CRAN Package Check Results for Package PSCBS

Last updated on 2017-04-27 10:48:39.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.62.0 10.20 276.76 286.97 OK
r-devel-linux-x86_64-debian-gcc 0.62.0 10.05 270.05 280.09 OK
r-devel-linux-x86_64-fedora-clang 0.62.0 565.07 OK --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 0.62.0 540.19 OK --no-stop-on-test-error
r-devel-windows-ix86+x86_64 0.62.0 23.00 501.00 524.00 OK
r-patched-linux-x86_64 0.62.0 10.18 275.88 286.06 OK
r-patched-solaris-sparc 0.62.0 3371.40 OK --no-build-vignettes
r-patched-solaris-x86 0.62.0 827.90 OK
r-release-linux-x86_64 0.62.0 10.60 276.01 286.61 OK
r-release-windows-ix86+x86_64 0.62.0 18.00 422.00 440.00 OK
r-release-osx-x86_64 0.62.0 ERROR
r-oldrel-windows-ix86+x86_64 0.62.0 17.00 549.00 566.00 OK
r-oldrel-osx-x86_64 0.62.0 OK

Check Details

Version: 0.62.0
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘aroma.light’
Flavor: r-release-osx-x86_64

Version: 0.62.0
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘aroma.light’
Flavor: r-release-osx-x86_64

Version: 0.62.0
Check: examples
Result: ERROR
    Running examples in ‘PSCBS-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: segmentByNonPairedPSCBS
    > ### Title: Segment total copy numbers and allele B fractions using the
    > ### Non-paired PSCBS method
    > ### Aliases: segmentByNonPairedPSCBS.default segmentByNonPairedPSCBS
    > ### segmentByNonPairedPSCBS.data.frame
    > ### segmentByNonPairedPSCBS.PairedPSCBS segmentByNonPairedPSCBS
    > ### Keywords: IO
    >
    > ### ** Examples
    >
    > verbose <- R.utils::Arguments$getVerbose(-10*interactive(), timestamp=TRUE)
    >
    > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    > # Load SNP microarray data
    > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    > data <- PSCBS::exampleData("paired.chr01")
    > str(data)
    'data.frame': 73346 obs. of 6 variables:
     $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ...
     $ x : int 1145994 2224111 2319424 2543484 2926730 2941694 3084986 3155127 3292731 3695086 ...
     $ CT : num 1.625 1.071 1.406 1.18 0.856 ...
     $ betaT : num 0.757 0.771 0.834 0.778 0.229 ...
     $ CN : num 2.36 2.13 2.59 1.93 1.71 ...
     $ betaN : num 0.827 0.875 0.887 0.884 0.103 ...
    >
    >
    > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    > # Paired PSCBS segmentation
    > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    > # Drop single-locus outliers
    > dataS <- dropSegmentationOutliers(data)
    >
    > # Speed up example by segmenting fewer loci
    > dataS <- dataS[seq(from=1, to=nrow(data), by=20),]
    >
    > str(dataS)
    'data.frame': 3668 obs. of 6 variables:
     $ chromosome: int 1 1 1 1 1 1 1 1 1 1 ...
     $ x : int 1145994 4276892 5034491 6266412 8418532 11211748 13928296 14370144 15014887 16589707 ...
     $ CT : num 1.63 1.16 1.35 1.39 1.55 ...
     $ betaT : num 0.7574 0.0576 0.8391 0.7917 0.8141 ...
     $ CN : num 2.36 2.32 2.33 2.97 2.31 ...
     $ betaN : num 0.8274 0.0421 0.9406 0.869 0.6045 ...
    >
    > R.oo::attachLocally(dataS)
    >
    > # Non-Paired PSCBS segmentation
    > fit <- segmentByNonPairedPSCBS(CT, betaT=betaT,
    + chromosome=chromosome, x=x,
    + seed=0xBEEF, verbose=verbose)
    Warning in parseRepos(sets = repos, where = where, fallback = fallback, :
     Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’
    [2017-04-21 00:23:01] Exception: Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
    
     at #06. installPkg(pkg, version = version, repos = repos, ..., quietly = quietly,
     verbose = verbose)
     - installPkg() is local of the calling function
    
     at #05. use.default(package, ..., how = "load")
     - use.default() is in environment 'R.utils'
    
     at #04. use(package, ..., how = "load")
     - use() is in environment 'R.utils'
    
     at #03. .use("findPeaksAndValleys", package = "aroma.light")
     - .use() is in environment 'PSCBS'
    
     at #02. segmentByNonPairedPSCBS.default(CT, betaT = betaT, chromosome = chromosome,
     x = x, seed = 48879, verbose = verbose)
     - segmentByNonPairedPSCBS.default() is in environment 'PSCBS'
    
     at #01. segmentByNonPairedPSCBS(CT, betaT = betaT, chromosome = chromosome,
     x = x, seed = 48879, verbose = verbose)
     - segmentByNonPairedPSCBS() is in environment 'PSCBS'
    
    Error: Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.62.0
Check: tests
Result: ERROR
     Running ‘PairedPSCBS,boot.R’ [3s/4s]
    Running the tests in ‘tests/PairedPSCBS,boot.R’ failed.
    Last 13 lines of output:
     at #02. segmentByPairedPSCBS.data.frame(dataS, knownSegments = knownSegments,
     avgDH = "median", seed = 48879)
     - segmentByPairedPSCBS.data.frame() is in environment 'PSCBS'
    
     at #01. segmentByPairedPSCBS(dataS, knownSegments = knownSegments, avgDH = "median",
     seed = 48879)
     - segmentByPairedPSCBS() is in environment 'PSCBS'
    
     Error: Package 'aroma.light' is not available from any of the repositories: 'http://cran.r-project.org'
     In addition: Warning messages:
     1: In segmentByPairedPSCBS.default(CT = data$CT, thetaT = data$thetaT, :
     Argument 'preserveScale' for segmentByPairedPSCBS() now defaults to FALSE. Prior to PSCBS v0.50.0 (October 2015) the default was TRUE. To avoid this warning, explicitly specify this argument when calling segmentByPairedPSCBS() or make sure to set option 'PSCBS/preserveScale' to either TRUE or FALSE. This warning will be removed in a future version.
     2: In parseRepos(sets = repos, where = where, fallback = fallback, :
     Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: '@CRAN@' -> 'http://cran.r-project.org'
     Execution halted
Flavor: r-release-osx-x86_64

Version: 0.62.0
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in ‘PairedPSCBS.tex.rsp’
     ...
     Calling genotypes from normal allele B fractions...
     num [1:73346] 0.827 0.875 0.887 0.884 0.103 ...
    Warning in parseRepos(sets = repos, where = where, fallback = fallback, :
     Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’
     Calling genotypes from normal allele B fractions...done
    Segmenting paired tumor-normal signals using Paired PSCBS...done
    
     When sourcing ‘PairedPSCBS.R’:
    Error: Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
    Execution halted
Flavor: r-release-osx-x86_64

Version: 0.62.0
Check: re-building of vignette outputs
Result: NOTE
    Error in re-building vignettes:
     ...
     Cluster #4 of 5...done
     Cluster #5 of 5...
     Segments in cluster:
     int 8
     Left indices of neighboring segments:
     int(0)
     Cluster #5 of 5...done
     Left indices of segments to be merged:
     int 6
     Merging neighboring segments within each cluster...done
     Merging segments...
     Merging segments...done
     Updating segment means...
     Updating segment means...done
    Prune segments by hierarchical clustering...done
    Segmenting paired tumor-normal signals using Paired PSCBS...
     Calling genotypes from normal allele B fractions...
     num [1:73346] 0.827 0.875 0.887 0.884 0.103 ...
    Warning in parseRepos(sets = repos, where = where, fallback = fallback, :
     Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: ‘@CRAN@’ -> ‘http://cran.r-project.org’
     Calling genotypes from normal allele B fractions...done
    Segmenting paired tumor-normal signals using Paired PSCBS...done
    Error: processing vignette 'PairedPSCBS.tex.rsp' failed with diagnostics:
    Package 'aroma.light' is not available from any of the repositories: ‘http://cran.r-project.org’
    Execution halted
Flavor: r-release-osx-x86_64