R CMD check NOTES:
Issue #32
resolved
* checking DESCRIPTION meta-information ... NOTE
Deprecated license: CC BY-NC-SA 3.0
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking R code for possible problems ... NOTE
countClones: no visible binding for global variable ‘SEQ_COUNT’
countClones: no visible binding for global variable ‘COPY_COUNT’
countGenes: no visible binding for global variable ‘SEQ_COUNT’
countGenes: no visible binding for global variable ‘COPY_COUNT’
estimateAbundance: no visible binding for global variable ‘COUNT’
estimateAbundance: no visible binding for global variable ‘P’
getPropertyData: no visible binding for global variable ‘aaindex’
getPropertyData: no visible binding for global variable ‘pK’
plotAbundance: no visible binding for global variable ‘RANK’
plotAbundance: no visible binding for global variable ‘P’
plotAbundance: no visible binding for global variable ‘GROUP’
plotAbundance: no visible binding for global variable ‘.x’
plotAbundance: no visible binding for global variable ‘LOWER’
plotAbundance: no visible binding for global variable ‘UPPER’
plotDiversityCurve: no visible binding for global variable ‘group’
plotDiversityCurve: no visible binding for global variable ‘lower’
plotDiversityCurve: no visible binding for global variable ‘upper’
plotDiversityCurve: no visible binding for global variable ‘.x’
rarefyDiversity: no visible binding for global variable ‘COUNT’
rarefyDiversity: no visible binding for global variable ‘SEQUENCES’
testDiversity: no visible binding for global variable ‘COUNT’
testDiversity: no visible binding for global variable ‘SEQUENCES’
Comments (6)
-
reporter -
Valid licenses according to CRAN: https://svn.r-project.org/R/trunk/share/licenses/license.db
-
reporter CRAN says we need to use 'CC BY-NC-SA 4.0'. Using this also solves NOTE 1. We can just delete the file for NOTE 2.
-
reporter - edited description
-
reporter These:
getPropertyData: no visible binding for global variable ‘aaindex’ getPropertyData: no visible binding for global variable ‘pK’
Are due to loading data objects from seqinr. Had to do some non-sense with the
with
function and a temporary environment to fix them.These:
plotAbundance: no visible binding for global variable ‘.x’ plotDiversityCurve: no visible binding for global variable ‘.x’
Are due to the special variable in
math_format(10^.x)
calls. I couldn't find a satisfactory fix, so I went with adding.x <- NULL
right before the plotting routines.Everything else could be fixed by using standard evaluation.
-
reporter - changed status to resolved
Fixed all no visible binding notes and updated license to CC BY-NC-SA 4.0 in 6f28192.
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Using
License: file LICENSE
in the DESCRIPTION file solves the first two.Avoiding non-standard evaluation in dplyr, tidyr and ggplot calls should solve the third.