CRAN Package Check Results for Package DRomics

Last updated on 2020-01-22 00:48:54 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0-1 36.60 568.90 605.50 OK
r-devel-linux-x86_64-debian-gcc 2.0-1 31.07 416.28 447.35 OK
r-devel-linux-x86_64-fedora-clang 2.0-1 681.64 OK
r-devel-linux-x86_64-fedora-gcc 2.0-1 683.85 OK
r-devel-windows-ix86+x86_64 2.0-1 100.00 625.00 725.00 ERROR
r-devel-windows-ix86+x86_64-gcc8 2.0-1 97.00 630.00 727.00 ERROR
r-patched-linux-x86_64 2.0-1 29.47 492.18 521.65 OK
r-patched-solaris-x86 2.0-1 901.70 NOTE
r-release-linux-x86_64 2.0-1 31.74 483.80 515.54 OK
r-release-windows-ix86+x86_64 2.0-1 65.00 656.00 721.00 OK
r-release-osx-x86_64 2.0-1 ERROR
r-oldrel-windows-ix86+x86_64 2.0-1 39.00 451.00 490.00 OK
r-oldrel-osx-x86_64 2.0-1 OK

Check Details

Version: 2.0-1
Check: examples
Result: ERROR
    Running examples in 'DRomics-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: RNAseqdata
    > ### Title: Import, check and normalization and transformation of RNAseq
    > ### data
    > ### Aliases: RNAseqdata print.RNAseqdata plot.RNAseqdata
    >
    > ### ** Examples
    >
    > # (1) import, check, normalization and transformation of RNAseq data
    > # An example on a subsample of a data set published by Zhou et al. 2017
    > # (in Toxicological sciences, 160, 95-110)
    > # Effect on kidney transcriptomes of tetrachloroethylene
    > #
    > datafilename <- system.file("extdata", "RNAseq_sample.txt", package="DRomics")
    > (o <- RNAseqdata(datafilename, check = TRUE, transfo.method = "rlog"))
    Just wait, the transformation using regularized logarithm (rlog)
     may take a few minutes.
    converting counts to integer mode
    Error in is(listData[[1L]], getClass("Annotated")) :
     trying to get slot "className" from an object of a basic class ("character") with no slots
    Calls: RNAseqdata ... DESeqDataSetFromMatrix -> DESeqDataSet -> DataFrame -> is
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8

Version: 2.0-1
Check: tests
Result: ERROR
     Running 'examplewithLprobit.R' [45s]
     Running 'examplewithRNAseq.R' [17s]
     Running 'examplewithmetabolomic.R' [39s]
     Running 'examplewithmicroarray.R' [147s]
     Running 'testthat.R' [17s]
    Running the tests in 'tests/examplewithRNAseq.R' failed.
    Complete output:
     > library(DRomics)
     Loading required package: limma
     Loading required package: DESeq2
     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 object is masked from 'package:limma':
    
     plotMA
    
     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
    
     Attaching package: 'IRanges'
    
     The following object is masked from 'package:grDevices':
    
     windows
    
     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
    
     Loading required package: BiocParallel
    
     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
    
     > # importation and check of RNAseq data and normalization
     > # with respect to library size and transformation
     > # options to put in shiny : transfo.method (2 methods, rlog or vst)
     > datafilename <- system.file("extdata", "RNAseq_sample.txt", package="DRomics")
     > (o <- RNAseqdata(datafilename, check = TRUE, transfo.method = "rlog"))
     Just wait, the transformation using regularized logarithm (rlog)
     may take a few minutes.
     converting counts to integer mode
     Error in is(listData[[1L]], getClass("Annotated")) :
     trying to get slot "className" from an object of a basic class ("character") with no slots
     Calls: RNAseqdata ... DESeqDataSetFromMatrix -> DESeqDataSet -> DataFrame -> is
     Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 2.0-1
Check: tests
Result: ERROR
     Running 'examplewithLprobit.R' [45s]
     Running 'examplewithRNAseq.R' [17s]
     Running 'examplewithmetabolomic.R' [39s]
     Running 'examplewithmicroarray.R' [146s]
     Running 'testthat.R' [18s]
    Running the tests in 'tests/examplewithRNAseq.R' failed.
    Complete output:
     > library(DRomics)
     Loading required package: limma
     Loading required package: DESeq2
     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 object is masked from 'package:limma':
    
     plotMA
    
     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
    
     Attaching package: 'IRanges'
    
     The following object is masked from 'package:grDevices':
    
     windows
    
     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
    
     Loading required package: BiocParallel
    
     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
    
     > # importation and check of RNAseq data and normalization
     > # with respect to library size and transformation
     > # options to put in shiny : transfo.method (2 methods, rlog or vst)
     > datafilename <- system.file("extdata", "RNAseq_sample.txt", package="DRomics")
     > (o <- RNAseqdata(datafilename, check = TRUE, transfo.method = "rlog"))
     Just wait, the transformation using regularized logarithm (rlog)
     may take a few minutes.
     converting counts to integer mode
     Error in is(listData[[1L]], getClass("Annotated")) :
     trying to get slot "className" from an object of a basic class ("character") with no slots
     Calls: RNAseqdata ... DESeqDataSetFromMatrix -> DESeqDataSet -> DataFrame -> is
     Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 2.0-1
Check: installed package size
Result: NOTE
     installed size is 5.2Mb
     sub-directories of 1Mb or more:
     DRomics-shiny 1.8Mb
     extdata 3.1Mb
Flavor: r-patched-solaris-x86

Version: 2.0-1
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-release-osx-x86_64