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pathview log file (check_x86_64_linux)

Mon Apr  7 22:19:01 2014: Checking package pathview (SVN revision 41) ...
* using log directory ‘/mnt/building/build_2014-04-07-22-08/RF_PKG_CHECK/PKGS/pathview.Rcheck’
* using R version 3.0.3 Patched (2014-03-06 r65382)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘pathview/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pathview’ version ‘1.3.5’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Weijun Luo ’
Package duplicated from http://www.bioconductor.org/packages/2.13/bioc
Vignette sources in ‘inst/doc’ with no ‘vignettes’ directory:
  ‘pathview.Rnw’
A ‘vignettes’ directory has been preferred since R 2.14.0
and will be required as from 3.1.0.
* 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 ‘pathview’ can be installed ... [19s/35s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file found at top level:
  ‘test’
* 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 ... NOTE
Packages in Depends field not imported from:
  ‘KEGGgraph’ ‘org.Hs.eg.db’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
File ‘pathview/R/zzz.R’:
  .onLoad calls:
    installed.packages()
    packageStartupMessage(wordwrap(disclaimer, 80))

Package startup functions should not call ‘installed.packages’.
See section ‘Good practice’ in '?.onAttach'.

render.kegg.node: warning in sliced.shapes(plot.data$x, height -
  plot.data$y, plot.data$width/2 - 0.5, plot.data$height/2 - 0.25, col
  = cols.ts, draw.border = F, shape = "rectangle"): partial argument
  match of 'col' to 'cols'
col.key: no visible binding for global variable ‘node.sizes’
cpd2kegg: no visible binding for global variable ‘rn.list’
cpdidmap: no visible binding for global variable ‘cpd.accs’
cpdkegg2name: no visible binding for global variable ‘kegg.met’
cpdname2kegg: no visible binding for global variable ‘cpd.names’
eg2id: no visible global function definition for ‘biocLite’
id2eg: no visible global function definition for ‘biocLite’
kegg.species.code: no visible binding for global variable ‘korg’
keggview.graph: no visible binding for global variable
  ‘KEGGEdgeSubtype’
keggview.graph: no visible binding for global variable ‘nplot’
keggview.native: no visible binding for global variable ‘nplot’
pathview: no visible binding for global variable ‘bods’
pathview: no visible binding for global variable ‘rn.list’
sim.mol.data: no visible binding for global variable ‘cpd.accs’
sim.mol.data: no visible binding for global variable ‘rn.list’
sim.mol.data: no visible binding for global variable ‘ko.ids’

Found the following calls to data() loading into the global environment:
File ‘pathview/R/cpd2kegg.R’:
  data(rn.list)
File ‘pathview/R/cpdidmap.R’:
  data(rn.list)
  data(cpd.accs)
File ‘pathview/R/cpdkegg2name.R’:
  data(rn.list)
  data(cpd.names)
  data(kegg.met)
File ‘pathview/R/eg2id.R’:
  data(gene.idtype.list)
File ‘pathview/R/id2eg.R’:
  data(gene.idtype.list)
File ‘pathview/R/kegg.legend.R’:
  data(KEGGEdgeSubtype)
File ‘pathview/R/kegg.species.code.R’:
  data(korg)
File ‘pathview/R/pathview.R’:
  data(bods)
  data(gene.idtype.list)
  data(rn.list)
File ‘pathview/R/sim.mol.data.R’:
  data(gene.idtype.list)
  data(cpd.accs)
  data(cpd.simtypes)
  data(rn.list)
  data(ko.ids)
File ‘pathview/R/zzz.R’:
  data(gene.idtype.list, package = "pathview")
  data(cpd.simtypes, package = "pathview")
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘pathview.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [51s/59s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
pathview      24.622   0.34  27.676
eg2id          9.413   0.20   9.644
download.kegg  0.060   0.00   5.113
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [15s/16s]
 [16s/16s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
   ‘pathview.Rnw’ ... [133s/148s] OK
 [133s/148s] OK
* checking re-building of vignette outputs ... [133s/147s] OK
* checking PDF version of manual ... OK

NOTE: There were 5 notes.
See
  ‘/mnt/building/build_2014-04-07-22-08/RF_PKG_CHECK/PKGS/pathview.Rcheck/00check.log’
for details.

Run time: 696.29 seconds.

Additional Logs:   00install.out
Thanks to:
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