CRAN Package Check Results for Package netClass

Last updated on 2014-10-26 01:48:11.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.2.1 14.24 118.25 132.49 NOTE
r-devel-linux-x86_64-debian-gcc 1.2.1 10.45 117.82 128.27 NOTE
r-devel-linux-x86_64-fedora-clang 1.2.1 313.99 NOTE
r-devel-linux-x86_64-fedora-gcc 1.2.1 299.12 NOTE
r-devel-osx-x86_64-clang 1.2.1 244.16 NOTE
r-devel-windows-ix86+x86_64 1.2.1 26.00 150.00 176.00 ERROR
r-patched-linux-x86_64 1.2.1 11.78 124.62 136.40 NOTE
r-patched-solaris-sparc 1.2.1 1652.30 NOTE
r-patched-solaris-x86 1.2.1 402.90 NOTE
r-release-linux-ix86 1.2.1 11.50 128.68 140.17 OK
r-release-linux-x86_64 1.2.1 10.10 111.25 121.35 OK
r-release-osx-x86_64-mavericks 1.2.1 ERROR
r-release-osx-x86_64-snowleopard 1.2.1 ERROR
r-release-windows-ix86+x86_64 1.2.1 24.00 158.00 182.00 OK
r-oldrel-windows-ix86+x86_64 1.2.1 27.00 151.00 178.00 ERROR

Check Details

Version: 1.2.1
Check: R code for possible problems
Result: NOTE
    XH: no visible binding for global variable ‘exprs’
    XIs: no visible binding for global variable ‘exprs’
    cv.aep: no visible global function definition for ‘mclapply’
    cv.frsvm: no visible global function definition for ‘mclapply’
    cv.hubc: no visible global function definition for ‘mclapply’
    cv.pac: no visible global function definition for ‘mclapply’
    cv.stsvm: no visible global function definition for ‘mclapply’
    probeset2pathway: no visible binding for global variable
     ‘KEGGEXTID2PATHID’
    probeset2pathwayTrain: no visible binding for global variable
     ‘KEGGEXTID2PATHID’
    spanbound: no visible global function definition for ‘param’
    spanbound: no visible global function definition for ‘error’
    spanbound: no visible global function definition for ‘kernelf’
    spanbound: no visible global function definition for ‘b’
    svm.predict: no visible global function definition for ‘b’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in 'netClass-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: cv.aep
    > ### Title: Cross validation for aepSVM (aepSVM)
    > ### Aliases: cv.aep
    > ### Keywords: aep
    >
    > ### ** Examples
    >
    > library(netClass)
    > data(expr)
    > data(ad.matrix)
    > x <- expr$genes
    > y <- expr$y
    >
    > library(KEGG.db)
    Loading required package: AnnotationDbi
    Loading required package: stats4
    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 object is masked from 'package:stats':
    
     xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
     eval, evalq, get, intersect, is.unsorted, lapply, mapply, match,
     mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
     rep.int, rownames, sapply, setdiff, sort, table, tapply, union,
     unique, unlist, unsplit
    
    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: GenomeInfoDb
    Loading required package: S4Vectors
    Loading required package: IRanges
    
    Attaching package: 'AnnotationDbi'
    
    The following object is masked from 'package:GenomeInfoDb':
    
     species
    
    Loading required package: DBI
    Error : .onLoad failed in loadNamespace() for 'KEGG.db', details:
     call: ls(envir, all.names = TRUE)
     error: 2 arguments passed to .Internal(ls) which requires 3
    Error: package or namespace load failed for 'KEGG.db'
    Error during wrapup: cannot open the connection
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.2.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘KEGG.db’
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in ‘netClass-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: cv.aep
    > ### Title: Cross validation for aepSVM (aepSVM)
    > ### Aliases: cv.aep
    > ### Keywords: aep
    >
    > ### ** Examples
    >
    > library(netClass)
    > data(expr)
    > data(ad.matrix)
    > x <- expr$genes
    > y <- expr$y
    >
    > library(KEGG.db)
    Error in library(KEGG.db) : there is no package called ‘KEGG.db’
    Execution halted
Flavors: r-release-osx-x86_64-mavericks, r-release-osx-x86_64-snowleopard

Version: 1.2.1
Check: R code for possible problems
Result: NOTE
    Error : .onLoad failed in loadNamespace() for 'KEGG.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
    probeset2pathway: no visible binding for global variable
     'KEGGEXTID2PATHID'
    probeset2pathwayTrain: no visible binding for global variable
     'KEGGEXTID2PATHID'
Flavor: r-oldrel-windows-ix86+x86_64

Version: 1.2.1
Check: examples
Result: ERROR
    Running examples in 'netClass-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: cv.aep
    > ### Title: Cross validation for aepSVM (aepSVM)
    > ### Aliases: cv.aep
    > ### Keywords: aep
    >
    > ### ** Examples
    >
    > library(netClass)
    > data(expr)
    > data(ad.matrix)
    > x <- expr$genes
    > y <- expr$y
    >
    > library(KEGG.db)
    Loading required package: AnnotationDbi
    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 object is masked from 'package:stats':
    
     xtabs
    
    The following objects are masked from 'package:base':
    
     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
     as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq,
     get, intersect, is.unsorted, lapply, mapply, match, mget, order,
     paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rep.int,
     rownames, sapply, setdiff, sort, table, tapply, union, unique,
     unlist
    
    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: DBI
    Error : .onLoad failed in loadNamespace() for 'KEGG.db', details:
     call: match.arg(synchronous, c("off", "normal", "full"))
     error: 'arg' must be NULL or a character vector
    Error: package or namespace load failed for 'KEGG.db'
    Error during wrapup: cannot open the connection
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64