CRAN Package Check Results for Package metaRNASeq

Last updated on 2020-09-22 14:05:02 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.2 2.17 304.74 306.91 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.2 1.55 200.87 202.42 NOTE
r-devel-linux-x86_64-fedora-clang 1.0.2 382.15 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.2 373.78 NOTE
r-devel-windows-ix86+x86_64 1.0.2 4.00 35.00 39.00 NOTE --no-vignettes
r-patched-linux-x86_64 1.0.2 1.80 304.23 306.03 NOTE
r-patched-solaris-x86 1.0.2 727.90 NOTE --no-build-vignettes
r-release-linux-x86_64 1.0.2 1.82 303.36 305.18 NOTE
r-release-macos-x86_64 1.0.2 WARN
r-release-windows-ix86+x86_64 1.0.2 4.00 33.00 37.00 NOTE --no-vignettes
r-oldrel-macos-x86_64 1.0.2 WARN
r-oldrel-windows-ix86+x86_64 1.0.2 3.00 45.00 48.00 NOTE --no-vignettes

Check Details

Version: 1.0.2
Check: R code for possible problems
Result: NOTE
    fishercomb: no visible global function definition for 'pchisq'
    fishercomb: no visible global function definition for 'p.adjust'
    invnorm : <anonymous>: no visible global function definition for
     'qnorm'
    invnorm: no visible global function definition for 'pnorm'
    invnorm: no visible global function definition for 'p.adjust'
    sim.function : <anonymous>: no visible global function definition for
     'rnorm'
    sim.function : <anonymous>: no visible global function definition for
     'rnbinom'
    Undefined global functions or variables:
     p.adjust pchisq pnorm qnorm rnbinom rnorm
    Consider adding
     importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
     "rnorm")
    to your NAMESPACE file.
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-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 1.0.2
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    fishercomb: no visible global function definition for 'pchisq'
    fishercomb: no visible global function definition for 'p.adjust'
    invnorm : <anonymous>: no visible global function definition for
     'qnorm'
    invnorm: no visible global function definition for 'pnorm'
    invnorm: no visible global function definition for 'p.adjust'
    sim.function : <anonymous>: no visible global function definition for
     'rnorm'
    sim.function : <anonymous>: no visible global function definition for
     'rnbinom'
    Undefined global functions or variables:
     p.adjust pchisq pnorm qnorm rnbinom rnorm
    Consider adding
     importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
     "rnorm")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.2
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    fishercomb: no visible global function definition for ‘pchisq’
    fishercomb: no visible global function definition for ‘p.adjust’
    invnorm : <anonymous>: no visible global function definition for
     ‘qnorm’
    invnorm: no visible global function definition for ‘pnorm’
    invnorm: no visible global function definition for ‘p.adjust’
    sim.function : <anonymous>: no visible global function definition for
     ‘rnorm’
    sim.function : <anonymous>: no visible global function definition for
     ‘rnbinom’
    Undefined global functions or variables:
     p.adjust pchisq pnorm qnorm rnbinom rnorm
    Consider adding
     importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
     "rnorm")
    to your NAMESPACE file.
Flavor: r-patched-solaris-x86

Version: 1.0.2
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘HTSFilter’
Flavor: r-release-macos-x86_64

Version: 1.0.2
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘metaRNASeq.Rnw’
     ...
     estimateSizeFactorsForMatrix,
     getVarianceStabilizedData,
     varianceStabilizingTransformation
    
    
    > library(HTSFilter)
    
     When sourcing ‘metaRNASeq.R’:
    Error: there is no package called ‘HTSFilter’
    Execution halted
    
     ‘metaRNASeq.Rnw’... failed
Flavor: r-release-macos-x86_64

Version: 1.0.2
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
    --- re-building ‘metaRNASeq.Rnw’ using Sweave
    Loading required package: S4Vectors
    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: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, colnames, dirname, do.call, duplicated,
     eval, evalq, get, grep, grepl, intersect,
     is.unsorted, lapply, mapply, match, mget, order,
     paste, pmax, pmax.int, pmin, pmin.int, rank,
     rbind, rownames, sapply, setdiff, sort, table,
     tapply, union, unique, unsplit, which, which.max,
     which.min
    
    
    Attaching package: ‘S4Vectors’
    
    The following object is masked from ‘package:base’:
    
     expand.grid
    
    Loading required package: IRanges
    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: SummarizedExperiment
    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: DelayedArray
    Loading required package: matrixStats
    
    Attaching package: ‘matrixStats’
    
    The following objects are masked from ‘package:Biobase’:
    
     anyMissing, rowMedians
    
    
    Attaching package: ‘DelayedArray’
    
    The following objects are masked from ‘package:matrixStats’:
    
     colMaxs, colMins, colRanges, rowMaxs, rowMins,
     rowRanges
    
    The following objects are masked from ‘package:base’:
    
     aperm, apply, rowsum
    
    converting counts to integer mode
    estimating size factors
    estimating dispersions
    gene-wise dispersion estimates
    mean-dispersion relationship
    final dispersion estimates
    fitting model and testing
    converting counts to integer mode
    estimating size factors
    estimating dispersions
    gene-wise dispersion estimates
    mean-dispersion relationship
    final dispersion estimates
    fitting model and testing
    Loading required package: locfit
    locfit 1.5-9.4 2020-03-24
    Loading required package: lattice
     Welcome to 'DESeq'. For improved performance,
     usability and functionality, please consider
     migrating to 'DESeq2'.
    
    Attaching package: ‘DESeq’
    
    The following objects are masked from ‘package:DESeq2’:
    
     estimateSizeFactorsForMatrix,
     getVarianceStabilizedData,
     varianceStabilizingTransformation
    
    
    Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
     chunk 9 (label = DESeq1study)
    Error in library(HTSFilter) : there is no package called ‘HTSFilter’
    
    --- failed re-building ‘metaRNASeq.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘metaRNASeq.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-macos-x86_64

Version: 1.0.2
Check: package dependencies
Result: NOTE
    Packages suggested but not available for checking:
     'HTSFilter', 'DESeq', 'DESeq2'
Flavor: r-oldrel-macos-x86_64

Version: 1.0.2
Check: running R code from vignettes
Result: WARN
    Errors in running code in vignettes:
    when running code in ‘metaRNASeq.Rnw’
     ...
    
    > options(width = 60)
    
    > library(metaRNASeq)
    
    > library(DESeq2)
    
     When sourcing ‘metaRNASeq.R’:
    Error: there is no package called ‘DESeq2’
    Execution halted
Flavor: r-oldrel-macos-x86_64

Version: 1.0.2
Check: re-building of vignette outputs
Result: NOTE
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘metaRNASeq.Rnw’ using Sweave
    
    Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
     chunk 2 (label = loadparameters)
    Error in library(DESeq2) : there is no package called ‘DESeq2’
    
    --- failed re-building ‘metaRNASeq.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘metaRNASeq.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-oldrel-macos-x86_64