gclust.rsvt, gclust.app, getAICc and their Rd

igraph / xdata-igraph

xdata igraph, has been merged into igraph/igraph

GNU General Public License v2.0

18 stars 3 forks source link

~/works/igraph/nhlee/interfaces/R (develop)$ R CMD check igraph_0.7.999-315.tar.gz 
* using log directory ‘/Users/gaborcsardi/works/igraph/nhlee/interfaces/R/igraph.Rcheck’
* using R version 3.1.0 (2014-04-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* checking for file ‘igraph/DESCRIPTION’ ... OK
* this is package ‘igraph’ version ‘0.7.999-315’
* 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 ‘igraph’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘clue’
Namespace in Imports field not imported from: ‘clue’
  All declared Imports should be used.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gclust.app: no visible global function definition for ‘nmf’
gclust.app: no visible global function definition for ‘basis’
gclust.rsvt: no visible global function definition for ‘irlba’
gclust.rsvt: no visible global function definition for ‘nmf’
gclust.rsvt: no visible global function definition for ‘basis’
sgm: no visible global function definition for ‘solve_LSAP’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'getAICc' but not in code:
  getAIC

Codoc mismatches from documentation object 'gclust.app':
gclust.app
  Code: function(glist, r = 1, nmfout = FALSE, maxit = 10000, nmfmethod
                 = "lee")
  Docs: function(glist, r = 1)
  Argument names in code not in docs:
    nmfout maxit nmfmethod

Codoc mismatches from documentation object 'gclust.rsvt':
gclust.rsvt
  Code: function(glist, r = 1, maxsvt = 10, nmfout = FALSE, maxit =
                 10000, nmfmethod = "lee")
  Docs: function(glist, r = 1)
  Argument names in code not in docs:
    maxsvt nmfout maxit nmfmethod

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'gclust.app':
  ‘nmfout’ ‘maxit’ ‘nmfmethod’

Documented arguments not in \usage in documentation object 'gclust.rsvt':
  ‘maxsvt’ ‘nmfout’ ‘maxit’ ‘nmfmethod’

Objects in \usage without \alias in documentation object 'getAICc':
  ‘getAIC’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' calls not declared from:
  ‘NMF’ ‘irlba’
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There were 2 notes.
See
  ‘/Users/gaborcsardi/works/igraph/nhlee/interfaces/R/igraph.Rcheck/00check.log’
for details.

~/works/igraph/nhlee/interfaces/R (develop)$ R CMD check igraph_0.7.999-318.tar.gz * using log directory ‘/Users/gaborcsardi/works/igraph/nhlee/interfaces/R/igraph.Rcheck’ * using R version 3.1.0 (2014-04-10) * using platform: x86_64-apple-darwin10.8.0 (64-bit) * using session charset: UTF-8 * checking for file ‘igraph/DESCRIPTION’ ... OK * this is package ‘igraph’ version ‘0.7.999-318’ * 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 ‘igraph’ can be installed ... OK * checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: libs 4.6Mb * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * 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 dependencies in R code ... WARNING 'library' or 'require' call not declared from: ‘clue’ Namespace in Imports field not imported from: ‘clue’ All declared Imports should be used. See the information on DESCRIPTION files in the chapter ‘Creating R packages’ of the ‘Writing R Extensions’ manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE gclust.app: no visible global function definition for ‘nmf’ gclust.app: no visible global function definition for ‘basis’ gclust.rsvt: no visible global function definition for ‘irlba’ gclust.rsvt: no visible global function definition for ‘nmf’ gclust.rsvt: no visible global function definition for ‘basis’ sgm: no visible global function definition for ‘solve_LSAP’ * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'gclust.rsvt': gclust.rsvt Code: function(glist, r = 1, maxsvt = 10, nmfout = FALSE, maxit = 10000, nmfmethod = "lee") Docs: function(glist, r = 1, , nmfout = FALSE, maxit = 10000, nmfmethod = "lee") Argument names in code not in docs: maxsvt Argument names in docs not in code: Mismatches in argument names: Position: 3 Code: maxsvt Docs: Codoc mismatches from documentation object 'getAICc': getAICc Code: function(gfit) Docs: function(x) Argument names in code not in docs: gfit Argument names in docs not in code: x Mismatches in argument names: Position: 1 Code: gfit Docs: x * checking Rd \usage sections ... WARNING Undocumented arguments in documentation object 'gclust.rsvt' ‘’ Documented arguments not in \usage in documentation object 'gclust.rsvt': ‘maxsvt’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See the chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... WARNING 'library' or 'require' calls not declared from: ‘NMF’ ‘irlba’ * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... OK * checking examples ... OK * checking PDF version of manual ... OK WARNING: There were 4 warnings. NOTE: There were 2 notes. See ‘/Users/gaborcsardi/works/igraph/nhlee/interfaces/R/igraph.Rcheck/00check.log’ for details.

igraph / xdata-igraph

gclust.rsvt, gclust.app, getAICc and their Rd #47