    The following object(s) are masked from total ( position 3 ) :

     acid base cell_evalue cell_hit charged freq_cell freq_hypo freq_intra
gene_id gene_name hydrophobic hypo_evalue hypo_hit log_cell log_hypo
log_pfam num_cell num_genes operon_id outcome pfam_align pfam_evalue
pfam_per_id polar position target total_length






--
Sincerely,
Changbin
--

        [[alternative HTML version deleted]]

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Re: help in attach function

Steve Lianoglou-6
Hi,

On Wed, Apr 7, 2010 at 4:24 PM, Changbin Du <[hidden email]> wrote:
> Hi, r-community,
>
> This morning, I MET the following problem several times when I try to attach
> the data set.
>
> When I closed the current console and reopen the R console, the problem
> disappear. BUt with the time passed on, the problem occurs again.
>
> Can anyone help me with this?

Yes, please read the documentation in ?attach

>> attach(total)
>
>    The following object(s) are masked from total ( position 3 ) :
>
>     acid base cell_evalue cell_hit charged freq_cell freq_hypo freq_intra
> gene_id gene_name hydrophobic hypo_evalue hypo_hit log_cell log_hypo
> log_pfam num_cell num_genes operon_id outcome pfam_align pfam_evalue
> pfam_per_id polar position target total_length

Specifically see the documentation for the `warn.conflicts` parameter.

I'm guessing you have (global) variables in your workspace that have
the same name as some of the columns in your `total` data.frame

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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Re: help in attach function

Don MacQueen
You can also read the help page for the conflicts() function. And try
a commend like
    find('acid')
(or any of the objects listed as being masked)
to find out where the two or more objects with the same name are located.

Oh, and looking at ?search would be good also.

-Don

At 4:31 PM -0400 4/7/10, Steve Lianoglou wrote:

>Hi,
>
>On Wed, Apr 7, 2010 at 4:24 PM, Changbin Du <[hidden email]> wrote:
>>  Hi, r-community,
>>
>>  This morning, I MET the following problem several times when I try to attach
>>  the data set.
>>
>>  When I closed the current console and reopen the R console, the problem
>>  disappear. BUt with the time passed on, the problem occurs again.
>>
>>  Can anyone help me with this?
>
>Yes, please read the documentation in ?attach
>
>>>  attach(total)
>>
>>     The following object(s) are masked from total ( position 3 ) :
>>
>>      acid base cell_evalue cell_hit charged freq_cell freq_hypo freq_intra
>>  gene_id gene_name hydrophobic hypo_evalue hypo_hit log_cell log_hypo
>>  log_pfam num_cell num_genes operon_id outcome pfam_align pfam_evalue
>>  pfam_per_id polar position target total_length
>
>Specifically see the documentation for the `warn.conflicts` parameter.
>
>I'm guessing you have (global) variables in your workspace that have
>the same name as some of the columns in your `total` data.frame
>
>--
>Steve Lianoglou
>Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
>Contact Info: http://*cbio.mskcc.org/~lianos/contact
>
>______________________________________________
>[hidden email] mailing list
>https://*stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://*www.*R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.


--
--------------------------------------
Don MacQueen
Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
925-423-1062

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Re: help in attach function

Duncan Murdoch
In reply to this post by Changbin Du
On 07/04/2010 4:24 PM, Changbin Du wrote:

> Hi, r-community,
>
> This morning, I MET the following problem several times when I try to attach
> the data set.
>
> When I closed the current console and reopen the R console, the problem
> disappear. BUt with the time passed on, the problem occurs again.
>
> Can anyone help me with this?
>
>> attach(total)
>
>     The following object(s) are masked from total ( position 3 ) :
>
>      acid base cell_evalue cell_hit charged freq_cell freq_hypo freq_intra
> gene_id gene_name hydrophobic hypo_evalue hypo_hit log_cell log_hypo
> log_pfam num_cell num_genes operon_id outcome pfam_align pfam_evalue
> pfam_per_id polar position target total_length

It appears you are attaching it multiple times, and never detaching it.
  So the most recent one masks an earlier one.

This is a very easy error to make, which is one reason I always
discourage this kind of use of attach().  (There are other common errors
associated with it too.  Just don't use it.)

Duncan Murdoch

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Re: help in attach function

Changbin Du
Thanks so much! Duncan, I appreciated!

On Thu, Apr 8, 2010 at 5:03 AM, Duncan Murdoch <[hidden email]> wrote:

> On 07/04/2010 4:24 PM, Changbin Du wrote:
>
>> Hi, r-community,
>>
>> This morning, I MET the following problem several times when I try to
>> attach
>> the data set.
>>
>> When I closed the current console and reopen the R console, the problem
>> disappear. BUt with the time passed on, the problem occurs again.
>>
>> Can anyone help me with this?
>>
>>  attach(total)
>>>
>>
>>    The following object(s) are masked from total ( position 3 ) :
>>
>>     acid base cell_evalue cell_hit charged freq_cell freq_hypo freq_intra
>> gene_id gene_name hydrophobic hypo_evalue hypo_hit log_cell log_hypo
>> log_pfam num_cell num_genes operon_id outcome pfam_align pfam_evalue
>> pfam_per_id polar position target total_length
>>
>
> It appears you are attaching it multiple times, and never detaching it.  So
> the most recent one masks an earlier one.
>
> This is a very easy error to make, which is one reason I always discourage
> this kind of use of attach().  (There are other common errors associated
> with it too.  Just don't use it.)
>
> Duncan Murdoch
>



--
Sincerely,
Changbin
--

Changbin Du
DOE Joint Genome Institute
Bldg 400 Rm 457
2800 Mitchell Dr
Walnut Creet, CA 94598
Phone: 925-927-2856

        [[alternative HTML version deleted]]

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.