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Package 347/514HostnameOS / ArchBUILDCHECKBUILD BIN
oligoClasses 1.16.0
Benilton Carvalho and Robert Scharpf
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/oligoClasses
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: oligoClasses
Version: 1.16.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings oligoClasses_1.16.0.tar.gz
StartedAt: 2012-03-24 01:45:31 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:47:51 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 139.6 seconds
RetCode: 0
Status:  OK 
CheckDir: oligoClasses.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/oligoClasses.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.16.0’
* 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 whether package ‘oligoClasses’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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
* 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 for unstated 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
createFF: no visible global function definition for ‘ff’
delCluster: no visible global function definition for ‘stopCluster’
initializeBigMatrix: no visible binding for global variable ‘ffdf’
initializeBigVector: no visible global function definition for ‘ff’
initializeLMObject: no visible global function definition for
  ‘paramNames’
initializeLMObject: no visible binding for global variable ‘ffdf’
ocLapply: no visible global function definition for ‘parLapply’
ocProbesets: no visible global function definition for ‘clusterCall’
ocSamples: no visible global function definition for ‘clusterCall’
requireClusterPkg: no visible global function definition for
  ‘clusterCall’
setCluster: no visible global function definition for ‘makeCluster’
splitIndicesByNode: no visible global function definition for
  ‘clusterSplit’
* checking Rd files ... NOTE
prepare_Rd: CNSet-class.Rd:107: Dropping empty section \seealso
prepare_Rd: batch.Rd:44-46: Dropping empty section \details
* 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 ... NOTE
  ================================================================================
  Large dataset support for 'oligo/crlmm': Disabled
       - Load 'ff'
  ================================================================================
  Parallel computing support for 'oligo/crlmm': Disabled
       - Load 'ff'
       - Load 'snow'
       - Use options(cluster=makeCluster(...))
  ================================================================================
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

oligoClasses.Rcheck/00install.out:

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘oligoClasses’
Creating a generic function for ‘close’ from package ‘base’ in package ‘oligoClasses’
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================

* DONE (oligoClasses)

oligoClasses.Rcheck/oligoClasses-Ex.timings:

nameusersystemelapsed
AlleleSet-class0.3880.0000.389
AssayData-methods0.6880.0240.712
CNSet-class11.805 0.20012.131
CopyNumberSet-class0.0440.0000.048
FeatureSetExtensions-class0.3800.0360.434
PDInfo-methods0.8880.0200.933
RangedDataCNV-classes0.0000.0000.001
RangedDataCNV-utils1.3440.0001.389
SnpSet-methods0.0920.0000.101
SnpSuperSet-class0.2760.0000.277
addFeatureAnnotation4.3160.0844.637
affyPlatforms0.0000.0000.001
batch1.0200.0081.038
celfileDate0.0280.0000.027
checkExists0.0080.0000.006
checkOrder0.0920.0000.095
chromosome2integer000
data-efsExample0.0040.0000.002
data-scqsExample0.0000.0000.002
data-sfsExample0.0040.0000.002
data-sqsExample0.0040.0000.002
db000
ff_matrix000
fileConnections000
findOverlaps0.8240.0160.890
flags0.3160.0120.327
getBar000
i2p_p2i0.0000.0000.001
is.ffmatrix0.0000.0040.001
isPackageLoaded0.0000.0000.001
kind0.0640.0200.083
largeObjects000
ldOpts0.0000.0000.001
list.celfiles0.0280.0000.037
locusLevelData0.0640.0040.068
oligoSetExample0.0560.0000.055
order0.0600.0040.068
pdPkgFromBioC000
requireAnnotation000
splitVec0.0000.0000.002