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BioC 3.2: CHECK report for hiAnnotator on windows1.bioconductor.org

This page was generated on 2015-10-27 17:31:16 -0400 (Tue, 27 Oct 2015).

Package 490/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.4.0
Nirav V Malani
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/hiAnnotator
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hiAnnotator
Version: 1.4.0
Command: rm -rf hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && mkdir hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.4.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.4.0.tar.gz
StartedAt: 2015-10-27 02:42:11 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:45:53 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 221.8 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:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.4.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/hiAnnotator.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* 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 '1.4.0'
* 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 ... NOTE
Malformed Title field: should not end in a period.
* 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
* 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 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 'featureName'
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 'n'
getNearestFeature: no visible binding for global variable 'featureName'
getSitesInFeature: no visible global function definition for 'n'
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
  'seqlevels'
makeGRanges: no visible global function definition for 'IRanges'
makeGRanges: no visible global function definition for 'seqlengths'
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<-'
* 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' ... [14s] OK
** running examples for arch 'x64' ... [16s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [7s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [8s]
 [8s] 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: 3 NOTEs
See
  'C:/biocbld/bbs-3.2-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_1.4.0.zip
* DONE (hiAnnotator)

hiAnnotator.Rcheck/examples_i386/hiAnnotator-Ex.timings:

nameusersystemelapsed
cleanColname000
doAnnotation1.060.001.06
get2NearestFeature1.530.061.59
getFeatureCounts0.460.030.49
getFeatureCountsBig0.700.020.71
getLowestDists0.060.000.07
getNearestFeature1.030.011.05
getRelevantCol0.010.000.02
getSitesInFeature0.530.000.53
getUCSCtable000
getWindowLabel000
makeChunks0.650.000.64
makeGRanges0.430.000.43
makeUCSCsession000
plotdisFeature1.060.021.08

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

nameusersystemelapsed
cleanColname0.010.000.02
doAnnotation0.990.000.98
get2NearestFeature1.960.042.02
getFeatureCounts0.860.020.87
getFeatureCountsBig0.860.000.86
getLowestDists0.080.000.08
getNearestFeature1.320.011.34
getRelevantCol0.020.000.01
getSitesInFeature101
getUCSCtable000
getWindowLabel000
makeChunks0.460.000.47
makeGRanges0.430.020.44
makeUCSCsession000
plotdisFeature1.260.001.26