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BioC 3.4: CHECK report for Gviz on malbec1

This page was generated on 2017-04-15 16:10:47 -0400 (Sat, 15 Apr 2017).

Package 575/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.18.2
Florian Hahne
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Gviz
Last Changed Rev: 127378 / Revision: 128728
Last Changed Date: 2017-03-14 07:16:52 -0400 (Tue, 14 Mar 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Gviz
Version: 1.18.2
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Gviz_1.18.2.tar.gz
StartedAt: 2017-04-14 23:07:06 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 23:12:35 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 329.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Gviz.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Gviz_1.18.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Gviz.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.18.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Gviz’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.buildRange,IRanges-ANY-ANY-ANY: warning in GRanges(seqnames =
  .chrName(chromosome), range = range, strand = if
  (!is.null(args$strand)) args$strand else "*"): partial argument match
  of 'range' to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames = seqnames(r)[1],
  range = rtmp): partial argument match of 'range' to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames =
  chromosome(GdObject), range = ir, strand =
  unique(as.character(strand(GdObject)))): partial argument match of
  'range' to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames = 1, strand =
  strand(GdObject)[1], range = rr): partial argument match of 'range'
  to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames =
  seq_len(length(rr)), strand = st, range = rr): partial argument match
  of 'range' to 'ranges'
initialize,AlignedReadTrack: warning in GRanges(range = IRanges(start =
  from, end = to), strand = names(.Object@coverage), seqnames =
  .Object@chromosome): partial argument match of 'range' to 'ranges'
initialize,GenomeAxisTrack: warning in GRanges(range = range, seqnames
  = "dummy", id = ids): partial argument match of 'range' to 'ranges'
initialize,IdeogramTrack: warning in GRanges(seqnames = bnames, range =
  IRanges(start = bands$chromStart, end = bands$chromEnd), name =
  bnames, type = as.character(bands$gieStain)): partial argument match
  of 'range' to 'ranges'
subset,AlignedReadTrack: warning in GRanges(range = IRanges(start =
  from, end = to), strand = names(x@coverage), seqnames =
  x@chromosome): partial argument match of 'range' to 'ranges'
.computeGroupRange: no visible global function definition for
  'setNames'
.defaultVarMap: no visible global function definition for 'setNames'
.getBioColorIdeo: no visible global function definition for 'setNames'
.prepareDtData: no visible global function definition for
  'type.convert'
.supportsAlpha: no visible global function definition for 'dev.cur'
.supportsAlpha: no visible global function definition for 'dev.off'
plotTracks: no visible global function definition for 'dev.cur'
plotTracks: no visible global function definition for 'dev.off'
.buildRange,GRanges-ANY-ANY-ANY: no visible global function definition
  for 'setNames'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
  'cdsBy'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
  'fiveUTRsByTranscript'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
  'threeUTRsByTranscript'
drawGD,AlignmentsTrack: no visible global function definition for
  'setNames'
drawGD,AlignmentsTrack : <anonymous>: no visible global function
  definition for 'setNames'
Undefined global functions or variables:
  cdsBy dev.cur dev.off fiveUTRsByTranscript setNames
  threeUTRsByTranscript type.convert
Consider adding
  importFrom("grDevices", "dev.cur", "dev.off")
  importFrom("stats", "setNames")
  importFrom("utils", "type.convert")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'AlignedReadTrack,ANY,ANY,ANY'
  generic '[' and siglist 'DataTrack,ANY,ANY,ANY'
  generic '[' and siglist 'GenomeAxisTrack,ANY,ANY,ANY'
  generic '[' and siglist 'IdeogramTrack,ANY,ANY,ANY'
  generic '[' and siglist 'RangeTrack,ANY,ANY,ANY'
  generic '[' and siglist 'StackedTrack,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
AlignmentsTrack-class 7.82  0.236   8.063
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Gviz.Rcheck/00check.log’
for details.


Gviz.Rcheck/00install.out:

* installing *source* package ‘Gviz’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Gviz)

Gviz.Rcheck/Gviz-Ex.timings:

nameusersystemelapsed
AlignedReadTrack-class1.8280.0321.861
AlignmentsTrack-class7.8200.2368.063
AnnotationTrack-class3.5560.0083.566
BiomartGeneRegionTrack-class3.1200.0043.126
DataTrack-class0.4080.0040.409
DisplayPars-class0.0200.0000.022
GeneRegionTrack-class4.0400.0044.044
GenomeAxisTrack-class2.2240.0002.225
IdeogramTrack-class0.2080.0000.211
SequenceTrack-class2.3320.1042.440
plotTracks3.2280.0003.231