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Repitools log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/Repitools.Rcheck'
* using R version 2.15.2 Patched (2013-01-31 r61797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'Repitools/DESCRIPTION' ... OK
* this is package 'Repitools' version '1.81'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Mark Robinson '
Package duplicated from http://www.bioconductor.org/packages/2.11/bioc
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'RepitoolsExamples'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking whether package 'Repitools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  LGPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
  LGPL (>= 2.0)
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.blocksStats: warning in matrix(NA, nr = nrow(coordinatesTable), nc =
  ncol(diffs), dimnames = list(NULL, colnames(design))): partial
  argument match of 'nr' to 'nrow'
.blocksStats: warning in matrix(NA, nr = nrow(coordinatesTable), nc =
  ncol(diffs), dimnames = list(NULL, colnames(design))): partial
  argument match of 'nc' to 'ncol'
.fdrTable: warning in matrix(, nr = length(cuts), nc = 4): partial
  argument match of 'nr' to 'nrow'
.fdrTable: warning in matrix(, nr = length(cuts), nc = 4): partial
  argument match of 'nc' to 'ncol'
.regionStats: warning in matrix(, nr = nrow(diffs), nc = ncol(diffs)):
  partial argument match of 'nr' to 'nrow'
.regionStats: warning in matrix(, nr = nrow(diffs), nc = ncol(diffs)):
  partial argument match of 'nc' to 'ncol'
.regionStats : : warning in matrix(NA, nr = nrow(diffs), nc
  = nPermutations): partial argument match of 'nr' to 'nrow'
.regionStats : : warning in matrix(NA, nr = nrow(diffs), nc
  = nPermutations): partial argument match of 'nc' to 'ncol'
.regionStats : : warning in .fdrTable(tmeanReal[, col], u,
  ch, sp, 40, nProbes, maxGap, twoSides, maxCut = mx, verbose =
  verbose): partial argument match of 'maxCut' to 'maxCutoff'
checkProbes: warning in pdf(paste(outFile, ".pdf", sep = ""), h = 8, w
  = 12): partial argument match of 'w' to 'width'
checkProbes: warning in pdf(paste(outFile, ".pdf", sep = ""), h = 8, w
  = 12): partial argument match of 'h' to 'height'
genQC: warning in pdf(paste("QC ", exptName, ".pdf", sep = ""), h =
  8.3, w = 11.7): partial argument match of 'w' to 'width'
genQC: warning in pdf(paste("QC ", exptName, ".pdf", sep = ""), h =
  8.3, w = 11.7): partial argument match of 'h' to 'height'
multiHeatmap: warning in viewport(x = start[i], y = ystarts[1], w =
  (end[i] - start[i]), h = diff(ystarts[1:2]), just = c("left",
  "bottom"), name = "vp1"): partial argument match of 'w' to 'width'
multiHeatmap: warning in viewport(x = start[i], y = ystarts[1], w =
  (end[i] - start[i]), h = diff(ystarts[1:2]), just = c("left",
  "bottom"), name = "vp1"): partial argument match of 'h' to 'height'
multiHeatmap: warning in viewport(x = end[i], y = ystarts[3], w =
  min(cwidth * nc/tw), h = diff(ystarts[3:4]), just = c("right",
  "bottom"), name = "vp2"): partial argument match of 'w' to 'width'
multiHeatmap: warning in viewport(x = end[i], y = ystarts[3], w =
  min(cwidth * nc/tw), h = diff(ystarts[3:4]), just = c("right",
  "bottom"), name = "vp2"): partial argument match of 'h' to 'height'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'AffymetrixCelSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 contents of 'data' directory ... WARNING
Files not of a type allowed in a 'data' directory:
  'expr.Rdata' 'samplesList.Rdata'
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... ERROR
Running examples in 'Repitools-Ex.R' failed
The error most likely occurred in:

> ### Name: annotationBlocksLookup
> ### Title: Forms a mapping between probe locations and chromosomal blocks
> ###   (regions)
> ### Aliases: annotationBlocksLookup
> 
> ### ** Examples
> 
> # create example set of probes and gene start sites
> probeTab <- data.frame(position=seq(1000,3000,by=200), chr="chrX", strand="+")
> genes <- data.frame(chr="chrX", start=c(2100,2200), end=c(2500, 2400), strand=c("+","-"))
> rownames(genes) <- paste("gene",1:2,sep="")
> 
> # Call annotationLookup() and look at output
> annotationBlocksLookup(probeTab, genes)
Processing mapping between probes and genes.
Error in tapply(anno.overlaps@matchMatrix[, 1], anno.overlaps@matchMatrix[,  : 
  error in evaluating the argument 'X' in selecting a method for function 'tapply': Error: no slot of name "matchMatrix" for this object of class "Hits"
Calls: annotationBlocksLookup -> processChromosome -> tapply
Execution halted
Run time: 138.83 seconds.

Additional Logs:   00install.out
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