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clusterpath log file (check_x86_64_linux)

Mon Jun 29 17:57:27 2020: Checking package clusterpath (SVN revision 97) ...
* using log directory ‘/srv/rf/building/build_2020-06-29-17-56/RF_PKG_CHECK/PKGS/clusterpath.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-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 is:
‘Fast agglomerative convex clustering, non-Rcpp implementation’
In title case that is:
‘Fast Agglomerative Convex Clustering, Non-Rcpp Implementation’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
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 serialization versions ... OK
* checking whether package ‘clusterpath’ can be installed ... [11s/12s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [8s/8s] NOTE
calcstats : : no visible global function definition for
  ‘dist’
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 global function definition for
  ‘dist’
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’
clusterpath.l2.general: no visible global function definition for
  ‘dist’
cut.clusterpath: no visible binding for global variable ‘lambda’
cut.clusterpath.labels: no visible binding for global variable ‘lambda’
cvxmod.cluster: no visible global function definition for ‘dist’
cvxmod.cluster: no visible global function definition for ‘write.table’
cvxmod.cluster: no visible binding for global variable ‘mclapply’
fillin: no visible global function definition for ‘approx’
gendata: no visible global function definition for ‘rnorm’
gendata : : no visible global function definition for
  ‘rnorm’
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 ‘dist’
get.best.eigenvectors : try.gamma: no visible global function
  definition for ‘Diagonal’
get.best.eigenvectors : try.gamma: no visible global function
  definition for ‘kmeans’
get.old.best : : no visible global function definition for
  ‘dist’
get.old.best : : no visible global function definition for
  ‘Diagonal’
get.old.best : : no visible global function definition for
  ‘kmeans’
halfmoon.cluster : halfcircle: no visible global function definition
  for ‘runif’
halfmoon.cluster : halfcircle: no visible global function definition
  for ‘rnorm’
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 ‘.’
Undefined global functions or variables:
  . Diagonal Matrix aes approx coord_equal dcast ddply dist geom_path
  geom_point ggplot ggtitle kmeans lambda mclapply panel.splom
  panel.xyplot plot3d rename rnorm runif scale_size solver splom
  strip.custom write.table xyplot
Consider adding
  importFrom("stats", "approx", "dist", "kmeans", "rnorm", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘clusterpath/libs/clusterpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking examples ... [115s/106s] NOTE
Examples with CPU or elapsed time > 5s
                         user system elapsed
clusterpath.l2.general 17.099  0.456  17.786
plotpath3d             16.606  0.364  16.915
cluster3d              16.030  0.741  17.152
clusterpath.l2         16.400  0.345  16.717
plotpathmatrix         14.113  0.023  14.137
cluster.points         11.067  0.040  11.379
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 9 NOTEs
See
  ‘/srv/rf/building/build_2020-06-29-17-56/RF_PKG_CHECK/PKGS/clusterpath.Rcheck/00check.log’
for details.


Run time: 174.41 seconds.
Additional Logs:   00install.out
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