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BioC 3.2: CHECK report for SplicingGraphs on linux1.bioconductor.org

This page was generated on 2015-10-27 17:25:54 -0400 (Tue, 27 Oct 2015).

Package 1010/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.10.0
H. Pages
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/SplicingGraphs
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  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 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: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.10.0.tar.gz
StartedAt: 2015-10-27 08:25:19 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 08:30:20 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 301.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SplicingGraphs.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [16s/16s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [104s/104s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 26.779  0.020  26.817
toy_data                16.630  0.004  16.634
countReads-methods       6.134  0.000   6.140
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’ [13s/13s]
 [14s/14s] 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
  ‘/home/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-class2.0610.0962.158
SplicingGraphs-package0.0010.0000.001
assignReads2.850.002.85
bubbles-methods3.5410.0083.549
countReads-methods6.1340.0006.140
plotTranscripts-methods26.779 0.02026.817
rsgedgesByGene-methods3.0940.0003.094
sgedges-methods3.4920.0083.501
sgedgesByGene-methods2.7470.0002.747
sgraph-methods1.5330.0041.537
toy_data16.630 0.00416.634
txpath-methods2.7850.0002.785