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mpcbs log file (check_x86_64_linux)

Mon Apr 16 15:07:05 2012: Checking package mpcbs (SVN revision 30) ...
* using log directory ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/mpcbs.Rcheck’
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘mpcbs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mpcbs’ version ‘1.1.1’
* checking CRAN incoming feasibility ... NOTE
New submission
Non-FOSS package license (What license is it under?)
* 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 whether package ‘mpcbs’ can be installed ... [4s/4s] 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 ... WARNING
Non-standard license specification:
  What license is it under?
Standardizable: FALSE
* 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 ... WARNING
merge:
  function(x, y, ...)
merge.pos:
  function(pos, anchors)

plot:
  function(x, ...)
plot.crossplatform:
  function(pos, y, anchor, chpts, ranking, yhat, platform.names,
           num.panels, xlim, ...)

update:
  function(object, ...)
update.bic.baseline:
  function(this.y, segbag, carriers, this.sum.deltasq,
           this.sum.deltasqwin, newchpt, samp.ord, win, y.var,
           PRIOR.CARRIER.PROB, PRIOR.SEGCOUNT, do.plots)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ComputeZ.R: no visible binding for global variable ‘y’
computeZ.test: no visible binding for global variable ‘z’
fscan.max: no visible binding for global variable ‘MIN.SNPS’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘ComputeProjectedZ.fromS.R.segments’
Undocumented data sets:
  ‘mpcbs.example’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'compute.var':
compute.var
  Code: function(y, use.mean = TRUE)
  Docs: function(y)
  Argument names in code not in docs:
    use.mean

Codoc mismatches from documentation object 'merge.pos':
merge.pos
  Code: function(pos, anchors = NULL)
  Docs: function(pos, anchors = 1)
  Mismatches in argument default values:
    Name: 'anchors' Code: NULL Docs: 1

Codoc mismatches from documentation object 'mpcbs':
mpcbs
  Code: function(y, pos, anchor, win, Z = NULL, MIN.SNPs = 2,
                 MIN.BP.LEN = 10000, ALPHA = 0, rratio = NULL, f =
                 NULL, MAX.CHPTS = 50, WCHISQ.CUTOFF = NA,
                 platform.names = NULL, plots = TRUE, plotspdf = NULL,
                 use.filtered.scan = TRUE, useProjectedChisquare =
                 TRUE)
  Docs: function(y, pos, anchors)
  Argument names in code not in docs:
    anchor win Z MIN.SNPs MIN.BP.LEN ALPHA rratio f MAX.CHPTS
    WCHISQ.CUTOFF platform.names plots plotspdf use.filtered.scan
    useProjectedChisquare
  Argument names in docs not in code:
    anchors
  Mismatches in argument names:
    Position: 3 Code: anchor Docs: anchors

Codoc mismatches from documentation object 'mpcbs.mbic':
mpcbs.mbic
  Code: function(y, pos, anchor, MIN.SNPs = 2, MIN.BP.LEN = 1000,
                 rratio = NULL, f = NULL, MAX.CHPTS = 30,
                 platform.names = NULL, plots = TRUE, plotspdf = NULL,
                 use.filtered.scan = TRUE)
  Docs: function(y, pos, anchor, MIN.SNPs = 2, MAX.CHPTS = 30,
                 platform.names, plots = TRUE)
  Argument names in code not in docs:
    MIN.BP.LEN rratio f plotspdf use.filtered.scan
  Mismatches in argument names:
    Position: 5 Code: MIN.BP.LEN Docs: MAX.CHPTS
    Position: 6 Code: rratio Docs: platform.names
    Position: 7 Code: f Docs: plots
  Mismatches in argument default values:
    Name: 'platform.names' Code: NULL Docs: 

Codoc mismatches from documentation object 'mpscan':
mpscan
  Code: function(y, pos, anchors, win, Z = NULL, MIN.SNPs = 1, ALPHA =
                 0, WCHISQ.CUTOFF = NA)
  Docs: function(y, pos, anchors, win)
  Argument names in code not in docs:
    Z MIN.SNPs ALPHA WCHISQ.CUTOFF

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'compute.var':
  ‘use.mean’

Undocumented arguments in documentation object 'mpcbs'
  ‘anchors’
Documented arguments not in \usage in documentation object 'mpcbs':
  ‘anchor’ ‘MIN.SNPs’ ‘MIN.BP.LEN’ ‘WCHISQ.CUTOFF’ ‘rratio’
  ‘platform.names’ ‘plots’ ‘plotspdf’ ‘use.filtered.scan’

Documented arguments not in \usage in documentation object 'mpcbs.mbic':
  ‘MIN.BP.LEN’ ‘rratio’ ‘plotspdf’ ‘use.filtered.scan’

Undocumented arguments in documentation object 'mpscan'
  ‘anchors’
Documented arguments not in \usage in documentation object 'mpscan':
  ‘anchor’ ‘MIN.SNPs’ ‘WCHISQ.CUTOFF’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
S3 methods shown with full name in documentation object 'merge.pos':
  ‘merge.pos’

S3 methods shown with full name in documentation object 'plot.crossplatform':
  ‘plot.crossplatform’

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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ... OK
* checking examples ... [161s/161s] OK
* checking PDF version of manual ... OK

WARNING: There were 5 warnings.
NOTE: There were 2 notes.
See
  ‘/mnt/building/build_2012-04-13-10-57/RF_PKG_CHECK/PKGS/mpcbs.Rcheck/00check.log’
for details.

Run time: 207.85 seconds.