Gviz 1.15.7
Florian Hahne
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz | | Last Changed Rev: 116136 / Revision: 116626 | | Last Changed Date: 2016-04-11 02:57:10 -0700 (Mon, 11 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | 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 Gviz_1.15.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Gviz.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.15.7’
* 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 ‘Gviz’ can be installed ... [34s/35s] OK
* checking installed package size ... NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
doc 1.6Mb
extdata 2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.buildRange,IRanges-ANY-ANY-ANY: warning in GRanges(seqnames =
.chrName(chromosome), range = range, strand = if
(!is.null(args$strand)) args$strand else "*"): partial argument match
of 'range' to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames = seqnames(r)[1],
range = rtmp): partial argument match of 'range' to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames =
chromosome(GdObject), range = ir, strand =
unique(as.character(strand(GdObject)))): partial argument match of
'range' to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames = 1, strand =
strand(GdObject)[1], range = rr): partial argument match of 'range'
to 'ranges'
collapseTrack,DataTrack: warning in GRanges(seqnames =
seq_len(length(rr)), strand = st, range = rr): partial argument match
of 'range' to 'ranges'
initialize,AlignedReadTrack: warning in GRanges(range = IRanges(start =
from, end = to), strand = names(.Object@coverage), seqnames =
.Object@chromosome): partial argument match of 'range' to 'ranges'
initialize,GenomeAxisTrack: warning in GRanges(range = range, seqnames
= "dummy", id = ids): partial argument match of 'range' to 'ranges'
initialize,IdeogramTrack: warning in GRanges(seqnames = bnames, range =
IRanges(start = bands$chromStart, end = bands$chromEnd), name =
bnames, type = as.character(bands$gieStain)): partial argument match
of 'range' to 'ranges'
subset,AlignedReadTrack: warning in GRanges(range = IRanges(start =
from, end = to), strand = names(x@coverage), seqnames =
x@chromosome): partial argument match of 'range' to 'ranges'
.computeGroupRange: no visible global function definition for
'setNames'
.defaultVarMap: no visible global function definition for 'setNames'
.getBioColorIdeo: no visible global function definition for 'setNames'
.prepareDtData: no visible global function definition for
'type.convert'
.supportsAlpha: no visible global function definition for 'dev.cur'
.supportsAlpha: no visible global function definition for 'dev.off'
plotTracks: no visible global function definition for 'dev.cur'
plotTracks: no visible global function definition for 'dev.off'
.buildRange,GRanges-ANY-ANY-ANY: no visible global function definition
for 'setNames'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
'cdsBy'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
'fiveUTRsByTranscript'
.buildRange,TxDb-ANY-ANY-ANY: no visible global function definition for
'threeUTRsByTranscript'
drawGD,AlignmentsTrack: no visible global function definition for
'setNames'
drawGD,AlignmentsTrack : <anonymous>: no visible global function
definition for 'setNames'
Undefined global functions or variables:
cdsBy dev.cur dev.off fiveUTRsByTranscript setNames
threeUTRsByTranscript type.convert
Consider adding
importFrom("grDevices", "dev.cur", "dev.off")
importFrom("stats", "setNames")
importFrom("utils", "type.convert")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'AlignedReadTrack,ANY,ANY,ANY'
generic '[' and siglist 'DataTrack,ANY,ANY,ANY'
generic '[' and siglist 'GenomeAxisTrack,ANY,ANY,ANY'
generic '[' and siglist 'IdeogramTrack,ANY,ANY,ANY'
generic '[' and siglist 'RangeTrack,ANY,ANY,ANY'
generic '[' and siglist 'StackedTrack,ANY,ANY,ANY'
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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [65s/68s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AlignmentsTrack 10.261 1.136 11.801
SequenceTrack-class 8.909 0.939 11.068
GeneRegionTrack-class 6.877 0.051 7.146
AnnotationTrack-class 5.739 0.033 6.103
plotTracks 5.145 0.012 5.248
* 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: 1 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/Gviz.Rcheck/00check.log’
for details.