An embedded and charset-unspecified text was scrubbed... Name: not available URL: <https://stat.ethz.ch/pipermail/bioc-devel/attachments/20100717/65b5f7a7/attachment.pl>
[Bioc-devel] suppressing warn from Biobase
4 messages · Bazeley, Peter, Patrick Aboyoun
?suppressWarnings Patrick
On 7/16/10 11:23 PM, Bazeley, Peter wrote:
Dear List, I am creating a package, where one function's name is "combine.quantile.freqs". There is a "combine" method in package Biobase. My package Depends on Biobase, so it is installed. I get the following warning message the first time I use combine.quantile.freqs in a session: Warning message: In findGeneric(f,parent.frame()) : 'combine' is a formal generic function; S3 methods will not likely be found My naming scheme of "combine" followed by a period is causing R to think this is class method (or something along those lines). Is there someway I can suppress this warning message? I could just use a different naming scheme, but I like the way it is. Thank you, Peter Bazeley [[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Oops. I didn't read you message closely enough. Rather placing Biobase in the Depends field, I recommend you place it in the "Imports" field, and then in the NAMESPACE file, import only the symbols that you need. That being said, using "."'s in function names is generally a bad idea for this very reason and should be avoided. Consider using a camel case naming convention, e.g. combineQuantileFreqs, for all your function names. Cheers, Patrick
On 7/17/10 11:50 AM, Patrick Aboyoun wrote:
?suppressWarnings Patrick On 7/16/10 11:23 PM, Bazeley, Peter wrote:
Dear List,
I am creating a package, where one function's name is
"combine.quantile.freqs". There is a "combine" method in package
Biobase. My package Depends on Biobase, so it is installed. I get the
following warning message the first time I use combine.quantile.freqs
in a session:
Warning message:
In findGeneric(f,parent.frame()) :
'combine' is a formal generic function; S3 methods will not likely
be found
My naming scheme of "combine" followed by a period is causing R to
think this is class method (or something along those lines). Is there
someway I can suppress this warning message? I could just use a
different naming scheme, but I like the way it is.
Thank you,
Peter Bazeley
[[alternative HTML version deleted]]
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
1 day later
Thank you, Patrick. I went with the latter option. It seems like a safer move in the long run.
From: Patrick Aboyoun [paboyoun at fhcrc.org]
Sent: Saturday, July 17, 2010 2:02 PM
To: Bazeley, Peter
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] suppressing warn from Biobase
Sent: Saturday, July 17, 2010 2:02 PM
To: Bazeley, Peter
Cc: bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] suppressing warn from Biobase
Oops. I didn't read you message closely enough. Rather placing Biobase in the Depends field, I recommend you place it in the "Imports" field, and then in the NAMESPACE file, import only the symbols that you need. That being said, using "."'s in function names is generally a bad idea for this very reason and should be avoided. Consider using a camel case naming convention, e.g. combineQuantileFreqs, for all your function names. Cheers, Patrick On 7/17/10 11:50 AM, Patrick Aboyoun wrote: > ?suppressWarnings > > Patrick > > > On 7/16/10 11:23 PM, Bazeley, Peter wrote: >> Dear List, >> >> I am creating a package, where one function's name is >> "combine.quantile.freqs". There is a "combine" method in package >> Biobase. My package Depends on Biobase, so it is installed. I get the >> following warning message the first time I use combine.quantile.freqs >> in a session: >> >> Warning message: >> In findGeneric(f,parent.frame()) : >> 'combine' is a formal generic function; S3 methods will not likely >> be found >> >> My naming scheme of "combine" followed by a period is causing R to >> think this is class method (or something along those lines). Is there >> someway I can suppress this warning message? I could just use a >> different naming scheme, but I like the way it is. >> >> >> Thank you, >> Peter Bazeley >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-devel at stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > > _______________________________________________ > Bioc-devel at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel