setSigFuncs<- \S4method{setSigFuncs<-}{SignatureSet,character}
The argument of a replacement function which corresponds to the right
hand side must be named value.
[x] checking Rd files ... [0s/0s] WARNING
checkRd: (7) NanoStringRccSet-autoplot.Rd:14-49: Tag \code is invalid in a \usage block
prepare_Rd: SignatureSet.Rd:74-75: Dropping empty section \examples
prepare_Rd: geom_beeswarm_interactive.Rd:53-54: Dropping empty section \examples
checkRd: (7) normalize.Rd:10: Tag \code is invalid in a \usage block
checkRd: (7) setQCFlags.Rd:10-20: Tag \code is invalid in a \usage block
[x] checking Rd metadata ... WARNING
Rd files with duplicated alias 'autoplot.NanoStringRccSet':
NanoStringRccSet-autoplot.Rd NanoStringRccSet-class.Rd
Rd files with duplicated alias 'setQCFlags':
NanoStringRccSet-class.Rd setQCFlags.Rd
[x] checking for missing documentation entries ... WARNING
Undocumented code objects:
getSigFuncs groups groups<- setSignatureFuncs<-
setSignatureGroups<- signatureFuncs signatureGroups version
version<-
Undocumented S4 methods:
generic 'getSigFuncs' and siglist 'SignatureSet'
generic 'groups' and siglist 'SignatureSet'
generic 'groups<-' and siglist 'SignatureSet,ANY'
generic 'groups<-' and siglist 'SignatureSet,NULL'
generic 'groups<-' and siglist 'SignatureSet,factor'
generic 'setSignatureFuncs<-' and siglist
'NanoStringRccSet,character'
generic 'setSignatureGroups<-' and siglist
'NanoStringRccSet,character'
generic 'setSignatureGroups<-' and siglist 'NanoStringRccSet,factor'
generic 'signatureFuncs' and siglist 'NanoStringRccSet'
generic 'signatureGroups' and siglist 'NanoStringRccSet'
generic 'version' and siglist 'SignatureSet'
generic 'version<-' and siglist 'SignatureSet,ANY'
generic 'version<-' and siglist 'SignatureSet,NULL'
generic 'version<-' and siglist 'SignatureSet,character'
generic 'weights<-' and siglist 'SignatureSet,CompressedNumericList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter Writing R documentation files in the Writing R
Extensions manual.
[x] checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SignatureSet-class':
SignatureSet
Code: function(weights = NumericList(), groups = factor(), func =
character(), version = character(), ...)
Docs: function(weights = NumericList(), ...)
Argument names in code not in docs:
groups func version
Mismatches in argument names:
Position: 2 Code: groups Docs: ...
[x] checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'NanoStringRccSet-autoplot':
ERCCLoD = c(standardDeviations = 2)
[x] Checking for proper Description: field...
WARNING: Description field in the DESCRIPTION file is too concise
[x] Checking R Version dependency...
WARNING: Update R version dependency from 3.6 to 4.1.
[x] checking replacement functions ... WARNING
setSigFuncs<- \S4method{setSigFuncs<-}{SignatureSet,character} The argument of a replacement function which corresponds to the right hand side must be named value.
[x] checking Rd files ... [0s/0s] WARNING
checkRd: (7) NanoStringRccSet-autoplot.Rd:14-49: Tag \code is invalid in a \usage block prepare_Rd: SignatureSet.Rd:74-75: Dropping empty section \examples prepare_Rd: geom_beeswarm_interactive.Rd:53-54: Dropping empty section \examples checkRd: (7) normalize.Rd:10: Tag \code is invalid in a \usage block checkRd: (7) setQCFlags.Rd:10-20: Tag \code is invalid in a \usage block
Rd files with duplicated alias 'autoplot.NanoStringRccSet': NanoStringRccSet-autoplot.Rd NanoStringRccSet-class.Rd Rd files with duplicated alias 'setQCFlags': NanoStringRccSet-class.Rd setQCFlags.Rd
Undocumented code objects: getSigFuncs groups groups<- setSignatureFuncs<- setSignatureGroups<- signatureFuncs signatureGroups version version<- Undocumented S4 methods: generic 'getSigFuncs' and siglist 'SignatureSet' generic 'groups' and siglist 'SignatureSet' generic 'groups<-' and siglist 'SignatureSet,ANY' generic 'groups<-' and siglist 'SignatureSet,NULL' generic 'groups<-' and siglist 'SignatureSet,factor' generic 'setSignatureFuncs<-' and siglist 'NanoStringRccSet,character' generic 'setSignatureGroups<-' and siglist 'NanoStringRccSet,character' generic 'setSignatureGroups<-' and siglist 'NanoStringRccSet,factor' generic 'signatureFuncs' and siglist 'NanoStringRccSet' generic 'signatureGroups' and siglist 'NanoStringRccSet' generic 'version' and siglist 'SignatureSet' generic 'version<-' and siglist 'SignatureSet,ANY' generic 'version<-' and siglist 'SignatureSet,NULL' generic 'version<-' and siglist 'SignatureSet,character' generic 'weights<-' and siglist 'SignatureSet,CompressedNumericList' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter Writing R documentation files in the Writing R Extensions manual.
Codoc mismatches from documentation object 'SignatureSet-class': SignatureSet Code: function(weights = NumericList(), groups = factor(), func = character(), version = character(), ...) Docs: function(weights = NumericList(), ...) Argument names in code not in docs: groups func version Mismatches in argument names: Position: 2 Code: groups Docs: ...
Assignments in \usage in documentation object 'NanoStringRccSet-autoplot': ERCCLoD = c(standardDeviations = 2)
[x] Checking for proper Description: field...
[x] Checking R Version dependency...