Re: [Bioc-devel] ddply causes error during R check

2019-02-14 Thread web working 

Hi Martin,

thank you for this approach. I will check my code and see where I can 
use it.


Tobias

Am 12.02.19 um 14:58 schrieb Martin Morgan:

use `globalVariables()` to declare these symbols and quieten warnings, at the 
expense of quietening warnings about undefined variables in _all_ code and 
potentially silencing true positives. Avoid non-standard evaluation (this is 
what ddply is doing, using special rules to resolve symbols like `name`) by 
using base R functionality; note also that non-standard evaluation is prone to 
typos, e.g., looking for the typo `hpx` in the calling environment rather than 
the data frame


hpx = 1
ddply(mtcars, "cyl", "summarize", value = mean(hpx)).  ## oops, meant 
`mean(hp)`.

   cyl summarize
1   4 1
2   6 1
3   8 1

Marginally better is


aggregate(hp ~ cyl, mtcars, mean)

   cylhp
1   4  82.63636
2   6 122.28571
3   8 209.21429

where R recognizes symbols in the formula ~ as intentionally unresolved. The 
wizards on the list might point to constructs in the rlang package.

Martin

On 2/12/19, 2:35 AM, "Bioc-devel on behalf of web working" 
 wrote:

 Hi,
 
 I am developing a Bioconductor package and can not get rid of some

 warning messages. During devtools::check() I get the following warning
 messages:
 
 ...

 summarizeDataFrame: no visible binding for global variable ‘name’
 summarizeDataFrame: no visible binding for global variable ‘gene’
 summarizeDataFrame: no visible binding for global variable ‘value’
 ...
 
 Here a short version of the function:
 
 #' Collapse rows with duplicated name column

 #'
 #' @param dat a \cite{tibble} with the columns name, gene and value
 #' @importFrom plyr ddply
 #' @import tibble
 #' @return a \cite{tibble}
 #' @export
 #'
 #' @examples
 #' dat <- tibble(name = c(paste0("position", 1:5), paste0("position",
 c(1:3))), gene = paste0("gene", 1:8), value = 1:8)
 #' summarizeDataFrame(dat)
 summarizeDataFrame <- function(dat){
ddply(dat, "name", "summarize",
  name=unique(name),
  gene=paste(unique(gene), collapse = ","),
  value=mean(value))
 }
 
 R interprets the "name", "gene" and "value" column names as variables

 during the check. Does anyone has an idea how to change the syntax of
 ddply or how to get rid of the warning message?
 
 Thanks in advance!
 
 Tobias
 
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Re: [Bioc-devel] ddply causes error during R check

2019-02-14 Thread web working 
Hi Mike,

thank you for pointing out that there are other package which have the 
same situation.

Tobias

Am 12.02.19 um 14:47 schrieb Mike Smith:
> If you're sure these are false positives (and it looks like they are) 
> then you can use utils::globalVariables() outside of your function to 
> get rid of the note.  It might also be worth pointing out that there 
> are also plenty of Bioconductor packages that don't do this and simply 
> have this mentioned in the check results e.g 
> http://bioconductor.org/checkResults/devel/bioc-LATEST/beadarray/malbec2-checksrc.html
>  
> .
>
> Mike
>
> On Tue, 12 Feb 2019 at 08:35, web working  > wrote:
>
> Hi,
>
> I am developing a Bioconductor package and can not get rid of some
> warning messages. During devtools::check() I get the following
> warning
> messages:
>
> ...
> summarizeDataFrame: no visible binding for global variable ‘name’
> summarizeDataFrame: no visible binding for global variable ‘gene’
> summarizeDataFrame: no visible binding for global variable ‘value’
> ...
>
> Here a short version of the function:
>
> #' Collapse rows with duplicated name column
> #'
> #' @param dat a \cite{tibble} with the columns name, gene and value
> #' @importFrom plyr ddply
> #' @import tibble
> #' @return a \cite{tibble}
> #' @export
> #'
> #' @examples
> #' dat <- tibble(name = c(paste0("position", 1:5), paste0("position",
> c(1:3))), gene = paste0("gene", 1:8), value = 1:8)
> #' summarizeDataFrame(dat)
> summarizeDataFrame <- function(dat){
>    ddply(dat, "name", "summarize",
>  name=unique(name),
>  gene=paste(unique(gene), collapse = ","),
>  value=mean(value))
> }
>
> R interprets the "name", "gene" and "value" column names as variables
> during the check. Does anyone has an idea how to change the syntax of
> ddply or how to get rid of the warning message?
>
> Thanks in advance!
>
> Tobias
>
> ___
> Bioc-devel@r-project.org  mailing
> list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] ddply causes error during R check

2019-02-12 Thread Martin Morgan 
use `globalVariables()` to declare these symbols and quieten warnings, at the 
expense of quietening warnings about undefined variables in _all_ code and 
potentially silencing true positives. Avoid non-standard evaluation (this is 
what ddply is doing, using special rules to resolve symbols like `name`) by 
using base R functionality; note also that non-standard evaluation is prone to 
typos, e.g., looking for the typo `hpx` in the calling environment rather than 
the data frame

> hpx = 1
> ddply(mtcars, "cyl", "summarize", value = mean(hpx)).  ## oops, meant 
> `mean(hp)`.
  cyl summarize
1   4 1
2   6 1
3   8 1

Marginally better is

> aggregate(hp ~ cyl, mtcars, mean)
  cylhp
1   4  82.63636
2   6 122.28571
3   8 209.21429

where R recognizes symbols in the formula ~ as intentionally unresolved. The 
wizards on the list might point to constructs in the rlang package.

Martin

On 2/12/19, 2:35 AM, "Bioc-devel on behalf of web working" 
 wrote:

Hi,

I am developing a Bioconductor package and can not get rid of some 
warning messages. During devtools::check() I get the following warning 
messages:

...
summarizeDataFrame: no visible binding for global variable ‘name’
summarizeDataFrame: no visible binding for global variable ‘gene’
summarizeDataFrame: no visible binding for global variable ‘value’
...

Here a short version of the function:

#' Collapse rows with duplicated name column
#'
#' @param dat a \cite{tibble} with the columns name, gene and value
#' @importFrom plyr ddply
#' @import tibble
#' @return a \cite{tibble}
#' @export
#'
#' @examples
#' dat <- tibble(name = c(paste0("position", 1:5), paste0("position", 
c(1:3))), gene = paste0("gene", 1:8), value = 1:8)
#' summarizeDataFrame(dat)
summarizeDataFrame <- function(dat){
   ddply(dat, "name", "summarize",
 name=unique(name),
 gene=paste(unique(gene), collapse = ","),
 value=mean(value))
}

R interprets the "name", "gene" and "value" column names as variables 
during the check. Does anyone has an idea how to change the syntax of 
ddply or how to get rid of the warning message?

Thanks in advance!

Tobias

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Re: [Bioc-devel] ddply causes error during R check

2019-02-12 Thread Mike Smith 
If you're sure these are false positives (and it looks like they are) then
you can use utils::globalVariables() outside of your function to get rid of
the note.  It might also be worth pointing out that there are also plenty
of Bioconductor packages that don't do this and simply have this mentioned
in the check results e.g
http://bioconductor.org/checkResults/devel/bioc-LATEST/beadarray/malbec2-checksrc.html
 .

Mike

On Tue, 12 Feb 2019 at 08:35, web working  wrote:

> Hi,
>
> I am developing a Bioconductor package and can not get rid of some
> warning messages. During devtools::check() I get the following warning
> messages:
>
> ...
> summarizeDataFrame: no visible binding for global variable ‘name’
> summarizeDataFrame: no visible binding for global variable ‘gene’
> summarizeDataFrame: no visible binding for global variable ‘value’
> ...
>
> Here a short version of the function:
>
> #' Collapse rows with duplicated name column
> #'
> #' @param dat a \cite{tibble} with the columns name, gene and value
> #' @importFrom plyr ddply
> #' @import tibble
> #' @return a \cite{tibble}
> #' @export
> #'
> #' @examples
> #' dat <- tibble(name = c(paste0("position", 1:5), paste0("position",
> c(1:3))), gene = paste0("gene", 1:8), value = 1:8)
> #' summarizeDataFrame(dat)
> summarizeDataFrame <- function(dat){
>ddply(dat, "name", "summarize",
>  name=unique(name),
>  gene=paste(unique(gene), collapse = ","),
>  value=mean(value))
> }
>
> R interprets the "name", "gene" and "value" column names as variables
> during the check. Does anyone has an idea how to change the syntax of
> ddply or how to get rid of the warning message?
>
> Thanks in advance!
>
> Tobias
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] ddply causes error during R check

2019-02-11 Thread web working 

Hi,

I am developing a Bioconductor package and can not get rid of some 
warning messages. During devtools::check() I get the following warning 
messages:


...
summarizeDataFrame: no visible binding for global variable ‘name’
summarizeDataFrame: no visible binding for global variable ‘gene’
summarizeDataFrame: no visible binding for global variable ‘value’
...

Here a short version of the function:

#' Collapse rows with duplicated name column
#'
#' @param dat a \cite{tibble} with the columns name, gene and value
#' @importFrom plyr ddply
#' @import tibble
#' @return a \cite{tibble}
#' @export
#'
#' @examples
#' dat <- tibble(name = c(paste0("position", 1:5), paste0("position", 
c(1:3))), gene = paste0("gene", 1:8), value = 1:8)

#' summarizeDataFrame(dat)
summarizeDataFrame <- function(dat){
  ddply(dat, "name", "summarize",
    name=unique(name),
    gene=paste(unique(gene), collapse = ","),
    value=mean(value))
}

R interprets the "name", "gene" and "value" column names as variables 
during the check. Does anyone has an idea how to change the syntax of 
ddply or how to get rid of the warning message?


Thanks in advance!

Tobias

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