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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).

Package 624/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hiAnnotator
Version: 1.10.0
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
StartedAt: 2017-08-16 00:29:22 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:35:05 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 342.4 seconds
RetCode: 0
Status:  OK  
CheckDir: hiAnnotator.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running 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
###
##############################################################################
##############################################################################


* 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:

nameusersystemelapsed
cleanColname0.020.000.02
doAnnotation1.860.121.98
get2NearestFeature3.270.053.31
getFeatureCounts0.710.051.45
getFeatureCountsBig0.680.030.72
getLowestDists0.190.000.19
getNearestFeature1.860.012.00
getRelevantCol000
getSitesInFeature0.620.020.64
getUCSCtable000
getWindowLabel000
makeChunks0.500.050.55
makeGRanges0.380.000.37
makeUCSCsession000
plotdisFeature2.500.062.56

hiAnnotator.Rcheck/examples_x64/hiAnnotator-Ex.timings:

nameusersystemelapsed
cleanColname000
doAnnotation1.940.001.93
get2NearestFeature2.310.042.34
getFeatureCounts0.480.010.50
getFeatureCountsBig0.430.030.46
getLowestDists0.120.000.12
getNearestFeature1.220.051.31
getRelevantCol000
getSitesInFeature0.590.010.61
getUCSCtable000
getWindowLabel000
makeChunks101
makeGRanges0.310.000.31
makeUCSCsession000
plotdisFeature3.110.023.13