SCM

R Development Page

FIRMAGene log file (check_x86_64_linux)

Wed May 29 12:17:15 2013: Checking package FIRMAGene (SVN revision 166) ...
* using log directory ‘/mnt/building/build_2013-05-29-12-07/RF_PKG_CHECK/PKGS/FIRMAGene.Rcheck’
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘FIRMAGene/DESCRIPTION’ ... OK
* this is package ‘FIRMAGene’ version ‘0.9.8’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Mark Robinson ’
New submission
* 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘FIRMAGene’ can be installed ... [2s/4s] WARNING
Found the following significant warnings:
  Warning: ignoring .First.lib() for package ‘FIRMAGene’
See ‘/mnt/building/build_2013-05-29-12-07/RF_PKG_CHECK/PKGS/FIRMAGene.Rcheck/00install.out’ for details.
* 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
plotDecompAroma:
  function(...)
plotDecompAroma.default:
  function(plm, id, col, lwd, vlines)

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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

FIRMAGene : : warning in matrix(sample(resMatrix, size = u *
  nSamples), nc = nSamples): partial argument match of 'nc' to 'ncol'
topSplices: warning in matrix(rank(-fgObj$firmaGeneScores), nc =
  ncol(fgObj$firmaGeneScores), dimnames = dimnames(fgObj$mufScores)):
  partial argument match of 'nc' to 'ncol'
* checking Rd files ... NOTE
prepare_Rd: mufMaxPositions.Rd:17-18: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘getDetails.ProbeLevelModel’ ‘plotDecompAroma.ProbeLevelModel’
  ‘plotDecompAroma.default’
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 'getDetails':
getDetails
  Code: function(...)
  Docs: function(plm, probesets, id = "7952953", mart = NULL,
                 verticalBars = FALSE, geneSymbolId =
                 "external_gene_id", transcriptClusterId =
                 "Transcript.Cluster.ID", colours = "blue", lwd = 1, o
                 = NULL, verbose = FALSE)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    plm probesets id mart verticalBars geneSymbolId transcriptClusterId
    colours lwd o verbose
  Mismatches in argument names:
    Position: 1 Code: ... Docs: plm

Codoc mismatches from documentation object 'plotDecompAroma':
plotDecompAroma
  Code: function(...)
  Docs: function(plm, id = "7952953", col = "black", lwd = 1, vlines =
                 NULL)
  Argument names in code not in docs:
    ...
  Argument names in docs not in code:
    plm id col lwd vlines
  Mismatches in argument names:
    Position: 1 Code: ... Docs: plm

* 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 use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
* checking examples ... [1s/2s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘FIRMAGene-Tests.R’
 [1s/2s] OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2013-05-29-12-07/RF_PKG_CHECK/PKGS/FIRMAGene.Rcheck/00check.log’
for details.

Run time: 80.77 seconds.

Additional Logs:   00install.out
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge