* using log directory ‘/home/bolker/lme4check2/check/lsmeans.Rcheck’
* using R Under development (unstable) (2015-06-08 r68489)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘lsmeans/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘lsmeans’ version ‘2.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘lsmeans’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import by ‘lme4::VarCorr’ when loading ‘lsmeans’
Warning: replacing previous import by ‘lme4::ranef’ when loading ‘lsmeans’
Warning: replacing previous import by ‘lme4::fixef’ when loading ‘lsmeans’
Warning: replacing previous import by ‘lme4::lmList’ when loading ‘lsmeans’
See ‘/home/bolker/lme4check2/check/lsmeans.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
contrastLC: no visible global function definition for ‘:=’
contrastLC: missing arguments not allowed in calls to ‘list’
* checking Rd files ... NOTE
prepare_Rd: CalculateMatrixofMeansAndStandardErrors.Rd:35-37: Dropping empty section \details
prepare_Rd: CalculateMatrixofMeansAndStandardErrors.Rd:49-51: Dropping empty section \note
prepare_Rd: CalculateMatrixofMeansAndStandardErrors.Rd:43-45: Dropping empty section \references
prepare_Rd: CalculateMmatrix.Rd:20-22: Dropping empty section \details
prepare_Rd: CalculateMmatrix.Rd:37-39: Dropping empty section \note
prepare_Rd: CalculateMmatrix.Rd:31-33: Dropping empty section \references
prepare_Rd: CalculateMmatrix.Rd:43-46: Dropping empty section \seealso
prepare_Rd: MeanAndVariance.Rd:35-37: Dropping empty section \details
prepare_Rd: MeanAndVariance.Rd:49-51: Dropping empty section \note
prepare_Rd: MeanAndVariance.Rd:43-45: Dropping empty section \references
prepare_Rd: MeanAndVariance.Rd:55-57: Dropping empty section \seealso
prepare_Rd: MeansComparison.Rd:46-48: Dropping empty section \details
prepare_Rd: MeansComparison.Rd:58-60: Dropping empty section \note
prepare_Rd: MeansComparison.Rd:52-54: Dropping empty section \references
prepare_Rd: MeansComparison.Rd:64-66: Dropping empty section \seealso
prepare_Rd: RSquare.Rd:21-23: Dropping empty section \details
prepare_Rd: RSquare.Rd:35-37: Dropping empty section \note
prepare_Rd: RSquare.Rd:29-31: Dropping empty section \references
prepare_Rd: RSquare.Rd:41-43: Dropping empty section \seealso
prepare_Rd: contrastLC.Rd:36-38: Dropping empty section \note
prepare_Rd: contrastLC.Rd:30-32: Dropping empty section \references
prepare_Rd: contrastLC.Rd:42-44: Dropping empty section \seealso
prepare_Rd: lsmeans-package.Rd:30-32: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'lsmeans-package.Rd':
‘Test_Contrast’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘AvgSEMeansDiff_and_AvgDMS’
‘FindGreatestDFForAGivenListOfMeansForA_lme_model’
‘Linear.combination.to.estimate.a.mean’ ‘RebuildFactorLevels’
‘RebuildTreatmentNames’ ‘ReduceModel’
‘SearchForASubstringInAListOfStrings’
‘SearchForASubstringInAListOfStringsWithSeparators’
‘SearchForASubstringInAStringWithSeparators’ ‘Test_Contrast’
‘TheModelCoefficients’ ‘TheModelCoefficientsCovar’ ‘TheModelTerms’
‘UpdateFormula’ ‘checklinearindependence’ ‘dfMixedModelTypeIAnova’
‘validCases’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 WARNINGs, 3 NOTEs