[R] rJython matrix message

[Steve Lianoglou]

Hi,

On Wed, Sep 14, 2011 at 12:01 PM, Ben qant <ccquant at gmail.com> wrote:
> That fixed it!! Thank you very much! I should have thought of that.

For the sake of others that might stumble on this thread -- what fixed
it, exactly?

Doing paste(errs, collapse="\\n"), or the writing to a tmp file thing, or?

-steve

>
> Thanks again,
>
> Ben
>
> On Wed, Sep 14, 2011 at 9:57 AM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>>
>> Hi,
>>
>> On Wed, Sep 14, 2011 at 11:44 AM, Ben qant <ccquant at gmail.com> wrote:
>> > Hello,
>> >
>> > I've posted something similar under a different subject and never
>> > received a
>> > solution. Trying again with (hopefully) a better description.
>> >
>> > Objective: Send a matrix of string data in an email message. The message
>> > must have authentication and be sent via an R script.
>> >
>> > I'm almost there!
>> >
>> > Here is where I am at:
>> > I collect long error message lines in 'errs', which is a matrix.
>>
>> (I might collect this into a list, but that's just a matter of style)
>>
>>
>> > Then I collapse them into a character vector via:
>> >
>> > errs = paste(errs, collapse = "")
>> >
>> > Then I send that in a email via rJython. The message is sent to an
>> > Microsoft
>> > Outlook address like this:
>> >
>> > mail = c(  ....etc...
>> > paste("msg = MIMEText('",errs,"')",sep=""),
>> > ...etc....)
>> >
>> > ...etc... [the rest of the rJython stuff to send a message omitted here]
>> >
>> > jython.exec(rJython,mail)
>> >
>> > The problem: The issue is that the message wraps the text in the body of
>> > the
>> > message so that the message just looks like one big line of text which
>> > makes
>> > it very difficult to read (aka is not acceptable).
>> >
>> > Notes:
>> > 1) The message must have authentication; therefore, I am using rJython.
>> > (My
>> > understanding is that there is no R way to send an email message with
>> > authentication.)
>> > 2) I have to receive the message in Outlook.
>> > 3) When I do errs = paste(errs, collapse = "\n"), and pass that as the
>> > message text, rJython gives me an error:
>> > Error in ls(envir = envir, all.names = private) :
>> >  invalid 'envir' argument
>>
>> It's hard to imagine why this would happen. using `paste(errs,
>> collapse="")` vs. `paste(errs, collapse="\n")` will provide you with
>> one character vector/string, so I've got to believe the problem is
>> somewhere else.
>>
>> Just a stab in the dark, but does `paste(errs, collapse="\\n")` give
>> you problems?
>>
>> What if you take your `errs = paste(errs, collapse="\n")` and call
>> `writeLines` on `errs` to a tmp file that you provide the path for to
>> rJython, which then reads the file and append into a message.
>>
>> Also -- if you want to be reading the file "normally" on windows,
>> shouldn't you be using windows line endings (I think "\r\n"), or does
>> outlook recognize "\n" as a new line (I'm imagining if you do get the
>> whole thing to work, outlook might still just show you one long line
>> since "\n" alone isn't recognized as a newline command on windows
>> (last time I checked)).
>>
>> -steve
>>
>> --
>> 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
>
>



-- 
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