Package: oligoClasses

Version: 1.15.9

Command: mkdir oligoClasses.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oligoClasses.buildbin-libdir oligoClasses_1.15.9.tar.gz >oligoClasses-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=oligoClasses.buildbin-libdir --install="check:oligoClasses-install.out" --force-multiarch --no-vignettes --timings oligoClasses_1.15.9.tar.gz && mv oligoClasses.buildbin-libdir/* oligoClasses.Rcheck/ && rmdir oligoClasses.buildbin-libdir

StartedAt: 2011-07-07 05:48:39 -0700 (Thu, 07 Jul 2011)

EndedAt: 2011-07-07 05:51:31 -0700 (Thu, 07 Jul 2011)

EllapsedTime: 171.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/oligoClasses.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-20 r56188)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* 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 name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.9-bioc/meat/oligoClasses.Rcheck/00check.log'
for details

install for i386

* 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(...))
================================================================================

add DLL for x64

* installing *source* package 'oligoClasses' ...
** 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(...))
================================================================================
* MD5 sums
packaged installation of 'oligoClasses' as oligoClasses_1.15.9.zip

* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.25	0.00	0.25
AssayData-methods	0.73	0.00	0.74
CNSet-class	7.94	0.06	8.00
FeatureSetExtensions-class	0.31	0.00	0.31
PDInfo-methods	0.97	0.04	1.00
SnpSet-methods	0.17	0.00	0.17
SnpSuperSet-class	0.21	0.00	0.21
addFeatureAnnotation	3.47	0.03	3.50
affyPlatforms	0	0	0
batch	0.35	0.00	0.35
celfileDate	0.04	0.00	0.04
checkExists	0	0	0
chromosome2integer	0	0	0
data-efsExample	0.01	0.00	0.01
data-scqsExample	0	0	0
data-sfsExample	0	0	0
data-sqsExample	0	0	0
db	0	0	0
ff_matrix	0	0	0
fileConnections	0	0	0
flags	0.16	0.01	0.19
getBar	0	0	0
i2p_p2i	0	0	0
is.ffmatrix	0.01	0.00	0.01
isPackageLoaded	0	0	0
kind	0.11	0.00	0.11
largeObjects	0	0	0
ldOpts	0.02	0.00	0.02
list.celfiles	0	0	0
pdPkgFromBioC	0	0	0
relocateObject	0	0	0
requireAnnotation	0	0	0
splitVec	0	0	0