BioC 3.5: CHECK report for hiAnnotator on toluca2
This page was generated on 2017-04-23 14:38:31 -0400 (Sun, 23 Apr 2017).
hiAnnotator 1.9.1 Nirav V Malani
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/hiAnnotator | Last Changed Rev: 128797 / Revision: 129046 | Last Changed Date: 2017-04-17 15:35:02 -0400 (Mon, 17 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK |  |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
Summary
Package: hiAnnotator |
Version: 1.9.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiAnnotator_1.9.1.tar.gz |
StartedAt: 2017-04-23 05:15:49 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 05:19:55 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 246.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: hiAnnotator.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings hiAnnotator_1.9.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/hiAnnotator.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘hiAnnotator/DESCRIPTION’ ... OK
* this is package ‘hiAnnotator’ version ‘1.9.1’
* 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 ‘hiAnnotator’ can be installed ... OK
* checking installed package size ... OK
* 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
get2NearestFeature: no visible global function definition for ‘IRanges’
get2NearestFeature: no visible global function definition for ‘mid’
get2NearestFeature : <anonymous>: no visible binding for global
variable ‘queryHits’
get2NearestFeature : <anonymous>: no visible binding for global
variable ‘dist’
get2NearestFeature : <anonymous>: no visible binding for global
variable ‘featureName’
getFeatureCounts: no visible global function definition for ‘as’
getFeatureCounts : <anonymous>: no visible global function definition
for ‘countQueryHits’
getFeatureCountsBig: no visible global function definition for ‘mid’
getNearestFeature: no visible global function definition for ‘IRanges’
getNearestFeature: no visible global function definition for ‘mid’
getNearestFeature: no visible binding for global variable ‘queryHits’
getNearestFeature: no visible binding for global variable ‘n’
getNearestFeature: no visible binding for global variable ‘featureName’
getNearestFeature: no visible binding for global variable ‘dist’
getSitesInFeature: no visible global function definition for
‘overlapsAny’
getSitesInFeature: no visible binding for global variable ‘queryHits’
getSitesInFeature: no visible global function definition for ‘n’
getSitesInFeature: no visible global function definition for ‘filter’
getSitesInFeature: no visible binding for global variable ‘featureName’
makeChunks: no visible global function definition for ‘breakInChunks’
makeChunks: no visible global function definition for ‘detectCores’
makeChunks : <anonymous>: no visible global function definition for
‘keepSeqlevels’
makeChunks : <anonymous>: no visible global function definition for
‘seqlevelsInUse’
makeGRanges: no visible global function definition for ‘IRanges’
makeGRanges: no visible global function definition for ‘seqlengths’
makeGRanges: no visible global function definition for ‘read.delim’
makeGRanges: no visible global function definition for ‘seqlevels<-’
makeGRanges: no visible global function definition for ‘sortSeqlevels’
makeGRanges: no visible global function definition for ‘seqlevels’
makeGRanges: no visible global function definition for ‘seqlengths<-’
plotdisFeature: no visible global function definition for ‘is’
plotdisFeature: no visible global function definition for ‘filter’
Undefined global functions or variables:
IRanges as breakInChunks countQueryHits detectCores dist featureName
filter is keepSeqlevels mid n overlapsAny queryHits read.delim
seqlengths seqlengths<- seqlevels seqlevels<- seqlevelsInUse
sortSeqlevels
Consider adding
importFrom("methods", "as", "is")
importFrom("stats", "dist", "filter")
importFrom("utils", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
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
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/hiAnnotator.Rcheck/00check.log’
for details.
hiAnnotator.Rcheck/00install.out:
* installing *source* package ‘hiAnnotator’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (hiAnnotator)
hiAnnotator.Rcheck/hiAnnotator-Ex.timings:
name | user | system | elapsed
|
cleanColname | 0.002 | 0.000 | 0.002 |
|
doAnnotation | 2.287 | 0.082 | 2.538 |
|
get2NearestFeature | 2.910 | 0.093 | 3.054 |
|
getFeatureCounts | 0.774 | 0.034 | 0.818 |
|
getFeatureCountsBig | 0.630 | 0.042 | 0.679 |
|
getLowestDists | 0.185 | 0.001 | 0.192 |
|
getNearestFeature | 1.535 | 0.058 | 1.595 |
|
getRelevantCol | 0.008 | 0.002 | 0.011 |
|
getSitesInFeature | 0.658 | 0.025 | 0.684 |
|
getUCSCtable | 0.001 | 0.000 | 0.000 |
|
getWindowLabel | 0.001 | 0.000 | 0.000 |
|
makeChunks | 0.395 | 0.028 | 0.424 |
|
makeGRanges | 0.378 | 0.037 | 0.416 |
|
makeUCSCsession | 0.001 | 0.000 | 0.001 |
|
plotdisFeature | 4.168 | 0.060 | 4.277 |
|