CRAN Package Check Results for Package MSIseq

Last updated on 2020-09-14 11:07:45 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.0 23.02 309.02 332.04 NOTE
r-devel-linux-x86_64-debian-gcc 1.0.0 18.48 108.09 126.57 WARN
r-devel-linux-x86_64-fedora-clang 1.0.0 437.81 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.0 215.72 WARN
r-devel-windows-ix86+x86_64 1.0.0 36.00 108.00 144.00 NOTE --no-vignettes
r-patched-linux-x86_64 1.0.0 20.57 302.53 323.10 NOTE
r-release-linux-x86_64 1.0.0 18.93 289.03 307.96 NOTE
r-release-macos-x86_64 1.0.0 NOTE
r-release-windows-ix86+x86_64 1.0.0 31.00 144.00 175.00 NOTE --no-vignettes
r-oldrel-macos-x86_64 1.0.0 WARN
r-oldrel-windows-ix86+x86_64 1.0.0 27.00 137.00 164.00 NOTE --no-vignettes

Check Details

Version: 1.0.0
Check: R code for possible problems
Result: NOTE
    MSIseq.classify: no visible global function definition for 'predict'
    Undefined global functions or variables:
     predict
    Consider adding
     importFrom("stats", "predict")
    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: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘MSIseq.Rnw’ using Sweave
    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, 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
    
    Loading required package: S4Vectors
    Loading required package: stats4
    
    Attaching package: ‘S4Vectors’
    
    The following object is masked from ‘package:base’:
    
     expand.grid
    
    Loading required package: RWeka
    Loading required package: rJava
    Loading required package: R.utils
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
    
    Attaching package: ‘R.oo’
    
    The following object is masked from ‘package:R.methodsS3’:
    
     throw
    
    The following object is masked from ‘package:rJava’:
    
     clone
    
    The following object is masked from ‘package:IRanges’:
    
     trim
    
    The following objects are masked from ‘package:methods’:
    
     getClasses, getMethods
    
    The following objects are masked from ‘package:base’:
    
     attach, detach, load, save
    
    R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
    
    Attaching package: ‘R.utils’
    
    The following object is masked from ‘package:utils’:
    
     timestamp
    
    The following objects are masked from ‘package:base’:
    
     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
     warnings
    
    trying URL ‘http://steverozen.net/data/Hg19repeats.rda’
    Content type 'unknown' length 66808496 bytes (63.7 MB)
    =========
    downloaded 11.5 MB
    
    Warning in download.file(url, file) :
     downloaded length 12050009 != reported length 66808496
    Warning in download.file(url, file) :
     URL 'http://steverozen.net/data/Hg19repeats.rda': status was 'Timeout was reached'
    
    Error: processing vignette 'MSIseq.Rnw' failed with diagnostics:
     chunk 3 (label = Hg19repeats)
    Error in download.file(url, file) :
     download from 'http://steverozen.net/data/Hg19repeats.rda' failed
    
    --- failed re-building ‘MSIseq.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘MSIseq.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.0
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘MSIseq.Rnw’ using Sweave
    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, 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
    
    Loading required package: S4Vectors
    Loading required package: stats4
    
    Attaching package: ‘S4Vectors’
    
    The following object is masked from ‘package:base’:
    
     expand.grid
    
    Loading required package: RWeka
    Loading required package: rJava
    Loading required package: R.utils
    Loading required package: R.oo
    Loading required package: R.methodsS3
    R.methodsS3 v1.8.1 (2020-08-26 16:20:06 UTC) successfully loaded. See ?R.methodsS3 for help.
    R.oo v1.24.0 (2020-08-26 16:11:58 UTC) successfully loaded. See ?R.oo for help.
    
    Attaching package: ‘R.oo’
    
    The following object is masked from ‘package:R.methodsS3’:
    
     throw
    
    The following object is masked from ‘package:rJava’:
    
     clone
    
    The following object is masked from ‘package:IRanges’:
    
     trim
    
    The following objects are masked from ‘package:methods’:
    
     getClasses, getMethods
    
    The following objects are masked from ‘package:base’:
    
     attach, detach, load, save
    
    R.utils v2.10.1 (2020-08-26 22:50:31 UTC) successfully loaded. See ?R.utils for help.
    
    Attaching package: ‘R.utils’
    
    The following object is masked from ‘package:utils’:
    
     timestamp
    
    The following objects are masked from ‘package:base’:
    
     cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
     warnings
    
    trying URL 'http://steverozen.net/data/Hg19repeats.rda'
    Content type 'unknown' length 66808496 bytes (63.7 MB)
    ==============================
    downloaded 39.2 MB
    
    Warning in download.file(url, file) :
     downloaded length 41122057 != reported length 66808496
    Warning in download.file(url, file) :
     URL 'http://steverozen.net/data/Hg19repeats.rda': status was 'Timeout was reached'
    
    Error: processing vignette 'MSIseq.Rnw' failed with diagnostics:
     chunk 3 (label = Hg19repeats)
    Error in download.file(url, file) :
     download from 'http://steverozen.net/data/Hg19repeats.rda' failed
    
    --- failed re-building ‘MSIseq.Rnw’
    
    SUMMARY: processing the following file failed:
     ‘MSIseq.Rnw’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.0.0
Flags: --no-vignettes
Check: R code for possible problems
Result: NOTE
    MSIseq.classify: no visible global function definition for 'predict'
    Undefined global functions or variables:
     predict
    Consider adding
     importFrom("stats", "predict")
    to your NAMESPACE file.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.0.0
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: package ‘IRanges’ was built under R version 3.6.1
     Warning: package ‘S4Vectors’ was built under R version 3.6.1
Flavor: r-oldrel-macos-x86_64