• using R version 2.15.3 (2013-03-01)
• using platform: i386-apple-darwin9.8.0 (32-bit)
• using session charset: ASCII
• checking for file 'rphast/DESCRIPTION' ... OK
• this is package 'rphast' version '1.4'
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Package suggested but not available for checking: 'seqLogo'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking whether package 'rphast' can be installed ... OK
• checking installed package size ... NOTE
  installed size is 6.1Mb
  sub-directories of 1Mb or more:
  doc 1.4Mb
  libs 3.0Mb
  NB: this package is only installed for sub-architecture 'i386'
• 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 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 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 ... OK
• checking Rd files ... OK
• 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 line endings in C/C++/Fortran sources/headers ... OK
• checking line endings in Makefiles ... OK
• checking for portable compilation flags in Makevars ... OK
• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... OK
• checking sizes of PDF files under 'inst/doc' ... OK
• checking installed files from 'inst/doc' ... OK
• checking examples ... OK
• checking for unstated dependencies in tests ... OK
• checking tests ... OK
  Running 'feat.examples.R'
  Running 'msa.examples.R'
  Running 'optim.examples.R'
  Running 'phyloP.examples.R'
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking running R code from vignettes ... WARNING
  Errors in running code in vignettes:
  when running code in 'vignette3.Rnw'
  ...
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'seqLogo'
  
  > m <- read.table("NRSF/NRSF.mtf")
  
  > pwm <- makePWM(t(m))
  
  When sourcing 'vignette3.R':
  Error: could not find function "makePWM"
  Execution halted
  
• checking re-building of vignette PDFs ... NOTE
  Error in re-building vignettes:
  ...
  numpar = 5
  Done. log(likelihood) = -104.384510 numeval=330
  Fitting tree model to alignment (category 17) using REV ...
  numpar = 5
  Done. log(likelihood) = -137.833746 numeval=158
  Fitting tree model to alignment (category 18) using REV ...
  numpar = 5
  Done. log(likelihood) = -178.603297 numeval=388
  Fitting tree model to alignment (category 19) using REV ...
  numpar = 5
  Done. log(likelihood) = -175.281397 numeval=118
  Fitting tree model to alignment (category 20) using REV ...
  numpar = 5
  Done. log(likelihood) = -187.919026 numeval=148
  Fitting tree model to alignment (category 21) using REV ...
  numpar = 5
  Done. log(likelihood) = -189.754697 numeval=161
  Loading required package: seqLogo
  Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
  there is no package called 'seqLogo'
  
  Error: processing vignette 'vignette3.Rnw' failed with diagnostics:
  chunk 6 (label = seqLogoPlot)
  Error in eval(expr, envir, enclos) : could not find function "makePWM"
  Execution halted
  
• checking PDF version of manual ... OK
  WARNING: There was 1 warning.
  NOTE: There were 3 notes.
  See
  '/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/rphast.Rcheck/00check.log'
  for details.
• elapsed time (check, wall clock): 2:26