davidTiling 1.17.0
Wolfgang Huber
| Snapshot Date: 2017-08-15 09:00:08 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/davidTiling | | Last Changed Rev: 4157 / Revision: 4227 | | Last Changed Date: 2017-04-24 16:19:55 -0400 (Mon, 24 Apr 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings davidTiling_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/davidTiling.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘davidTiling/DESCRIPTION’ ... OK
* this is package ‘davidTiling’ version ‘1.17.0’
* 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 ‘davidTiling’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 538.0Mb
sub-directories of 1Mb or more:
celfiles 305.9Mb
data 229.5Mb
website 2.3Mb
* checking package 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
‘Biobase’ ‘GO.db’ ‘tilingArray’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOHyperG: no visible global function definition for ‘phyper’
GOHyperG: no visible binding for global variable ‘GOTERM’
GOHyperG: no visible global function definition for
‘replaceSystematicByCommonName’
GOHyperG: no visible global function definition for ‘Term’
GOHyperG: no visible global function definition for ‘plot’
GOHyperG: no visible global function definition for ‘abline’
colMedians: no visible binding for global variable ‘median’
getAllGO: no visible binding for global variable ‘GOMFANCESTOR’
getAllGO: no visible binding for global variable ‘GOBPANCESTOR’
getAllGO: no visible binding for global variable ‘GOCCANCESTOR’
movingWindow: no visible global function definition for ‘median’
movingWindow : <anonymous>: no visible global function definition for
‘median’
scatterWithHist: no visible global function definition for ‘hist’
scatterWithHist: no visible global function definition for ‘layout’
scatterWithHist: no visible global function definition for ‘par’
scatterWithHist: no visible global function definition for ‘plot’
scatterWithHist: no visible global function definition for ‘barplot’
scatterWithHist: no visible global function definition for ‘text’
scoreSegments: no visible global function definition for ‘data’
scoreSegments: no visible binding for global variable ‘yeastFeatures’
scoreSegments: no visible binding for global variable ‘chrs’
scoreSegments: no visible global function definition for ‘otherStrand’
scoreSegments: no visible global function definition for ‘median’
scoreSegments: no visible global function definition for ‘posMin’
showDens: no visible global function definition for ‘hist’
showDens: no visible global function definition for ‘plot’
showDens: no visible global function definition for ‘axis’
showDens: no visible global function definition for ‘polygon’
zscore: no visible global function definition for ‘sd’
Undefined global functions or variables:
GOBPANCESTOR GOCCANCESTOR GOMFANCESTOR GOTERM Term abline axis
barplot chrs data hist layout median otherStrand par phyper plot
polygon posMin replaceSystematicByCommonName sd text yeastFeatures
Consider adding
importFrom("graphics", "abline", "axis", "barplot", "hist", "layout",
"par", "plot", "polygon", "text")
importFrom("stats", "median", "phyper", "sd")
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GOHyperG.Rd:34-35: Dropping empty section \examples
prepare_Rd: getGO.Rd:32-33: Dropping empty section \examples
prepare_Rd: scatterWithHist.Rd:19-20: Dropping empty section \details
prepare_Rd: scoreSegments.Rd:103-104: Dropping empty section \examples
* 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 files in ‘vignettes’ ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
‘Archi_RT_positions.txt’, ‘strongConservedNovelIsolated.txt’,
‘utrmap-GOcategories.txt’
Package has no Sweave vignette sources and no VignetteBuilder field.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
davidTiling 28.624 0.928 29.565
probeAnno 5.308 0.256 5.566
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/home/biocbuild/bbs-3.6-data-experiment/meat/davidTiling.Rcheck/00check.log’
for details.