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BioC 3.2: CHECK report for Gviz on oaxaca

This page was generated on 2015-10-27 17:39:56 -0400 (Tue, 27 Oct 2015).

Package 479/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.14.0
Florian Hahne
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Gviz
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: Gviz
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.14.0.tar.gz
StartedAt: 2015-10-27 04:32:04 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 04:37:58 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 354.7 seconds
RetCode: 0
Status:  OK 
CheckDir: Gviz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Gviz.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.14.0’
* 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 ... [29s/30s] OK
* checking installed package size ... NOTE
  installed size is  5.7Mb
  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 : .local: 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 : .local: warning in GRanges(seqnames =
  seqnames(r)[1], range = rtmp): partial argument match of 'range' to
  'ranges'
collapseTrack,DataTrack : .local: warning in GRanges(seqnames =
  chromosome(GdObject), range = ir, strand =
  unique(as.character(strand(GdObject)))): partial argument match of
  'range' to 'ranges'
collapseTrack,DataTrack : .local: warning in GRanges(seqnames = 1,
  strand = strand(GdObject)[1], range = rr): partial argument match of
  'range' to 'ranges'
collapseTrack,DataTrack : .local: warning in GRanges(seqnames =
  seq_len(length(rr)), strand = st, range = rr): partial argument match
  of 'range' to 'ranges'
initialize,AlignedReadTrack : .local: 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 : .local: warning in GRanges(range = range,
  seqnames = "dummy", id = ids): partial argument match of 'range' to
  'ranges'
initialize,IdeogramTrack : .local: 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 : .local: warning in GRanges(range =
  IRanges(start = from, end = to), strand = names(x@coverage), seqnames
  = x@chromosome): partial argument match of 'range' to 'ranges'
.buildRange,TxDb-ANY-ANY-ANY : .local: no visible global function
  definition for ‘cdsBy’
.buildRange,TxDb-ANY-ANY-ANY : .local: no visible global function
  definition for ‘fiveUTRsByTranscript’
.buildRange,TxDb-ANY-ANY-ANY : .local: no visible global function
  definition for ‘threeUTRsByTranscript’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
AlignmentsTrack       8.751  0.864   9.636
SequenceTrack-class   8.398  0.752   9.170
GeneRegionTrack-class 6.270  0.035   6.366
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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-class1.8310.0601.893
AlignmentsTrack8.7510.8649.636
AnnotationTrack-class4.9250.0314.987
BiomartGeneRegionTrack-class3.8750.0263.905
DataTrack-class0.6740.0140.689
DisplayPars-class0.0330.0020.035
GeneRegionTrack-class6.2700.0356.366
GenomeAxisTrack-class3.8710.0203.894
IdeogramTrack-class0.3490.0030.354
SequenceTrack-class8.3980.7529.170
plotTracks4.2730.0134.289