Gviz 1.14.7
Florian Hahne
| Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/Gviz | | Last Changed Rev: 116135 / Revision: 116712 | | Last Changed Date: 2016-04-11 02:56:57 -0700 (Mon, 11 Apr 2016) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| oaxaca | 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_1.14.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Gviz.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.14.7’
* 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 ... [32s/50s] 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 : .local: 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 : .local: warning in GRanges(seqnames =
seqnames(r)[1], range = rtmp): partial argument match of 'range' to
'ranges'
collapseTrack,DataTrack : .local: warning in GRanges(seqnames =
chromosome(GdObject), range = ir, strand =
unique(as.character(strand(GdObject)))): partial argument match of
'range' to 'ranges'
collapseTrack,DataTrack : .local: warning in GRanges(seqnames = 1,
strand = strand(GdObject)[1], range = rr): partial argument match of
'range' to 'ranges'
collapseTrack,DataTrack : .local: warning in GRanges(seqnames =
seq_len(length(rr)), strand = st, range = rr): partial argument match
of 'range' to 'ranges'
initialize,AlignedReadTrack : .local: 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 : .local: warning in GRanges(range = range,
seqnames = "dummy", id = ids): partial argument match of 'range' to
'ranges'
initialize,IdeogramTrack : .local: 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 : .local: warning in GRanges(range =
IRanges(start = from, end = to), strand = names(x@coverage), seqnames
= x@chromosome): partial argument match of 'range' to 'ranges'
.buildRange,TxDb-ANY-ANY-ANY : .local: no visible global function
definition for ‘cdsBy’
.buildRange,TxDb-ANY-ANY-ANY : .local: no visible global function
definition for ‘fiveUTRsByTranscript’
.buildRange,TxDb-ANY-ANY-ANY : .local: no visible global function
definition for ‘threeUTRsByTranscript’
* 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 ... [59s/65s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AlignmentsTrack 8.975 0.829 11.330
SequenceTrack-class 8.070 0.765 10.365
AnnotationTrack-class 5.706 0.041 5.840
GeneRegionTrack-class 5.576 0.030 5.756
* 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-3.2-bioc/meat/Gviz.Rcheck/00check.log’
for details.