CRAN Package Check Results for Package SNPtools

Last updated on 2018-07-03 10:54:37 CEST.

Flavor	Version	T_install	T_check	T_total	Status	Flags
r-devel-linux-x86_64-debian-clang	1.1	13.35	142.42	155.77	ERROR
r-devel-linux-x86_64-debian-gcc	1.1	10.04	120.52	130.56	ERROR
r-devel-linux-x86_64-fedora-clang	1.1			216.97	ERROR
r-devel-linux-x86_64-fedora-gcc	1.1			211.81	ERROR
r-devel-windows-ix86+x86_64	1.1	29.00	176.00	205.00	ERROR
r-patched-linux-x86_64	1.1	10.20	135.50	145.70	ERROR
r-patched-solaris-x86	1.1			224.50	ERROR	--no-build-vignettes
r-release-linux-x86_64	1.1	10.55	136.42	146.97	ERROR
r-release-windows-ix86+x86_64	1.1	27.00	213.00	240.00	NOTE
r-release-osx-x86_64	1.1				ERROR
r-oldrel-windows-ix86+x86_64	1.1	19.00	221.00	240.00	NOTE
r-oldrel-osx-x86_64	1.1				NOTE

Check Details

Version: 1.1
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Title field: should not end in a period.
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-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.1
Check: top-level files
Result: NOTE
Non-standard file/directory found at top level:
‘test’
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

Version: 1.1
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Rsamtools’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
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-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.1
Check: R code for possible problems
Result: NOTE
    cluster.strains: no visible global function definition for ‘hclust’
    cluster.strains: no visible global function definition for ‘as.dist’
    convert.genes.to.GRanges: no visible global function definition for
     ‘GRanges’
    convert.genes.to.GRanges: no visible global function definition for
     ‘IRanges’
    convert.genes.to.GRanges: no visible global function definition for
     ‘metadata<-’
    convert.pos.to.GRanges: no visible global function definition for
     ‘GRanges’
    convert.pos.to.GRanges: no visible global function definition for
     ‘IRanges’
    convert.variants.to.GRanges: no visible global function definition for
     ‘GRanges’
    convert.variants.to.GRanges: no visible global function definition for
     ‘IRanges’
    convert.variants.to.GRanges: no visible global function definition for
     ‘metadata<-’
    find.overlapping.genes: no visible global function definition for
     ‘findOverlaps’
    find.overlapping.genes: no visible global function definition for
     ‘subjectHits’
    gene.plot: no visible global function definition for ‘par’
    gene.plot: no visible global function definition for ‘plot’
    gene.plot: no visible global function definition for ‘strwidth’
    gene.plot: no visible global function definition for ‘strheight’
    gene.plot: no visible global function definition for ‘rect’
    gene.plot: no visible global function definition for ‘text’
    get.mgi.features: no visible global function definition for ‘TabixFile’
    get.mgi.features: no visible global function definition for
     ‘headerTabix’
    get.mgi.features: no visible global function definition for ‘scanTabix’
    get.strains: no visible global function definition for ‘TabixFile’
    get.strains: no visible global function definition for ‘headerTabix’
    get.variants: no visible global function definition for ‘TabixFile’
    get.variants: no visible global function definition for ‘headerTabix’
    get.variants: no visible global function definition for ‘scanTabix’
    snp.plot: no visible global function definition for ‘par’
    snp.plot: no visible global function definition for ‘layout’
    snp.plot: no visible global function definition for ‘image’
    snp.plot: no visible global function definition for ‘mtext’
    snp.plot: no visible global function definition for ‘abline’
    snp.plot: no visible global function definition for ‘axis’
    snp.plot: no visible global function definition for ‘rect’
    snp.plot: no visible global function definition for ‘rgb’
    snp.plot: no visible global function definition for ‘lines’
    snp.plot: no visible global function definition for ‘text’
    snp.plot: no visible global function definition for ‘approx’
    snp.plot: no visible global function definition for ‘quantile’
    snp.plot: no visible global function definition for ‘colorRampPalette’
    Undefined global functions or variables:
     GRanges IRanges TabixFile abline approx as.dist axis colorRampPalette
     findOverlaps hclust headerTabix image layout lines metadata<- mtext
     par plot quantile rect rgb scanTabix strheight strwidth subjectHits
     text
    Consider adding
     importFrom("grDevices", "colorRampPalette", "rgb")
     importFrom("graphics", "abline", "axis", "image", "layout", "lines",
     "mtext", "par", "plot", "rect", "strheight", "strwidth",
     "text")
     importFrom("stats", "approx", "as.dist", "hclust", "quantile")
    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-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 1.1
Check: examples
Result: ERROR
    Running examples in ‘SNPtools-Ex.R’ failed
    The error most likely occurred in:

    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: categorize.variants
    > ### Title: categorize.variants
    > ### Aliases: categorize.variants
    >
    > ### ** Examples
    >
    > data(example.snps)
    > snp.type = categorize.variants(variants = example.snps[1:50,])
    Error in open.TabixFile(con) :
     [khttp_connect_file] fail to open file (HTTP code: 404).
    Calls: categorize.variants -> get.mgi.features -> open -> open.TabixFile
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: IRanges
    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, colMeans, colSums, 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, rowMeans, rowSums,
     rownames, sapply, setdiff, sort, table, tapply, union, unique,
     unsplit, which, which.max, which.min

    Loading required package: S4Vectors
    Loading required package: stats4

    Attaching package: ‘S4Vectors’

    The following object is masked from ‘package:base’:

     expand.grid

    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: Biostrings
    Loading required package: XVector

    Attaching package: ‘Biostrings’

    The following object is masked from ‘package:base’:

     strsplit

    Loading required package: Rsamtools

    Error: processing vignette ‘SNPtools.Rnw’ failed with diagnostics:
     chunk 3
    Error in open.TabixFile(con) :
     [khttp_connect_file] fail to open file (HTTP code: 404).

    Execution halted
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

Version: 1.1
Check: examples
Result: ERROR
    Running examples in ‘SNPtools-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: categorize.variants
    > ### Title: categorize.variants
    > ### Aliases: categorize.variants
    >
    > ### ** Examples
    >
    > data(example.snps)
    > snp.type = categorize.variants(variants = example.snps[1:50,])
    Error in open.TabixFile(con) :
     [khttp_connect_file] fail to open file (HTTP code: 404).
    Calls: categorize.variants -> get.mgi.features -> open -> open.TabixFile
    Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.1
Check: examples
Result: ERROR
    Running examples in 'SNPtools-Ex.R' failed
    The error most likely occurred in:

    > ### Name: categorize.variants
    > ### Title: categorize.variants
    > ### Aliases: categorize.variants
    >
    > ### ** Examples
    >
    > data(example.snps)
    > snp.type = categorize.variants(variants = example.snps[1:50,])
    [khttp_connect_file] fail to open file (HTTP code: 404).
    Error in open.TabixFile(con) : failed to open file
    Calls: categorize.variants -> get.mgi.features -> open -> open.TabixFile
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: IRanges
    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, 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: S4Vectors
    Loading required package: stats4

    Attaching package: 'S4Vectors'

    The following object is masked from 'package:base':

     expand.grid


    Attaching package: 'IRanges'

    The following object is masked from 'package:grDevices':

     windows

    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: Biostrings
    Loading required package: XVector

    Attaching package: 'Biostrings'

    The following object is masked from 'package:base':

     strsplit

    Loading required package: Rsamtools

    [khttp_connect_file] fail to open file (HTTP code: 404).
    Error: processing vignette 'SNPtools.Rnw' failed with diagnostics:
     chunk 3
    Error in open.TabixFile(con) : failed to open file
    Execution halted
Flavor: r-devel-windows-ix86+x86_64

Version: 1.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Loading required package: IRanges
    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, 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: S4Vectors
    Loading required package: stats4

    Attaching package: ‘S4Vectors’

    The following object is masked from ‘package:base’:

     expand.grid

    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: Biostrings
    Loading required package: XVector

    Attaching package: ‘Biostrings’

    The following object is masked from ‘package:base’:

     strsplit

    Loading required package: Rsamtools

    Error: processing vignette ‘SNPtools.Rnw’ failed with diagnostics:
     chunk 3
    Error in open.TabixFile(con) :
     [khttp_connect_file] fail to open file (HTTP code: 404).

    Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64

Version: 1.1
Flags: --no-build-vignettes
Check: DESCRIPTION meta-information
Result: NOTE
Malformed Title field: should not end in a period.
Flavor: r-patched-solaris-x86

Version: 1.1
Flags: --no-build-vignettes
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Rsamtools’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavor: r-patched-solaris-x86

Version: 1.1
Flags: --no-build-vignettes
Check: R code for possible problems
Result: NOTE
    cluster.strains: no visible global function definition for ‘hclust’
    cluster.strains: no visible global function definition for ‘as.dist’
    convert.genes.to.GRanges: no visible global function definition for
     ‘GRanges’
    convert.genes.to.GRanges: no visible global function definition for
     ‘IRanges’
    convert.genes.to.GRanges: no visible global function definition for
     ‘metadata<-’
    convert.pos.to.GRanges: no visible global function definition for
     ‘GRanges’
    convert.pos.to.GRanges: no visible global function definition for
     ‘IRanges’
    convert.variants.to.GRanges: no visible global function definition for
     ‘GRanges’
    convert.variants.to.GRanges: no visible global function definition for
     ‘IRanges’
    convert.variants.to.GRanges: no visible global function definition for
     ‘metadata<-’
    find.overlapping.genes: no visible global function definition for
     ‘findOverlaps’
    find.overlapping.genes: no visible global function definition for
     ‘subjectHits’
    gene.plot: no visible global function definition for ‘par’
    gene.plot: no visible global function definition for ‘plot’
    gene.plot: no visible global function definition for ‘strwidth’
    gene.plot: no visible global function definition for ‘strheight’
    gene.plot: no visible global function definition for ‘rect’
    gene.plot: no visible global function definition for ‘text’
    get.mgi.features: no visible global function definition for ‘TabixFile’
    get.mgi.features: no visible global function definition for
     ‘headerTabix’
    get.mgi.features: no visible global function definition for ‘scanTabix’
    get.strains: no visible global function definition for ‘TabixFile’
    get.strains: no visible global function definition for ‘headerTabix’
    get.variants: no visible global function definition for ‘TabixFile’
    get.variants: no visible global function definition for ‘headerTabix’
    get.variants: no visible global function definition for ‘scanTabix’
    snp.plot: no visible global function definition for ‘par’
    snp.plot: no visible global function definition for ‘layout’
    snp.plot: no visible global function definition for ‘image’
    snp.plot: no visible global function definition for ‘mtext’
    snp.plot: no visible global function definition for ‘abline’
    snp.plot: no visible global function definition for ‘axis’
    snp.plot: no visible global function definition for ‘rect’
    snp.plot: no visible global function definition for ‘rgb’
    snp.plot: no visible global function definition for ‘lines’
    snp.plot: no visible global function definition for ‘text’
    snp.plot: no visible global function definition for ‘approx’
    snp.plot: no visible global function definition for ‘quantile’
    snp.plot: no visible global function definition for ‘colorRampPalette’
    Undefined global functions or variables:
     GRanges IRanges TabixFile abline approx as.dist axis colorRampPalette
     findOverlaps hclust headerTabix image layout lines metadata<- mtext
     par plot quantile rect rgb scanTabix strheight strwidth subjectHits
     text
    Consider adding
     importFrom("grDevices", "colorRampPalette", "rgb")
     importFrom("graphics", "abline", "axis", "image", "layout", "lines",
     "mtext", "par", "plot", "rect", "strheight", "strwidth",
     "text")
     importFrom("stats", "approx", "as.dist", "hclust", "quantile")
    to your NAMESPACE file.
Flavor: r-patched-solaris-x86

Version: 1.1
Flags: --no-build-vignettes
Check: examples
Result: ERROR
    Running examples in ‘SNPtools-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: categorize.variants
    > ### Title: categorize.variants
    > ### Aliases: categorize.variants
    >
    > ### ** Examples
    >
    > data(example.snps)
    > snp.type = categorize.variants(variants = example.snps[1:50,])
    Error in open.TabixFile(con) :
     [khttp_connect_file] fail to open file (HTTP code: 404).
    Calls: categorize.variants -> get.mgi.features -> open -> open.TabixFile
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1
Flags: --no-build-vignettes
Check: running R code from vignettes
Result: ERROR
    Errors in running code in vignettes:
    when running code in ‘SNPtools.Rnw’
     ...

    > library(SNPtools)
    Loading required package: IRanges
    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, 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: S4Vectors
    Loading required package: stats4

    Attaching package: ‘S4Vectors’

    The following object is masked from ‘package:base’:

     expand.grid

    Loading required package: GenomicRanges
    Loading required package: GenomeInfoDb
    Loading required package: Biostrings
    Loading required package: XVector

    Attaching package: ‘Biostrings’

    The following object is masked from ‘package:base’:

     strsplit

    Loading required package: Rsamtools

    > snp.file = "http://cgd.jax.org/tools/SNPtools/Build38/sanger.snps.NCBI38.txt.gz"

    > mgi.file = "http://cgd.jax.org/tools/SNPtools/MGI/MGI.20130305.sorted.txt.gz"

    > available.strains = get.strains(snp.file)

     When sourcing ‘SNPtools.R’:
    Error: [khttp_connect_file] fail to open file (HTTP code: 404).
    Execution halted
Flavor: r-patched-solaris-x86

Version: 1.1
Check: package dependencies
Result: ERROR
    Package required but not available: ‘Rsamtools’

    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64