Please see the notes which are produced after run the BiocCheck function to test my package.
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 98 lines long
The longest 5 functions are:
predict.sigFeature() (R/predict.R, line 21): 98 lines
sigFeatureFrequency() (R/sigFeatureFrequency.R, line 22): 59 lines
svmrfeFeatureRanking() (R/svmrfeFeatureRanking.R, line 25): 30 lines
PlotErrors() (R/PlotErrors.R, line 20): 27 lines
sigFeature() (R/sigFeature.R, line 21): 27 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; 1 lines (0%) are > 80 characters long.
First 1 lines:
vignettes/vignettes.Rmd:2 title: "sigFeature: an R-package for significant feature selection using SVM-RFE & t...
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: 5
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; 1 lines (0%) are > 80 characters long."
[4] "Remove generated comments from man pages predict.Rd, sigCVError.Rd, sigFeaturePvalue.Rd, svmrfeFeatureRanking.Rd"
[5] "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"
Please anybody help me to address those NOTEs.
Thank you
regards
Pijush
