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BioC 2.13: CHECK report for bumphunter on moscato1

This page was generated on 2014-04-05 09:51:07 -0700 (Sat, 05 Apr 2014).

Package 104/750HostnameOS / ArchBUILDCHECKBUILD BIN
bumphunter 1.2.0
Rafael A. Irizarry
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/bumphunter
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: bumphunter
Version: 1.2.0
Command: rm -rf bumphunter.buildbin-libdir && mkdir bumphunter.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=bumphunter.buildbin-libdir bumphunter_1.2.0.tar.gz >bumphunter-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=bumphunter.buildbin-libdir --install="check:bumphunter-install.out" --force-multiarch --no-vignettes --timings bumphunter_1.2.0.tar.gz && mv bumphunter.buildbin-libdir/* bumphunter.Rcheck/ && rmdir bumphunter.buildbin-libdir
StartedAt: 2014-04-05 02:42:36 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:47:36 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 300.2 seconds
RetCode: 0
Status:  OK  
CheckDir: bumphunter.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/bumphunter.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'bumphunter/DESCRIPTION' ... OK
* this is package 'bumphunter' 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 'bumphunter' 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 ... NOTE
Unexported object imported by a ':::' call: 'doParallel:::.options'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'greaterOrEqual'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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' ... [26s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
bumphunter 0.37   0.02    9.89
smoother   0.09   0.00    5.88
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
bumphunter 0.59   0.02   10.50
smoother   0.11   0.00    7.41
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'runTests.R' [38s]
 [39s] OK
** running tests for arch 'x64'
  Running 'runTests.R' [41s]
 [41s] 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

NOTE: There was 1 note.
See
  'D:/biocbld/bbs-2.13-bioc/meat/bumphunter.Rcheck/00check.log'
for details.

bumphunter.Rcheck/00install.out:


install for i386

* installing *source* package 'bumphunter' ...
** R
** data
*** moving datasets to lazyload DB
** 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 'bumphunter' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'bumphunter' as bumphunter_1.2.0.zip
* DONE (bumphunter)

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

nameusersystemelapsed
annotateNearest2.860.082.93
bumphunter0.370.029.89
clusterMaker0.010.000.01
dummyData000
getSegments0.020.000.03
locfitByCluster0.040.000.05
loessByCluster0.520.000.52
pointMatch0.430.000.44
regionFinder0.030.010.05
runmedByCluster0.020.000.01
smoother0.090.005.88

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

nameusersystemelapsed
annotateNearest2.760.042.81
bumphunter 0.59 0.0210.50
clusterMaker0.030.000.03
dummyData0.020.000.02
getSegments0.030.000.55
locfitByCluster0.080.000.07
loessByCluster0.880.000.89
pointMatch0.460.000.46
regionFinder0.030.000.03
runmedByCluster0.020.000.02
smoother0.110.007.41