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Package 317/472HostnameOS / ArchBUILDCHECKBUILD BIN
oligoClasses 1.15.9
Benilton Carvalho and Robert Scharpf
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligoClasses
Last Changed Rev: 55800 / Revision: 56351
Last Changed Date: 2011-05-24 05:48:19 -0700 (Tue, 24 May 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: oligoClasses
Version: 1.15.9
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.15.9.tar.gz
StartedAt: 2011-06-22 04:24:21 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 04:27:14 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 173.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: oligoClasses.Rcheck
Warnings: 1

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/oligoClasses.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oligoClasses/DESCRIPTION’ ... OK
* this is package ‘oligoClasses’ version ‘1.15.9’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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’
relocateObject : f2: no visible global function definition for
  ‘physical<-’
relocateObject: no visible global function definition for ‘physical<-’
relocateObject : relocate.fxn: no visible binding for global variable
  ‘nmm’
relocateObject : relocate.fxn: no visible global function definition
  for ‘filename<-’
relocateObject : relocate.fxn: no visible global function definition
  for ‘physical<-’
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: batch.Rd:44-46: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘isFF’
Undocumented S4 methods:
  generic 'close' and siglist 'array'
  generic 'open' and siglist 'array'
  generic 'show' and siglist 'CNSet'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘hapmapsnp5’ ‘hapmapsnp6’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  Welcome to oligoClasses version 1.15.9
  ================================================================================
  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

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.9-bioc/meat/oligoClasses.Rcheck/00check.log’
for details

oligoClasses.Rcheck/00install.out:

* installing *source* package ‘oligoClasses’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Creating a generic function for "close" from package "base" in package “oligoClasses”
Creating a generic function for "open" from package "base" in package “oligoClasses”
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.9
================================================================================
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-class0.3420.0050.349
AssayData-methods0.7610.0390.839
CNSet-class11.239 0.25812.051
FeatureSetExtensions-class0.8680.0260.910
PDInfo-methods1.0310.0601.104
SnpSet-methods0.1770.0060.186
SnpSuperSet-class0.2900.0020.292
addFeatureAnnotation5.4320.1465.730
affyPlatforms0.0010.0010.002
batch1.0000.0331.091
celfileDate0.0470.0070.101
checkExists0.0110.0020.012
chromosome2integer0.0000.0000.001
data-efsExample0.0040.0010.005
data-scqsExample0.0030.0010.003
data-sfsExample0.0030.0000.003
data-sqsExample0.0030.0000.004
db0.0010.0000.001
ff_matrix0.0010.0000.001
fileConnections0.0010.0010.001
flags0.4040.0240.432
getBar0.0010.0010.001
i2p_p2i0.0000.0000.001
is.ffmatrix0.0020.0000.002
isPackageLoaded0.0000.0000.001
kind0.2250.0160.300
largeObjects0.0010.0000.002
ldOpts0.0020.0000.003
list.celfiles0.0060.0010.007
pdPkgFromBioC000
relocateObject0.0010.0000.000
requireAnnotation000
splitVec0.0020.0010.003