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BioC 3.0: CHECK report for DASiR on oaxaca

This page was generated on 2015-04-10 10:07:08 -0700 (Fri, 10 Apr 2015).

Package 221/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DASiR 1.6.0
Oscar Flores , Anna Mantsoki
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DASiR
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: DASiR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DASiR_1.6.0.tar.gz
StartedAt: 2015-04-09 22:46:08 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:48:33 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 144.5 seconds
RetCode: 0
Status:  OK 
CheckDir: DASiR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch DASiR_1.6.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/DASiR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DASiR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DASiR’ version ‘1.6.0’
* 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 ‘DASiR’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getCapabilities: no visible global function definition for ‘xmlSize’
.getCapabilities: no visible global function definition for ‘xmlAttrs’
.getFeature: no visible global function definition for ‘xmlAttrs’
.getFeature: no visible global function definition for ‘xmlSApply’
.getFeature: no visible binding for global variable ‘xmlValue’
.getGroup: no visible global function definition for ‘xmlAttrs’
.getSequence: no visible global function definition for ‘xmlValue’
.getStructure: no visible global function definition for ‘xmlAttrs’
.makeSegments: no visible global function definition for ‘seqnames’
getDasDsn: no visible global function definition for ‘xmlTreeParse’
getDasDsn: no visible global function definition for ‘xmlRoot’
getDasDsn: no visible global function definition for ‘xmlSApply’
getDasDsn : <anonymous>: no visible global function definition for
  ‘xmlAttrs’
getDasEntries: no visible global function definition for ‘xmlTreeParse’
getDasEntries : <anonymous>: no visible global function definition for
  ‘htmlTreeParse’
getDasEntries: no visible global function definition for ‘xmlRoot’
getDasEntries: no visible global function definition for ‘xmlApply’
getDasEntries: no visible binding for global variable ‘xmlAttrs’
getDasEntries: no visible global function definition for ‘GRanges’
getDasEntries: no visible global function definition for ‘IRanges’
getDasEntries: no visible global function definition for
  ‘elementMetadata<-’
getDasFeature: no visible global function definition for ‘xmlTreeParse’
getDasFeature: no visible global function definition for ‘xmlRoot’
getDasFeature: no visible global function definition for ‘xmlSize’
getDasFeature: no visible global function definition for ‘xmlApply’
getDasSequence: no visible global function definition for
  ‘xmlTreeParse’
getDasSequence: no visible global function definition for ‘xmlRoot’
getDasSequence: no visible global function definition for ‘xmlApply’
getDasSource: no visible global function definition for ‘xmlTreeParse’
getDasSource: no visible global function definition for ‘xmlRoot’
getDasSource: no visible global function definition for ‘xmlSApply’
getDasSource : <anonymous>: no visible global function definition for
  ‘xmlAttrs’
getDasStructure: no visible global function definition for
  ‘xmlTreeParse’
getDasStructure: no visible global function definition for ‘xmlRoot’
getDasStructure: no visible global function definition for ‘xmlSApply’
getDasStructure: no visible binding for global variable ‘xmlAttrs’
getDasTypes: no visible global function definition for ‘xmlTreeParse’
getDasTypes: no visible global function definition for ‘xmlRoot’
getDasTypes: no visible global function definition for ‘xmlSApply’
getDasTypes : <anonymous>: no visible global function definition for
  ‘xmlAttrs’
plotFeatures: no visible global function definition for ‘IRanges’
plotFeatures: no visible global function definition for ‘disjointBins’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/27s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getDasStructure 4.410  0.036    7.14
DASiR-package   1.714  0.021   10.04
* 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/DASiR.Rcheck/00check.log’
for details.

DASiR.Rcheck/00install.out:

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

DASiR.Rcheck/DASiR-Ex.timings:

nameusersystemelapsed
DASiR-package 1.714 0.02110.040
getDas-functions0.1400.0032.405
getDasFeature0.0520.0010.374
getDasSequence0.0380.0010.359
getDasStructure4.4100.0367.140
plotFeatures0.0390.0010.449