• using R Under development (unstable) (2012-08-14 r60253)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘mcsm/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘mcsm’ version ‘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 whether package ‘mcsm’ 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 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 ... NOTE
  EMcenso : like: warning in pnorm(the - a, log = T): partial argument
  match of 'log' to 'log.p'
  adapump: warning in rgamma(1, sha = gamma + 10 * alpha): partial
  argument match of 'sha' to 'shape'
  adapump: warning in rgamma(10, sha = data + alpha): partial argument
  match of 'sha' to 'shape'
  adapump: warning in rgamma(1, sha = gamma + (10 * alpha)): partial
  argument match of 'sha' to 'shape'
  gibbsmix: warning in matrix(0, nco = 250, nro = 250): partial argument
  match of 'nro' to 'nrow'
  gibbsmix: warning in matrix(0, nco = 250, nro = 250): partial argument
  match of 'nco' to 'ncol'
  kscheck: warning in rgamma(1, sha = gamma + 10 * alpha): partial
  argument match of 'sha' to 'shape'
  kscheck: warning in rgamma(10, sha = data + alpha): partial argument
  match of 'sha' to 'shape'
  kscheck: warning in rgamma(1, sha = gamma + (10 * alpha)): partial
  argument match of 'sha' to 'shape'
  logima: warning in matrix(0, ncol = 130, nro = 100): partial argument
  match of 'nro' to 'nrow'
  logima: warning in rnorm(N, m = -0.72, sd = 0.55): partial argument
  match of 'm' to 'mean'
  logima: warning in rnorm(N, m = 0.1, sd = 0.212): partial argument
  match of 'm' to 'mean'
  logima: warning in dnorm(sim[, 1], m = -0.72, sd = 0.55): partial
  argument match of 'm' to 'mean'
  logima: warning in dnorm(sim[, 2], m = 0.1, sd = 0.2121): partial
  argument match of 'm' to 'mean'
  logima: warning in sample(1:N, N, rep = TRUE, pro = weit): partial
  argument match of 'rep' to 'replace'
  logima: warning in sample(1:N, N, rep = TRUE, pro = weit): partial
  argument match of 'pro' to 'prob'
  mhmix: warning in matrix(0, nco = 250, nro = 250): partial argument
  match of 'nro' to 'nrow'
  mhmix: warning in matrix(0, nco = 250, nro = 250): partial argument
  match of 'nco' to 'ncol'
  mhmix: warning in dnorm(prop, curmean, lo = T): partial argument match
  of 'lo' to 'log'
  mhmix: warning in dnorm(the[iter, ], meanprop, lo = T): partial
  argument match of 'lo' to 'log'
  mochoice : gocho: warning in sample(c(0, 1), lga, rep = T): partial
  argument match of 'rep' to 'replace'
  pimamh : like: warning in pnorm(q = a + outer(X = b, Y = da[, 2], FUN =
  "*"), log = T): partial argument match of 'log' to 'log.p'
  pimamh : like: warning in pnorm(q = -a - outer(X = b, Y = da[, 2], FUN
  = "*"), log = T): partial argument match of 'log' to 'log.p'
  pimamh: warning in dnorm(prop, mean = curmean, sd = scale, lo = T):
  partial argument match of 'lo' to 'log'
  pimamh: warning in dnorm(the[t - 1, ], mean = propmean, sd = scale, lo
  = T): partial argument match of 'lo' to 'log'
  pimamh: warning in matrix(0, ncol = 130, nro = 100): partial argument
  match of 'nro' to 'nrow'
  pimax : like: warning in pnorm(q = a + outer(X = b, Y = da[, 2], FUN =
  "*"), log = T): partial argument match of 'log' to 'log.p'
  pimax : like: warning in pnorm(q = -a - outer(X = b, Y = da[, 2], FUN =
  "*"), log = T): partial argument match of 'log' to 'log.p'
  pimax : newlike: warning in pnorm(q = a + outer(X = b, Y = da[, 2], FUN
  = "*"), log = T): partial argument match of 'log' to 'log.p'
  pimax : newlike: warning in pnorm(q = -a - outer(X = b, Y = da[, 2],
  FUN = "*"), log = T): partial argument match of 'log' to 'log.p'
  randogibs: warning in sample(c(-1, 0, 1), n * m, rep = T): partial
  argument match of 'rep' to 'replace'
  randogit: warning in sample(c(-1, 0, 1), n * m, rep = TRUE): partial
  argument match of 'rep' to 'replace'
  SAmix : like: no visible binding for global variable ‘da’
  betagen: no visible binding for global variable ‘x’
  challenge: no visible binding for global variable ‘challenger’
  maximple: no visible global function definition for ‘h’
  randomeff: no visible binding for global variable ‘Energy’
• 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking examples ... [23s/23s] OK
• checking PDF version of manual ... OK
  NOTE: There was 1 note.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/mcsm.Rcheck/00check.log’
  for details.