BioC 3.5: CHECK report for hiAnnotator on tokay2
This page was generated on 2017-08-16 13:23:18 -0400 (Wed, 16 Aug 2017).
hiAnnotator 1.10.0 Nirav V Malani
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/hiAnnotator | Last Changed Rev: 129126 / Revision: 131943 | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 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 |  |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
Summary
Package: hiAnnotator
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Version: 1.10.0
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Command: rm -rf hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && mkdir hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.10.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.10.0.tar.gz
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StartedAt: 2017-08-16 00:29:22 -0400 (Wed, 16 Aug 2017)
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EndedAt: 2017-08-16 00:35:05 -0400 (Wed, 16 Aug 2017)
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EllapsedTime: 342.4 seconds
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RetCode: 0
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Status: OK
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CheckDir: hiAnnotator.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && mkdir hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.10.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.10.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/hiAnnotator.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hiAnnotator/DESCRIPTION' ... OK
* this is package 'hiAnnotator' version '1.10.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... 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' ... NOTE
The following directory looks like a leftover from 'knitr':
'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/hiAnnotator.Rcheck/00check.log'
for details.
hiAnnotator.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'hiAnnotator' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'hiAnnotator' as hiAnnotator_1.10.0.zip
* DONE (hiAnnotator)
hiAnnotator.Rcheck/examples_i386/hiAnnotator-Ex.timings:
name | user | system | elapsed
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cleanColname | 0.02 | 0.00 | 0.02 |
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doAnnotation | 1.86 | 0.12 | 1.98 |
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get2NearestFeature | 3.27 | 0.05 | 3.31 |
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getFeatureCounts | 0.71 | 0.05 | 1.45 |
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getFeatureCountsBig | 0.68 | 0.03 | 0.72 |
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getLowestDists | 0.19 | 0.00 | 0.19 |
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getNearestFeature | 1.86 | 0.01 | 2.00 |
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getRelevantCol | 0 | 0 | 0 |
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getSitesInFeature | 0.62 | 0.02 | 0.64 |
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getUCSCtable | 0 | 0 | 0 |
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getWindowLabel | 0 | 0 | 0 |
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makeChunks | 0.50 | 0.05 | 0.55 |
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makeGRanges | 0.38 | 0.00 | 0.37 |
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makeUCSCsession | 0 | 0 | 0 |
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plotdisFeature | 2.50 | 0.06 | 2.56 |
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hiAnnotator.Rcheck/examples_x64/hiAnnotator-Ex.timings:
name | user | system | elapsed
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cleanColname | 0 | 0 | 0 |
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doAnnotation | 1.94 | 0.00 | 1.93 |
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get2NearestFeature | 2.31 | 0.04 | 2.34 |
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getFeatureCounts | 0.48 | 0.01 | 0.50 |
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getFeatureCountsBig | 0.43 | 0.03 | 0.46 |
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getLowestDists | 0.12 | 0.00 | 0.12 |
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getNearestFeature | 1.22 | 0.05 | 1.31 |
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getRelevantCol | 0 | 0 | 0 |
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getSitesInFeature | 0.59 | 0.01 | 0.61 |
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getUCSCtable | 0 | 0 | 0 |
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getWindowLabel | 0 | 0 | 0 |
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makeChunks | 1 | 0 | 1 |
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makeGRanges | 0.31 | 0.00 | 0.31 |
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makeUCSCsession | 0 | 0 | 0 |
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plotdisFeature | 3.11 | 0.02 | 3.13 |
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