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clusterpath log file (check_x86_64_linux)

Thu Apr 23 11:06:29 2015: Checking package clusterpath (SVN revision 97) ...
* using log directory ‘/mnt/building/build_2015-04-23-10-50/RF_PKG_CHECK/PKGS/clusterpath.Rcheck’
* using R version 3.2.0 Patched (2015-04-21 r68221)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘clusterpath/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clusterpath’ version ‘1.2’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Toby Dylan Hocking ’
New submission

The Title field should be in title case, current version then in title case:
‘Fast agglomerative convex clustering, non-Rcpp implementation’
‘Fast Agglomerative Convex Clustering, Non-Rcpp Implementation’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped

Depends: includes the non-default packages:
  ‘lattice’ ‘ggplot2’ ‘plyr’ ‘reshape2’ ‘latticeExtra’ ‘Matrix’ ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘clusterpath’ can be installed ... [8s/17s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘etc’
* 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘parallel’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘latticeExtra’ ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  cut.clusterpath cut.clusterpath.labels plot.clusterpath plot.l2
  plot.predictclusterpath predict.clusterpath
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
castbreakpoints: no visible global function definition for ‘dcast’
castbreakpoints: no visible global function definition for ‘rename’
castbreakpoints: no visible global function definition for ‘ddply’
castbreakpoints: no visible global function definition for ‘.’
cluster3d: no visible global function definition for ‘plot3d’
clusterpath.l1.general: no visible binding for global variable
  ‘mclapply’
clusterpath.l1.general : : no visible binding for global
  variable ‘lambda’
clusterpath.l1.id: no visible binding for global variable ‘mclapply’
cut.clusterpath: no visible binding for global variable ‘lambda’
cut.clusterpath.labels: no visible binding for global variable ‘lambda’
cvxmod.cluster: no visible binding for global variable ‘mclapply’
get.best.eigenvectors : get.vectors: no visible global function
  definition for ‘Diagonal’
get.best.eigenvectors : get.vectors: no visible global function
  definition for ‘Matrix’
get.best.eigenvectors : try.gamma: no visible global function
  definition for ‘Matrix’
get.best.eigenvectors : try.gamma: no visible global function
  definition for ‘Diagonal’
get.old.best : : no visible global function definition for
  ‘Diagonal’
halfmoon.cluster: no visible global function definition for ‘xyplot’
plot.clusterpath: no visible global function definition for
  ‘strip.custom’
plot.clusterpath: no visible global function definition for ‘xyplot’
plot2d: no visible global function definition for ‘ggplot’
plot2d: no visible global function definition for ‘geom_path’
plot2d: no visible global function definition for ‘aes’
plot2d: no visible global function definition for ‘coord_equal’
plot2d: no visible global function definition for ‘geom_point’
plot2d: no visible binding for global variable ‘lambda’
plot2d: no visible global function definition for ‘scale_size’
plot2d: no visible global function definition for ‘ggtitle’
plotpath3d: no visible global function definition for ‘plot3d’
plotpathmatrix: no visible global function definition for ‘splom’
plotpathmatrix : : no visible global function definition for
  ‘panel.splom’
plotpathmatrix : : no visible global function definition for
  ‘panel.xyplot’
predict.clusterpath : calc1: no visible binding for global variable
  ‘solver’
predict.clusterpath: no visible global function definition for ‘ddply’
predict.clusterpath: no visible global function definition for ‘.’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'cvxmod.cluster.Rd':
  \usage lines wider than 90 characters:
         verbose = FALSE, s = NULL, weight.pts = pts, W = exp(-as.numeric(as.character(gamma)) * 

Rd file 'plot.clusterpath.Rd':
  \usage lines wider than 90 characters:
     plot(x, type = "l", main = "The entire regularization path of optimal solutions for each variable", 

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking examples ... [157s/268s] OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
clusterpath.l2         28.838  0.456  56.906
plotpath3d             28.009  0.440  41.617
cluster3d              25.425  1.208  53.318
plotpathmatrix         24.014  0.036  36.748
clusterpath.l2.general 15.204  0.736  31.439
cluster.points         14.025  0.016  28.568
cvxcheck                7.953  0.432   0.628
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/mnt/building/build_2015-04-23-10-50/RF_PKG_CHECK/PKGS/clusterpath.Rcheck/00check.log’
for details.

Run time: 391.21 seconds.

Additional Logs:   00install.out
Thanks to:
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