Gviz 1.15.0
Florian Hahne
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Gviz | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings Gviz_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/Gviz.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Gviz/DESCRIPTION’ ... OK
* this is package ‘Gviz’ version ‘1.15.0’
* 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 ... [21s/21s] OK
* checking installed package size ... NOTE
installed size is 5.7Mb
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'
.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’
Undefined global functions or variables:
cdsBy fiveUTRsByTranscript threeUTRsByTranscript
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
AlignmentsTrack 5.857 0.308 6.171
GeneRegionTrack-class 5.368 0.016 5.394
* 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 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/Gviz.Rcheck/00check.log’
for details.