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BioC 3.5: CHECK report for Gviz on toluca2

This page was generated on 2017-04-23 14:36:17 -0400 (Sun, 23 Apr 2017).

Package 608/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Gviz 1.19.3
Florian Hahne
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz
Last Changed Rev: 127985 / Revision: 129046
Last Changed Date: 2017-04-03 06:00:46 -0400 (Mon, 03 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Gviz
Version: 1.19.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.19.3.tar.gz
StartedAt: 2017-04-23 05:07:50 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 05:15:15 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 445.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Gviz.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Gviz_1.19.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Gviz.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.19.3’
* 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  6.0Mb
  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,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'
Undefined global functions or variables:
  cdsBy fiveUTRsByTranscript threeUTRsByTranscript
* 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 'GenomeAxisTrack,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 sizes of PDF files under ‘inst/doc’ ... 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  13.098  0.965  14.224
AnnotationTrack-class   8.563  0.047   8.681
SequenceTrack-class     7.232  0.632   7.936
GeneRegionTrack-class   6.923  0.039   7.036
AlignedReadTrack-class  5.229  0.116   8.336
* 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
  ‘/Users/biocbuild/bbs-3.5-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-class5.2290.1168.336
AlignmentsTrack-class13.098 0.96514.224
AnnotationTrack-class8.5630.0478.681
BiomartGeneRegionTrack-class3.9520.0254.051
DataTrack-class0.9310.0140.951
DisplayPars-class0.0410.0020.043
GeneRegionTrack-class6.9230.0397.036
GenomeAxisTrack-class3.4360.0093.484
IdeogramTrack-class0.5620.0040.574
SequenceTrack-class7.2320.6327.936
plotTracks4.4800.0454.633