Question: (Closed) Please help to address the BiocCheck NOTEs
0
gravatar for Pijush Das
2.9 years ago by
Pijush Das10
India
Pijush Das10 wrote:

Please see the notes produced by the BiocCheck after run the BiocCheck function.

>This is BiocCheck version 1.15.9. BiocCheck is a work in progress. Output and severity of issues may
>
>change. Installing package...
>
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set loaded
      with data(), or perhaps part of an object referenced in with() or within().
    object (function)
      as (predict.sigFeature)
      new (predict.sigFeature)
* Checking vignette directory...
    This is a software package
    # of chunks: 21, # of eval=FALSE: 0 (0%)
* Checking version number...
    Checking version number validity...
    Package version 0.99.0; pre-release
* Checking R Version dependency...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
    Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking unit tests...
    * NOTE: Consider adding unit tests. We strongly encourage them. See
      http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking library calls...
* Checking coding practice...
* Checking native routine registration...
* Checking for deprecated package usage...
* Checking parsed R code in R directory, examples, vignettes...
* Checking for direct slot access...
* Checking for T...
* Checking for F...
* Checking for browser()...
* Checking for <<-...
* Checking for library/require of sigFeature...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking function lengths........................
    The longest function is 83 lines long
    The longest 5 functions are:
    predict.sigFeature() (R/predict.R, line 21): 83 lines
    sigFeatureFrequency() (R/sigFeatureFrequency.R, line 22): 54 lines
    svmrfeFeatureRanking() (R/svmrfeFeatureRanking.R, line 25): 30 lines
    sigFeature() (R/sigFeature.R, line 21): 24 lines
    PlotErrors() (R/PlotErrors.R, line 20): 23 lines
* Checking man pages...
* Checking exported objects have runnable examples...
* Checking package NEWS...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source...
    * NOTE: Consider shorter lines; 161 lines (9%) are > 80 characters long.
    First 6 lines:
      R/PlotErrors.R:22     SigFe=unlist(lapply(featsweepSigFe, function(x) ifelse(is.null(x), NA, x$error)))
      R/PlotErrors.R:26     sigFeSD=unlist(lapply(featsweepSigFe, function(x) ifelse(is.null(x), NA, x$errorSD)))
      R/PlotErrors.R:34     plot(ym, SigFe_1, type="l", col="green", lwd=2, xlab="Number of Features", ylab="Mean ex...
      R/PlotErrors.R:38     plot(ym, sigFe_2, type="l", col="blue", lwd=2, xlab="Number of Features", ylab="Standard...
      R/predict.R:21 predict.sigFeature <- function (object, newdata, decision.values=FALSE, probability=FALSE, ... ...
      R/predict.R:32     newdata<-new("matrix.csr", ra=newdata$v[ind], ja=newdata$j[ind], ia=as.integer(cumsum(c(1, ...
    * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
    First 1 lines:
      man/PlotErrors.Rd:23     .. ..$ :'data.frame':    1 obs. of  4 variables:
    * NOTE: Consider multiples of 4 spaces for line indents, 356 lines(20%) are not.
    First 6 lines:
      R/predict.R:23   if(missing(newdata)){ return(fitted(object)) }
      R/predict.R:24   if(object$tot.nSV < 1){stop("Model is empty!")}
      R/predict.R:25   if(inherits(newdata, "Matrix")){
      R/predict.R:26      loadNamespace("SparseM")
      R/predict.R:27      loadNamespace("Matrix")
      R/predict.R:28      newdata <- as(newdata, "matrix.csr")}
    See http://bioconductor.org/developers/how-to/coding-style/
* Checking for canned comments in man pages...
    * NOTE: Remove generated comments from man pages predict.Rd, sigCVError.Rd, sigFeaturePvalue.Rd,
      svmrfeFeatureRanking.Rd
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
    * NOTE: Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires
      admin credentials).  Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
    Maintainer is registered at support site.


Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 7
For detailed information about these checks, see the BiocCheck vignette, available at
https://bioconductor.org/packages/3.7/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
$`error`
character(0)

$warning
character(0)

$note
[1] "Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set loaded with data(), or perhaps part of an object referenced in with() or within()."        
[2] "Consider adding unit tests. We strongly encourage them. See\n  http://bioconductor.org/developers/how-to/unitTesting-guidelines/."                                                
[3] "Consider shorter lines; 161 lines (9%) are > 80 characters long."                                                                                                                 
[4] "Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs."                                                                                                                    
[5] "Consider multiples of 4 spaces for line indents, 356 lines(20%) are not."                                                                                                         
[6] "Remove generated comments from man pages predict.Rd, sigCVError.Rd, sigFeaturePvalue.Rd, svmrfeFeatureRanking.Rd"                                                                 
[7] "Cannot determine whether maintainer is subscribed to the bioc-devel mailing list (requires admin\ncredentials).  Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel"

Can anybody help me to understand all the NOTEs generated by the BiocCheck 1) How to do the unit test in the package? When I am writing a line it automatically change its length if I move the screen size in RStudio. I do not understand how to maintain the line size less than 80 characters. If you move the screen size of the RStudio the line can be made big or small. So how can I determine the 80 characters size. Please help

2) I do not understand the NOTE no 4 and 5 . I have backspace the line and press the spaces with 4 number multiple times but Each time it shows the same results.

3) I do not understand what is "generated comments" commands. Please help me to understand that.

4) I already have enlisted my email id in bioc-devel mailing list but Whay the last NOTE is showing I do not know.

Please help me.

R • 998 views
ADD COMMENTlink modified 2.9 years ago by GenoMax96k • written 2.9 years ago by Pijush Das10

This looks better suited to the Bioconductor forum.

ADD REPLYlink written 2.9 years ago by Jean-Karim Heriche24k

Hello Pijush Das!

We believe that this post does not fit the main topic of this site.

Please ask https://support.bioconductor.org

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 2.9 years ago by Ram32k
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