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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Repitools_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Repitools.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Repitools/DESCRIPTION’ ... OK
* this is package ‘Repitools’ version ‘1.14.0’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Repitools’ can be installed ... [42s/46s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 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
clusterPlots,ClusteredScoresList : .local : <anonymous>: warning in
axis(2, at = c(y.min, (y.min + y.max)/2, y.max), label =
score.labels): partial argument match of 'label' to 'labels'
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
function definition for ‘nbrOfArrays’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
function definition for ‘extract’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible binding for
global variable ‘verbose’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
function definition for ‘getCdf’
.blocksStats,AffymetrixCelSet-GRanges : .local: no visible global
function definition for ‘extractMatrix’
.featureScores,AffymetrixCelSet-GRanges : .local: no visible global
function definition for ‘getCdf’
.featureScores,AffymetrixCelSet-GRanges : .local: no visible binding
for global variable ‘verbose’
.featureScores,AffymetrixCelSet-GRanges : .local: no visible global
function definition for ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
variable ‘Arguments’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘pushState’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘popState’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘nbrOfArrays’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘getCdf’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘getMainCdf’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘nbrOfUnits’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘indexOf’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘enter’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘getCellIndices’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘exit’
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
variable ‘AromaCellSequenceFile’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘getChipType’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘countBases’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘extract’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘getNames’
cpgBoxplots,AffymetrixCelSet : .local: no visible global function
definition for ‘extractMatrix’
cpgBoxplots,AffymetrixCelSet : .local: no visible binding for global
variable ‘AromaCellCpgFile’
cpgBoxplots,matrix : .local: no visible binding for global variable
‘Arguments’
cpgBoxplots,matrix : .local: no visible global function definition for
‘pushState’
cpgBoxplots,matrix : .local: no visible global function definition for
‘popState’
cpgBoxplots,matrix : .local: no visible global function definition for
‘enter’
cpgBoxplots,matrix : .local: no visible global function definition for
‘exit’
cpgDensityCalc,GRanges-BSgenome : .local: no visible global function
definition for ‘DNAString’
getProbePositionsDf,AffymetrixCdfFile : .local: no visible global
function definition for ‘getCellIndices’
getProbePositionsDf,AffymetrixCdfFile : .local: no visible binding for
global variable ‘AromaCellPositionFile’
getProbePositionsDf,AffymetrixCdfFile : .local: no visible global
function definition for ‘getChipType’
regionStats,AffymetrixCelSet : .local: no visible global function
definition for ‘getCdf’
regionStats,AffymetrixCelSet : .local: no visible global function
definition for ‘getCellIndices’
regionStats,AffymetrixCelSet : .local: no visible global function
definition for ‘nbrOfArrays’
regionStats,AffymetrixCelSet : .local: no visible binding for global
variable ‘AromaCellPositionFile’
regionStats,AffymetrixCelSet : .local: no visible global function
definition for ‘getChipType’
regionStats,AffymetrixCelSet : .local: no visible global function
definition for ‘extract’
regionStats,AffymetrixCelSet : .local: no visible global function
definition for ‘extractMatrix’
sequenceCalc,GRanges-BSgenome : .local : <anonymous>: no visible global
function definition for ‘matchPattern’
writeWig,AffymetrixCelSet : .local: no visible global function
definition for ‘getNames’
writeWig,AffymetrixCelSet : .local: no visible global function
definition for ‘extract’
writeWig,AffymetrixCelSet : .local: no visible global function
definition for ‘getCdf’
writeWig,AffymetrixCelSet : .local: no visible global function
definition for ‘extractMatrix’
* checking Rd files ... OK
* 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 ... OK
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘Repitools-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cpgDensityCalc
> ### Title: Calculate CpG Density in a Window
> ### Aliases: cpgDensityCalc cpgDensityCalc,data.frame,BSgenome-method
> ### cpgDensityCalc,GRangesList,BSgenome-method
> ### cpgDensityCalc,GRanges,BSgenome-method
>
> ### ** Examples
>
> if(require(BSgenome.Hsapiens.UCSC.hg18))
+ {
+ TSSTable <- data.frame(chr = c("chr1", "chr2"), position = c(100000, 200000))
+ cpgDensityCalc(TSSTable, organism = Hsapiens, window = 600)
+ }
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Loading required package: BSgenome
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Attaching package: ‘rtracklayer’
The following object is masked from ‘package:Repitools’:
blocks
Error in start(matchPattern(pattern, organism[[x]], fixed = fixed)) :
error in evaluating the argument 'x' in selecting a method for function 'start': Error in matchPattern(pattern, organism[[x]], fixed = fixed) :
error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': Error: error reading from connection
Calls: cpgDensityCalc ... RangesList -> lapply -> lapply -> FUN -> IRanges -> is -> start
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘tests.R’ [23s/23s]
ERROR
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
> correctLookupTable[6, c(51, 52)] <- 7
>
> if(!all(lookupTable == correctLookupTable, na.rm = TRUE))
+ stop("Error in makeWindowLookupTable function")
> cat("makeWindowLookupTable tested fine.\n")
makeWindowLookupTable tested fine.
>
> cpgDensity <- cpgDensityCalc(genes, organism = Hsapiens, window = 500, w.function="linear")
Error in start(matchPattern(pattern, organism[[x]], fixed = fixed)) :
error in evaluating the argument 'x' in selecting a method for function 'start': Error in matchPattern(pattern, organism[[x]], fixed = fixed) :
error in evaluating the argument 'subject' in selecting a method for function 'matchPattern': Error: error reading from connection
Calls: cpgDensityCalc ... RangesList -> lapply -> lapply -> FUN -> IRanges -> is -> start
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 NOTE
See
‘/Users/biocbuild/bbs-3.1-bioc/meat/Repitools.Rcheck/00check.log’
for details.