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BioC 3.4: CHECK report for SplicingGraphs on malbec1

This page was generated on 2017-04-15 16:11:25 -0400 (Sat, 15 Apr 2017).

Package 1183/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.14.0
H. Pagès
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/SplicingGraphs
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: SplicingGraphs
Version: 1.14.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.14.0.tar.gz
StartedAt: 2017-04-15 01:26:51 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:31:42 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 291.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: SplicingGraphs.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.0’
* package encoding: UTF-8
* 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 ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
  Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/SplicingGraphs.Rcheck/00install.out’ for details.
* 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.
':::' calls which should be '::':
  'S4Vectors:::matchIntegerPairs' 'S4Vectors:::orderIntegerPairs'
  'S4Vectors:::selfmatchIntegerPairs'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'BiocGenerics:::testPackage' 'GenomicAlignments:::fillJunctionGaps'
  'GenomicFeatures:::.collapse_df' 'IRanges:::newCompressedList0'
  'IRanges:::regroupBySupergroup' '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 '[' and siglist 'SplicingGraphs,ANY,ANY,ANY'
  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 ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 27.468  0.036  28.136
toy_data                13.712  0.012  13.733
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 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: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.


SplicingGraphs.Rcheck/00install.out:

* installing *source* package ‘SplicingGraphs’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::from’ by ‘Rgraphviz::from’ when loading ‘SplicingGraphs’
Warning: replacing previous import ‘IRanges::to’ by ‘Rgraphviz::to’ when loading ‘SplicingGraphs’
* DONE (SplicingGraphs)

SplicingGraphs.Rcheck/SplicingGraphs-Ex.timings:

nameusersystemelapsed
SplicingGraphs-class1.9640.0562.024
SplicingGraphs-package000
assignReads2.8080.0082.815
bubbles-methods2.5440.0042.548
countReads-methods4.5800.0084.591
plotTranscripts-methods27.468 0.03628.136
rsgedgesByGene-methods3.7840.0043.789
sgedges-methods3.2040.0043.210
sgedgesByGene-methods2.3640.0002.365
sgraph-methods1.8320.0081.841
toy_data13.712 0.01213.733
txpath-methods2.5360.0162.556