SplicingGraphs 1.6.0
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| 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/SplicingGraphs | | 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 | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch SplicingGraphs_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/SplicingGraphs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’
‘GenomicFeatures’ ‘GenomicAlignments’ ‘Rgraphviz’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [38s/41s] 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:
‘BiocGenerics’ ‘IRanges’ ‘GenomicRanges’ ‘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
Loading required package: parallel
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 object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: stats4
.buildEdgeList2: no visible global function definition for
‘buildEdgeList’
.buildEdgeList2 : <anonymous>: no visible global function definition
for ‘from’
.buildEdgeList2 : <anonymous>: no visible global function definition
for ‘to’
.make_Ragraph_from_graphNEL: no visible global function definition for
‘buildNodeList’
.make_Ragraph_from_graphNEL: no visible global function definition for
‘edgemode’
.subsetByOverlapWithSingleRange: no visible global function definition
for ‘seqlevels<-’
.subsetByOverlapWithSingleRange: no visible global function definition
for ‘seqlevels’
toy_reads_bam: no visible global function definition for ‘asBam’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'countReads-methods.Rd':
‘[IRanges]{DataFrame}’
Missing link or links in documentation object 'SplicingGraphs-class.Rd':
‘[IRanges]{DataFrame}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... [187s/193s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotTranscripts-methods 47.547 0.176 47.906
toy_data 28.836 0.066 28.980
countReads-methods 8.692 0.037 8.785
sgedges-methods 5.738 0.018 5.837
assignReads 4.974 0.037 5.050
SplicingGraphs-class 3.270 0.210 8.378
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘run_unitTests.R’ [23s/23s]
[24s/24s] 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
WARNING: There were 3 warnings.
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/SplicingGraphs.Rcheck/00check.log’
for details.