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BioC 3.2: CHECK report for SplicingGraphs on oaxaca

This page was generated on 2015-08-24 10:57:36 -0700 (Mon, 24 Aug 2015).

Package 979/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SplicingGraphs 1.9.1
H. Pages
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SplicingGraphs
Last Changed Rev: 103928 / Revision: 107696
Last Changed Date: 2015-05-18 12:54:28 -0700 (Mon, 18 May 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: 1.9.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SplicingGraphs_1.9.1.tar.gz
StartedAt: 2015-08-24 04:08:30 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:15:20 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 410.0 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_1.9.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SplicingGraphs/DESCRIPTION’ ... OK
* this is package ‘SplicingGraphs’ version ‘1.9.1’
* 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’
  ‘IRanges:::newCompressedList0’ ‘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 ... NOTE

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, as.vector, cbind, colnames, do.call, duplicated,
    eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rep.int, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unlist, unsplit

* 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 ... [141s/154s] OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
plotTranscripts-methods 38.676  0.129  39.337
toy_data                22.934  0.040  23.063
countReads-methods       7.472  0.031   7.552
sgedges-methods          5.554  0.026   5.593
SplicingGraphs-class     2.912  0.123  14.900
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’ [15s/15s]
 [15s/15s] 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, 3 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-class 2.912 0.12314.900
SplicingGraphs-package0.0010.0000.001
assignReads3.4190.0173.461
bubbles-methods4.1250.0134.258
countReads-methods7.4720.0317.552
plotTranscripts-methods38.676 0.12939.337
rsgedgesByGene-methods4.2940.0134.331
sgedges-methods5.5540.0265.593
sgedgesByGene-methods3.8820.0163.907
sgraph-methods2.2420.0072.255
toy_data22.934 0.04023.063
txpath-methods3.5880.0183.613