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bvsflex log file (check_x86_64_linux)

Thu Nov 12 10:38:42 2015: Checking package bvsflex (SVN revision 53) ...
* using log directory ‘/mnt/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bvsflex.Rcheck’
* using R version 3.2.2 Patched (2015-11-06 r69607)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘bvsflex/DESCRIPTION’ ... OK
* this is package ‘bvsflex’ version ‘0.48’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Manuela Zucknick ’
New submission

The Title field should be in title case, current version then in title case:
‘Integrative Bayesian variable selection with flexible priors’
‘Integrative Bayesian Variable Selection with Flexible Priors’

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* 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 ‘bvsflex’ can be installed ... [2s/2s] OK
* checking installed package size ... OK
* checking package directory ... 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘Matrix’ ‘ggplot2’ ‘gplots’ ‘grid’
'library' or 'require' calls in package code:
  ‘Matrix’ ‘ROCR’ ‘ggplot2’ ‘gplots’ ‘grid’ ‘pROC’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
print:
  function(x, ...)
print.summary.bvsflex:
  function(object, ...)

summary:
  function(object, ...)
summary.bvsflex:
  function(object, cutoff)

summary:
  function(object, ...)
summary.bvsflex:
  function(object, cutoff)

predict:
  function(object, ...)
predict.bvsflex:
  function(object, X2, sdX, which)

predict:
  function(object, ...)
predict.bvsflex:
  function(object, X2, sdX, which)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  print.summary.bvsflex
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ROC: no visible binding for global variable ‘r1’
ROC: no visible global function definition for ‘prediction’
ROC: no visible global function definition for ‘performance’
callBVS: no visible binding for global variable ‘dvec’
callBVS: no visible binding for global variable ‘p’
callBVS: no visible binding for global variable ‘k’
callBVS: possible error in logisticVS(X = X, Y = Y, b = b, v = v, k =
  k, d = eval(parse(text = dvec[i])) + shrink, block = block, Cupdate =
  FALSE, Piupdate = TRUE, MCMC = BVS.TOT, thinn = BVS.thin, burnin =
  burnin, seed = 1234, outdir = NULL): unused arguments (v = v, k = k,
  d = eval(parse(text = dvec[i])) + shrink, Cupdate = FALSE, burnin =
  burnin)
callBVS: no visible binding for global variable ‘X’
callBVS: no visible binding for global variable ‘Y’
callBVS: no visible binding for global variable ‘b’
callBVS: no visible binding for global variable ‘v’
callBVS: no visible binding for global variable ‘block’
callBVS: no visible binding for global variable ‘BVS.TOT’
callBVS: no visible binding for global variable ‘BVS.thin’
callBVS: no visible binding for global variable ‘burnin’
callBVS: no visible binding for global variable ‘annoX’
callBVSelicit: no visible binding for global variable ‘dvec’
callBVSelicit: no visible binding for global variable ‘p’
callBVSelicit: no visible binding for global variable ‘k’
callBVSelicit: no visible global function definition for ‘elicitBeta’
callBVSelicit: no visible binding for global variable ‘rangeModelsize’
callBVSelicit: no visible binding for global variable ‘coverage’
callBVSelicit: no visible global function definition for
  ‘logisticVSbeta’
callBVSelicit: no visible binding for global variable ‘X’
callBVSelicit: no visible binding for global variable ‘Y’
callBVSelicit: no visible binding for global variable ‘b’
callBVSelicit: no visible binding for global variable ‘v’
callBVSelicit: no visible binding for global variable ‘block’
callBVSelicit: no visible binding for global variable ‘BVS.TOT’
callBVSelicit: no visible binding for global variable ‘BVS.thin’
callBVSelicit: no visible binding for global variable ‘burnin’
callBVSelicit: no visible binding for global variable ‘annoX’
getBVSflex: no visible global function definition for ‘sparseMatrix’
plotGamma: no visible global function definition for ‘plotCI’
plotPaths: no visible global function definition for ‘grid.newpage’
plotPaths: no visible global function definition for ‘pushViewport’
plotPaths: no visible global function definition for ‘viewport’
plotPaths: no visible global function definition for ‘grid.layout’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘FDR’ ‘ROC’ ‘VarOfVar’ ‘callBVS’ ‘callBVSelicit’ ‘elicitGamma’
  ‘elicitPhi’ ‘find.delta’ ‘find.var’ ‘getBVSflex’ ‘plotACF’ ‘plotBeta’
  ‘plotBetaGamma’ ‘plotGamma’ ‘plotPaths’ ‘predict.bvsflex’
  ‘print.summary.bvsflex’ ‘resampleVar’ ‘rtruncBeta’ ‘summary.bvsflex’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING
  apparently PKG_LIBS is missing $(FLIBS) in ‘src/Makevars’
* checking compiled code ... OK
* checking examples ... [39s/40s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
logisticVS 38.72  0.076  39.521
* checking PDF version of manual ... OK
* DONE

Status: 4 WARNINGs, 3 NOTEs
See
  ‘/mnt/building/build_2015-11-12-10-14/RF_PKG_CHECK/PKGS/bvsflex.Rcheck/00check.log’
for details.


Run time: 62.2 seconds.