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BioC 3.2: CHECK report for SplicingGraphs on perceval

This page was generated on 2015-11-10 14:48:07 -0800 (Tue, 10 Nov 2015).

Package 1010/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.10.0
H. Pages
Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/SplicingGraphs
Last Changed Rev: 109589 / Revision: 110496
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SplicingGraphs
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.10.0.tar.gz
StartedAt: 2015-11-10 09:50:02 -0800 (Tue, 10 Nov 2015)
EndedAt: 2015-11-10 09:56:43 -0800 (Tue, 10 Nov 2015)
EllapsedTime: 400.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SplicingGraphs.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.10.0’
* 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 ‘SplicingGraphs’ can be installed ... [23s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GenomicFeatures’ ‘GenomicAlignments’ ‘Rgraphviz’ ‘igraph’
A package should be listed in only one of these fields.
* 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
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘GenomicAlignments:::fillJunctionGaps’
  ‘GenomicFeatures:::.collapse_df’ ‘IRanges:::newCompressedList0’
  ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::matchIntegerPairs’
  ‘S4Vectors:::orderIntegerPairs’ ‘S4Vectors:::selfmatchIntegerPairs’
  ‘S4Vectors:::setPrototypeFromObject’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘reportReads’
Undocumented S4 methods:
  generic 'reportReads' and siglist 'SplicingGraphs'
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 ... WARNING
Objects in \usage without \alias in documentation object 'countReads-methods':
  ‘reportReads’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [132s/137s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 35.926  0.116  36.048
toy_data                21.761  0.047  21.843
countReads-methods       6.657  0.023   6.681
SplicingGraphs-class     2.569  0.230   7.409
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’ [16s/16s]
 [16s/16s] OK
* 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 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.


SplicingGraphs.Rcheck/00install.out:

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

SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings:

nameusersystemelapsed
SplicingGraphs-class2.5690.2307.409
SplicingGraphs-package0.0000.0000.001
assignReads3.2530.0193.273
bubbles-methods3.7850.0113.797
countReads-methods6.6570.0236.681
plotTranscripts-methods35.926 0.11636.048
rsgedgesByGene-methods3.7090.0183.729
sgedges-methods4.8000.0154.815
sgedgesByGene-methods3.4500.0183.469
sgraph-methods2.1600.0112.171
toy_data21.761 0.04721.843
txpath-methods3.3420.0213.366