• using R Under development (unstable) (2012-02-23 r58468)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘Rknots/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘Rknots’ version ‘1.2’
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘bio3d’
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package ‘Rknots’ can be installed ... OK
• checking installed package size ... OK
• checking package directory ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level 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 for unstated 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
  loadProtein: no visible global function definition for ‘read.pdb’
  makeExampleKnot: no visible binding for global variable ‘Rolfsen.table’
  makeExampleKnot: no visible binding for global variable ‘link.table’
  plotComponent: warning in texts3d(points3D[2:(nrow(points3D) - 1), ],
  text = as.character(2:(nrow(points3D) - 1)), cex = 0.8, adj = 1.35,
  col = "black"): partial argument match of 'text' to 'texts'
  plotComponent: warning in texts3d(points3D[c(1, nrow(points3D)), ],
  text = c("N", "C"), cex = 1.5, adj = 1.35, col = "red"): partial
  argument match of 'text' to 'texts'
  rMatrix: warning in matrix(c(cos(theta), -sin(theta), 0, sin(theta),
  cos(theta), 0, 0, 0, 1), nc = 3, byrow = TRUE): partial argument
  match of 'nc' to 'ncol'
  xClean: warning in matrix(c(torusShift(k[1], 1), 1), nr = 1): partial
  argument match of 'nr' to 'nrow'
  xClean: warning in matrix(c(k[1], 2), nr = 1): partial argument match
  of 'nr' to 'nrow'
  xClean: warning in matrix(c(k[1], 2, torusShift(k[2], 1), 1), nr = 2,
  byrow = TRUE): partial argument match of 'nr' to 'nrow'
• checking Rd files ... NOTE
  prepare_Rd: AlexanderBriggs.Rd:24-26: Dropping empty section \details
  prepare_Rd: Rknots-package.Rd:68-71: Dropping empty section \seealso
  prepare_Rd: Rolfsen.table.Rd:26-28: Dropping empty section \details
  prepare_Rd: centroidClosure.Rd:25-27: Dropping empty section \details
• checking Rd metadata ... 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 examples ... [87s/80s] OK
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in ‘inst/doc’ ... OK
• checking running R code from vignettes ... [0s/0s] OK
• checking re-building of vignette PDFs ... [0s/1s] OK
• checking PDF version of manual ... OK
  NOTE: There were 3 notes.
  See
  ‘/home/hornik/tmp/R.check/r-devel/Work/PKGS/Rknots.Rcheck/00check.log’
  for details.