CRAN Package Check Results for Maintainer ‘Aurélie Siberchicot <aurelie.siberchicot at univ-lyon1.fr>’

Last updated on 2020-01-22 16:48:07 CET.

Package ERROR WARN NOTE OK
ade4 8 5
ade4TkGUI 2 11
adegraphics 1 12
CINID 13
DRomics 3 1 9
fitdistrplus 13
Interatrix 13
LDcorSV 13
MareyMap 13
Mondrian 13
OnAge 13

Package ade4

Current CRAN status: NOTE: 8, OK: 5

Version: 1.7-13
Check: installed package size
Result: NOTE
     installed size is 7.8Mb
     sub-directories of 1Mb or more:
     R 1.4Mb
     data 2.8Mb
     pictures 2.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Package ade4TkGUI

Current CRAN status: WARN: 2, OK: 11

Version: 0.3-0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: loading Rplot failed
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: dependencies in R code
Result: NOTE
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: S3 generic/method consistency
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    See section ‘Generic functions and methods’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: replacement functions
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    The argument of a replacement function which corresponds to the right
    hand side must be named ‘value’.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: foreign function calls
Result: NOTE
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: R code for possible problems
Result: NOTE
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: for missing documentation entries
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    All user-level objects in a package should have documentation entries.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: for code/documentation mismatches
Result: WARN
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.3-0
Check: Rd \usage sections
Result: NOTE
    No protocol specified
    No protocol specified
    No protocol specified
    No protocol specified
    The \usage entries for S3 methods should use the \method markup and not
    their full name.
    See chapter ‘Writing R documentation files’ in the ‘Writing R
    Extensions’ manual.
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Package adegraphics

Current CRAN status: NOTE: 1, OK: 12

Version: 1.0-15
Check: installed package size
Result: NOTE
     installed size is 5.1Mb
     sub-directories of 1Mb or more:
     R 1.5Mb
     doc 3.0Mb
Flavor: r-patched-solaris-x86

Package CINID

Current CRAN status: OK: 13

Package DRomics

Current CRAN status: ERROR: 3, NOTE: 1, OK: 9

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

Package fitdistrplus

Current CRAN status: OK: 13

Package Interatrix

Current CRAN status: OK: 13

Package LDcorSV

Current CRAN status: OK: 13

Package MareyMap

Current CRAN status: OK: 13

Package Mondrian

Current CRAN status: OK: 13

Package OnAge

Current CRAN status: OK: 13