• 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 ‘multic/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘multic’ version ‘0.3.2’
• checking package dependencies ... NOTE
  Package suggested but not available for checking: ‘kinship’
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
  CRAN requires a NAMESPACE file for all submissions.
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking whether package ‘multic’ can be installed ... [14s/14s] 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 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
  File ‘multic/R/zzz.q’:
  .First.lib calls:
  require("kinship")
  cat(no.kinship.lib.string)
  cat("loading kinship library\n")
  library("kinship")
  cat("\nIf the kinship library could not be loaded\n", "(you would have seen an error message),\n", "Not all of multic's functionality will be present.\n", sep = "")
  
  Package startup functions should not change the search path.
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  addGE: warning in casefold(statistic, up = T): partial argument match
  of 'up' to 'upper'
  multic: warning in match.call(expand = FALSE): partial argument match
  of 'expand' to 'expand.dots'
  addGE: no visible global function definition for ‘unpaste’
  addGE: no visible global function definition for ‘key’
  apply.sequential.ids: no visible global function definition for
  ‘importData’
  calculate.cor.values: possible error in cor(cbind(trait, covariate),
  na.method = "omit"): unused argument(s) (na.method = "omit")
  calculate.cor.values: possible error in cor(ranked, na.method =
  "omit"): unused argument(s) (na.method = "omit")
  check.for.full.data: no visible binding for global variable ‘x.name’
  fixibd: no visible global function definition for ‘as.chacter’
  make.kinship.file: no visible global function definition for
  ‘makekinship’
  make.kinship.file: possible error in write.table(kinship, share.out,
  dimnames.write = FALSE, sep = "\t"): unused argument(s)
  (dimnames.write = FALSE)
  mergeWithKinship: possible error in write.table(this.mibd, file =
  "mloci.out", quote.strings = FALSE, dimnames.write = FALSE, sep =
  "\t", append = TRUE): unused argument(s) (quote.strings = FALSE,
  dimnames.write = FALSE)
  multic.is.dir: no visible global function definition for ‘is.dir’
  multic.mkdir: no visible global function definition for ‘mkdir’
  multic.skewness: no visible binding for global variable ‘stdev’
  multic.strsplit: no visible global function definition for
  ‘splitString’
  multic.system: no visible global function definition for ‘unix’
  multic.unlink: no visible global function definition for ‘rmdir’
  phi2share: possible error in write.table(share.out, "share.out",
  dimnames.write = FALSE, sep = "\t"): unused argument(s)
  (dimnames.write = FALSE)
  read.pedindex.out: no visible global function definition for
  ‘importData’
  residuals.multic : stdfn: no visible global function definition for
  ‘gchol’
  residuals.multic : q1fn: no visible global function definition for
  ‘gchol’
  residuals.multic : q2fn: no visible global function definition for
  ‘gchol’
  sw2mloci: no visible global function definition for ‘files.in.dir’
  trim: no visible global function definition for ‘regMatchPos’
• checking Rd files ... NOTE
  prepare_Rd: addGE.Rd:69: Dropping empty section \keyword
  prepare_Rd: expand.data.Rd:42: Dropping empty section \keyword
  prepare_Rd: expand.multic.Rd:61: Dropping empty section \keyword
  prepare_Rd: multic.Rd:215: Dropping empty section \keyword
  prepare_Rd: multic.control.Rd:127: Dropping empty section \keyword
  prepare_Rd: non.user.level.objects.Rd:113: Dropping empty section \keyword
  prepare_Rd: phi2share.Rd:77: Dropping empty section \keyword
  prepare_Rd: plot.family.lods.Rd:72: Dropping empty section \keyword
  prepare_Rd: plot.multic.Rd:23: Dropping empty section \keyword
  prepare_Rd: print.multic.Rd:25: Dropping empty section \keyword
  prepare_Rd: solar2mloci.Rd:92: Dropping empty section \keyword
  prepare_Rd: solar2multic.Rd:106: Dropping empty section \keyword
  prepare_Rd: subsets.Rd:60: Dropping empty section \keyword
  prepare_Rd: sw2mloci.Rd:79: Dropping empty section \keyword
  prepare_Rd: t.rank.Rd:33: Dropping empty section \keyword
  prepare_Rd: t.rank.Rd:25-27: Dropping empty section \seealso
• 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 ... NOTE
  S3 methods shown with full name in documentation object 'plot.family.lods':
  ‘plot.family.lods’
  
  S3 methods shown with full name in documentation object 'plot.multic':
  ‘plot.multic’
  
  S3 methods shown with full name in documentation object 'print.multic':
  ‘print.multic’
  
  S3 methods shown with full name in documentation object 't.rank':
  ‘t.rank’
  
  The \usage entries for S3 methods should use the \method markup and not
  their full name.
  See the chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.
• 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
• checking compiled code ... NOTE
  File ‘/data/blackswan/ripley/R/packages/tests-devel/multic.Rcheck/multic/libs/multic.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Objects: ‘Calculate.o’, ‘Likelihoodfun.o’, ‘Maxfun.o’,
  ‘ReadFamilyData.o’, ‘fixibd.o’, ‘getFamilySizes.o’,
  ‘loadFamilyLogLikelihoods.o’, ‘validateShareOut.o’
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Objects: ‘Calculate.o’, ‘Composite.o’, ‘Lib.o’, ‘Maxfun.o’,
  ‘Robust_Variance.o’, ‘fixibd.o’, ‘makeBlockIdPair.o’, ‘multic.o’,
  ‘solar2mloci.o’, ‘sw2mloci.o’
  Found ‘printf’, possibly from ‘printf’ (C)
  Objects: ‘Maxfun.o’, ‘Maxfun_source.o’, ‘fixibd.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Objects: ‘Maxfun.o’, ‘fixibd.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Objects: ‘Maxfun_source.o’, ‘fixibd.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
  Object: ‘fixibd.o’
  
  Compiled code should not call functions which might terminate R nor
  write to stdout/stderr instead of to the console.
  
  See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
• checking examples ... OK
• checking PDF version of manual ... OK
  NOTE: There were 6 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/multic.Rcheck/00check.log’
  for details.