CRAN Package Check Results for Package metaboGSE

Last updated on 2018-04-08 09:15:07 CEST.

Check Details

Version: 1.0.1
Check: installed package size
Result: NOTE
     installed size is 6.1Mb
     sub-directories of 1Mb or more:
     data 5.6Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in 'metaboGSE-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: submnet
    > ### Title: Simulation of gene removal-based submodels
    > ### Aliases: submnet
    >
    > ### ** Examples
    >
    > data(Ec_core)
    > mod <- rescue(Ec_core, target=0.1)
    Loading required package: glpkAPI
    using GLPK version 4.47
    > mod.weight <- changeObjFunc(mod$rescue, react=rownames(mod$coef), obj_coef=mod$coef)
    > expr <- matrix(replicate(2, rnorm(length(sybil::allGenes(mod.weight)), mean=5, sd=4)),
    + ncol=2,
    + dimnames=list(sybil::allGenes(mod.weight), c('rep.1', 'rep.2')))
    > gene.sets <- list(X1=head(rownames(expr)), X2=tail(rownames(expr)))
    > sgd <- submnet(model=mod.weight,
    + expr=expr, step=200, obj.react="Biomass_Ecoli_core_w_GAM", gene.sets=gene.sets)
    Error in pdf(paste0("/tmp/recoclusterweight_", gene.num, "_", draw.num, :
     cannot open file '/tmp/recoclusterweight_1_1000znlfz.pdf'
    Calls: submnet -> weightReacts -> pdf
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: sybil
    Loading required package: Matrix
    Loading required package: lattice
    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 objects are masked from 'package:Matrix':
    
     colMeans, colSums, rowMeans, rowSums, which
    
    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: 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: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:Matrix':
    
     expand
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    Loading required package: ape
    Loading required package: topGO
    Loading required package: graph
    
    Attaching package: 'graph'
    
    The following objects are masked from 'package:ape':
    
     complement, edges
    
    Loading required package: GO.db
    
    Loading required package: SparseM
    
    Attaching package: 'SparseM'
    
    The following object is masked from 'package:base':
    
     backsolve
    
    
    groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
    
    Attaching package: 'topGO'
    
    The following object is masked from 'package:IRanges':
    
     members
    
    The following objects are masked from 'package:sybil':
    
     algorithm, algorithm<-, allGenes, genes
    
    Loading required package: clpAPI
    using COIN OR Clp version 1.16.9
    Quitting from lines 156-159 (metaboGSE.Rmd)
    Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
    cannot open file '/tmp/recoclusterweight_1_1000clfbc.pdf'
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: sybil
    Loading required package: Matrix
    Loading required package: lattice
    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 objects are masked from 'package:Matrix':
    
     colMeans, colSums, rowMeans, rowSums, which
    
    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, cbind, colMeans, colSums, colnames, 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: 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: IRanges
    Loading required package: S4Vectors
    
    Attaching package: 'S4Vectors'
    
    The following object is masked from 'package:Matrix':
    
     expand
    
    The following object is masked from 'package:base':
    
     expand.grid
    
    Loading required package: ape
    Loading required package: topGO
    Loading required package: graph
    
    Attaching package: 'graph'
    
    The following objects are masked from 'package:ape':
    
     complement, edges
    
    Loading required package: GO.db
    
    Loading required package: SparseM
    
    Attaching package: 'SparseM'
    
    The following object is masked from 'package:base':
    
     backsolve
    
    
    groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
    
    Attaching package: 'topGO'
    
    The following object is masked from 'package:IRanges':
    
     members
    
    The following objects are masked from 'package:sybil':
    
     algorithm, algorithm<-, allGenes, genes
    
    Loading required package: clpAPI
    using COIN OR Clp version 1.16.9
    Quitting from lines 156-159 (metaboGSE.Rmd)
    Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
    cannot open file '/tmp/recoclusterweight_1_1000clfbc.pdf'
    Execution halted
Flavor: r-release-windows-ix86+x86_64

Version: 1.0.1
Check: package dependencies
Result: ERROR
    Package required and available but unsuitable version: ‘sybil’
    
    Packages suggested but not available for checking: ‘clpAPI’ ‘glpkAPI’ ‘ctc’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64