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BioC 3.1: CHECK report for hiAnnotator on moscato2

This page was generated on 2015-10-09 09:31:13 -0700 (Fri, 09 Oct 2015).

Package 461/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
hiAnnotator 1.2.0
Nirav V Malani
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/hiAnnotator
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: hiAnnotator
Version: 1.2.0
Command: rm -rf hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && mkdir hiAnnotator.buildbin-libdir hiAnnotator.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.2.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.2.0.tar.gz
StartedAt: 2015-10-09 02:50:20 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:54:37 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 256.7 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 && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=hiAnnotator.buildbin-libdir hiAnnotator_1.2.0.tar.gz >hiAnnotator.Rcheck\00install.out 2>&1 && cp hiAnnotator.Rcheck\00install.out hiAnnotator-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=hiAnnotator.buildbin-libdir --install="check:hiAnnotator-install.out" --force-multiarch --no-vignettes --timings hiAnnotator_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/hiAnnotator.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.2.0'
* 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'
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' ... [21s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
get2NearestFeature 5.55   0.03    5.58
** running examples for arch 'x64' ... [23s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
get2NearestFeature 6.98   0.04    7.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R' [7s]
 [8s] OK
** running tests for arch 'x64' ...
  Running 'runTests.R' [9s]
 [9s] 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
  'E:/biocbld/bbs-3.1-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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'hiAnnotator' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'hiAnnotator' as hiAnnotator_1.2.0.zip
* DONE (hiAnnotator)

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

nameusersystemelapsed
cleanColname000
doAnnotation1.840.001.84
get2NearestFeature5.550.035.58
getFeatureCounts0.810.000.81
getFeatureCountsBig0.80.00.8
getLowestDists0.110.000.11
getNearestFeature1.420.021.43
getRelevantCol0.010.000.02
getSitesInFeature0.630.000.62
getUCSCtable000
getWindowLabel000
makeChunks0.870.010.89
makeGRanges0.620.000.63
makeUCSCsession000
plotdisFeature1.310.001.31

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

nameusersystemelapsed
cleanColname000
doAnnotation1.340.001.35
get2NearestFeature6.980.047.02
getFeatureCounts0.560.030.59
getFeatureCountsBig0.90.00.9
getLowestDists0.130.000.13
getNearestFeature1.20.01.2
getRelevantCol0.010.000.02
getSitesInFeature0.940.000.93
getUCSCtable000
getWindowLabel000
makeChunks0.520.020.53
makeGRanges1.040.001.05
makeUCSCsession000
plotdisFeature1.520.001.62