CRAN Package Check Results for Package QNB

Last updated on 2018-03-05 09:05:26 CET.

Check Details

Version: 1.1.11
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: locfit
    locfit 1.5-9.1 2013-03-22
    Loading required package: GenomicFeatures
    Loading required package: BiocGenerics
    Loading required package: parallel
    
    Attaching package: ‘BiocGenerics’
    
    The following objects are masked from ‘package:parallel’:
    
     clusterApply, clusterApplyLB, clusterCall,
     clusterEvalQ, clusterExport, clusterMap,
     parApply, parCapply, parLapply, parLapplyLB,
     parRapply, parSapply, parSapplyLB
    
    The following objects are masked from ‘package:stats’:
    
     IQR, mad, sd, var, xtabs
    
    The following objects are masked from ‘package:base’:
    
     Filter, Find, Map, Position, Reduce,
     anyDuplicated, append, as.data.frame, basename,
     cbind, colMeans, colSums, colnames, dirname,
     do.call, duplicated, eval, evalq, get, grep,
     grepl, intersect, is.unsorted, lapply, lengths,
     mapply, match, mget, order, paste, pmax,
     pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
     rowSums, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max,
     which.min
    
    Loading required package: S4Vectors
    Loading required package: stats4
    
    Attaching package: ‘S4Vectors’
    
    The following object is masked from ‘package:base’:
    
     expand.grid
    
    Loading required package: IRanges
    Loading required package: GenomeInfoDb
    Loading required package: GenomicRanges
    Loading required package: AnnotationDbi
    Loading required package: Biobase
    Welcome to Bioconductor
    
     Vignettes contain introductory material; view
     with 'browseVignettes()'. To cite Bioconductor,
     see 'citation("Biobase")', and for packages
     'citation("pkgname")'.
    
    Loading required package: Rsamtools
    Loading required package: Biostrings
    Loading required package: XVector
    
    Attaching package: ‘Biostrings’
    
    The following object is masked from ‘package:base’:
    
     strsplit
    
    Loading required package: exomePeak
    Loading required package: rtracklayer
    Loading required package: GenomicAlignments
    Loading required package: SummarizedExperiment
    Loading required package: DelayedArray
    Loading required package: matrixStats
    
    Attaching package: ‘matrixStats’
    
    The following objects are masked from ‘package:Biobase’:
    
     anyMissing, rowMedians
    
    Loading required package: BiocParallel
    
    Attaching package: ‘DelayedArray’
    
    The following objects are masked from ‘package:matrixStats’:
    
     colMaxs, colMins, colRanges, rowMaxs, rowMins,
     rowRanges
    
    The following object is masked from ‘package:Biostrings’:
    
     type
    
    The following objects are masked from ‘package:base’:
    
     aperm, apply
    
    Import genomic features from the file as a GRanges object ... OK
    Prepare the 'metadata' data frame ... OK
    Make the TxDb object ... OK
    'select()' returned 1:many mapping between keys and
    columns
    
    Error: processing vignette ‘QNB-Overview.Rnw’ failed with diagnostics:
     chunk 7 (label = The complete processing flow)
    Error in makeTxDbFromUCSC(genome = "hg19") :
     Couldn't load the RMariaDB package. You need to
     install the RMariaDB package in order to use
     makeTxDbFromUCSC().
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.1.11
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    The following objects are masked from 'package:matrixStats':
    
     colMaxs, colMins, colRanges, rowMaxs, rowMins,
     rowRanges
    
    The following object is masked from 'package:Biostrings':
    
     type
    
    The following objects are masked from 'package:base':
    
     aperm, apply
    
    Import genomic features from the file as a GRanges object ... OK
    Prepare the 'metadata' data frame ... OK
    Make the TxDb object ... OK
    'select()' returned 1:many mapping between keys and
    columns
    Download the knownGene table ...
    Error: processing vignette 'QNB-Overview.Rnw' failed with diagnostics:
     chunk 7 (label = The complete processing flow)
    Error : Bad Request
    
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.1.11
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    The following objects are masked from 'package:matrixStats':
    
     colMaxs, colMins, colRanges, rowMaxs, rowMins,
     rowRanges
    
    The following object is masked from 'package:Biostrings':
    
     type
    
    The following object is masked from 'package:base':
    
     apply
    
    Import genomic features from the file as a GRanges object ... OK
    Prepare the 'metadata' data frame ... OK
    Make the TxDb object ... OK
    'select()' returned 1:many mapping between keys and
    columns
    Download the knownGene table ...
    Error: processing vignette 'QNB-Overview.Rnw' failed with diagnostics:
     chunk 7 (label = The complete processing flow)
    Error : Bad Request
    
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 1.1.11
Check: package dependencies
Result: ERROR
    Packages required but not available:
     ‘GenomicFeatures’ ‘Rsamtools’ ‘exomePeak’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64