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BioC 3.0: CHECK report for hiAnnotator on moscato1

This page was generated on 2015-04-10 09:50:31 -0700 (Fri, 10 Apr 2015).

Package 424/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.0.0
Nirav V Malani
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/hiAnnotator
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: hiAnnotator
Version: 1.0.0
Command: rm -rf hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && mkdir hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.0.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.0.0.tar.gz
StartedAt: 2015-04-10 02:10:09 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:16:34 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 385.4 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 && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.0.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/hiAnnotator.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'hiAnnotator/DESCRIPTION' ... OK
* this is package 'hiAnnotator' version '1.0.0'
* 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
* 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'
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'
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' ... OK
* checking examples ...
** running examples for arch 'i386' ... [36s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
get2NearestFeature 7.66      0    7.66
** running examples for arch 'x64' ... [38s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
get2NearestFeature 8.03   0.04    8.07
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [11s]
 [12s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [15s]
 [16s] 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-3.0-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_1.0.0.zip
* DONE (hiAnnotator)

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

nameusersystemelapsed
cleanColname000
doAnnotation2.840.022.85
get2NearestFeature7.660.007.66
getFeatureCounts3.210.003.21
getFeatureCountsBig3.580.003.58
getLowestDists0.20.00.2
getNearestFeature2.990.033.02
getRelevantCol000
getSitesInFeature1.450.001.45
getUCSCtable000
getWindowLabel000
makeChunks0.510.000.51
makeGRanges0.730.000.73
makeUCSCsession000
plotdisFeature1.950.001.95

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

nameusersystemelapsed
cleanColname0.010.000.02
doAnnotation3.280.003.27
get2NearestFeature8.030.048.07
getFeatureCounts3.820.003.82
getFeatureCountsBig3.140.003.14
getLowestDists0.140.000.14
getNearestFeature3.10.03.1
getRelevantCol0.020.000.02
getSitesInFeature1.640.001.63
getUCSCtable000
getWindowLabel000
makeChunks0.560.000.60
makeGRanges0.870.000.87
makeUCSCsession000
plotdisFeature2.060.032.09