CRAN Package Check Results for Package DRomics

Last updated on 2020-02-20 21:47:25 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.0-1 32.14 513.77 545.91 ERROR
r-devel-linux-x86_64-debian-gcc 2.0-1 32.09 390.84 422.93 ERROR
r-devel-linux-x86_64-fedora-clang 2.0-1 678.21 ERROR
r-devel-linux-x86_64-fedora-gcc 2.0-1 650.52 ERROR
r-devel-windows-ix86+x86_64 2.0-1 62.00 496.00 558.00 OK
r-devel-windows-ix86+x86_64-gcc8 2.0-1 101.00 642.00 743.00 ERROR
r-patched-linux-x86_64 2.0-1 30.75 489.04 519.79 OK
r-patched-solaris-x86 2.0-1 886.40 NOTE
r-release-linux-x86_64 2.0-1 32.02 482.82 514.84 OK
r-release-windows-ix86+x86_64 2.0-1 64.00 526.00 590.00 OK
r-release-osx-x86_64 2.0-1 ERROR
r-oldrel-windows-ix86+x86_64 2.0-1 40.00 472.00 512.00 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:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### 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 `assays<-`(`*tmp*`, value = `*vtmp*`) :
     please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
     withDimnames=FALSE)) <- value' when the dimnames on the supplied
     assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
    Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 2.0-1
Check: tests
Result: ERROR
     Running 'examplewithLprobit.R' [36s/40s]
     Running 'examplewithRNAseq.R' [16s/17s]
     Running 'examplewithmetabolomic.R' [32s/36s]
     Running 'examplewithmicroarray.R' [121s/133s]
     Running 'testthat.R' [15s/16s]
    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
     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 `assays<-`(`*tmp*`, value = `*vtmp*`) :
     please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
     withDimnames=FALSE)) <- value' when the dimnames on the supplied
     assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
     Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.0-1
Check: tests
Result: ERROR
     Running ‘examplewithLprobit.R’ [25s/36s]
     Running ‘examplewithRNAseq.R’ [12s/18s]
     Running ‘examplewithmetabolomic.R’ [25s/37s]
     Running ‘examplewithmicroarray.R’ [85s/121s]
     Running ‘testthat.R’ [11s/16s]
    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
     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 `assays<-`(`*tmp*`, value = `*vtmp*`) :
     please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
     withDimnames=FALSE)) <- value' when the dimnames on the supplied
     assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
     Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

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 `assays<-`(`*tmp*`, value = `*vtmp*`) :
     please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
     withDimnames=FALSE)) <- value' when the dimnames on the supplied
     assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
    Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 2.0-1
Check: tests
Result: ERROR
     Running ‘examplewithLprobit.R’ [43s/146s]
     Running ‘examplewithRNAseq.R’ [20s/58s]
     Running ‘examplewithmetabolomic.R’ [38s/124s]
     Running ‘examplewithmicroarray.R’ [138s/501s]
     Running ‘testthat.R’ [18s/64s]
    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
     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 `assays<-`(`*tmp*`, value = `*vtmp*`) :
     please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
     withDimnames=FALSE)) <- value' when the dimnames on the supplied
     assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
     Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.0-1
Check: tests
Result: ERROR
     Running ‘examplewithLprobit.R’ [43s/112s]
     Running ‘examplewithRNAseq.R’ [18s/42s]
     Running ‘examplewithmetabolomic.R’ [38s/100s]
     Running ‘examplewithmicroarray.R’ [134s/322s]
     Running ‘testthat.R’ [18s/45s]
    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
     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 `assays<-`(`*tmp*`, value = `*vtmp*`) :
     please use 'assay(x, withDimnames=FALSE)) <- value' or 'assays(x,
     withDimnames=FALSE)) <- value' when the dimnames on the supplied
     assay(s) are not identical to the dimnames on DESeqDataSet object 'x'
     Calls: RNAseqdata ... rlog -> estimateDispersionsGeneEst -> assays<- -> assays<-
     Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.0-1
Check: tests
Result: ERROR
     Running 'examplewithLprobit.R' [42s]
     Running 'examplewithRNAseq.R' [30s]
     Running 'examplewithmetabolomic.R' [39s]
     Running 'examplewithmicroarray.R' [133s]
     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
     Elements of the experimental design in order to check the coding of the data :
     Tested doses and number of replicates for each dose:
    
     0 0.22 0.67 2 6
     2 3 3 3 3
     Number of items: 999
     Identifiers of the first 20 items:
     [1] "NM_144958" "NR_102758" "NM_172405" "NM_029777" "NM_001130188"
     [6] "NM_207141" "NM_001162368" "NM_008117" "NM_001168290" "NM_010910"
     [11] "NM_001004147" "NM_001146318" "NM_145597" "NM_001161797" "NM_021483"
     [16] "NR_002862" "NR_033520" "NM_134027" "NM_010381" "NM_019388"
     Data were normalized with respect to library size
     and tranformed using the following method: rlog
     > plot(o)
     >
     > # item selection using the quadratic method
     > # options to put in shiny : select.method (3 methods), FDR (numerical positive value < 1)
     > (s_quad <- itemselect(o, select.method = "quadratic", FDR = 0.001))
     converting counts to integer mode
     the design formula contains a numeric variable with integer values,
     specifying a model with increasing fold change for higher values.
     did you mean for this to be a factor? if so, first convert
     this variable to a factor using the factor() function
     estimating size factors
     estimating dispersions
     gene-wise dispersion estimates
     mean-dispersion relationship
     final dispersion estimates
     fitting model and testing
     Error in .wrap_in_length_one_list_like_object(value, name, x) :
     failed to coerce 'list(value)' to a DESeqResults object of length 1
     Calls: itemselect ... .append_list_element -> .wrap_in_length_one_list_like_object
     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