Package: oligoClasses

Version: 1.19.3

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch oligoClasses_1.19.3.tar.gz

StartedAt: 2012-06-21 02:11:46 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 02:15:24 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 218.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: oligoClasses.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/oligoClasses.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'oligoClasses/DESCRIPTION' ... OK
* this is package 'oligoClasses' version '1.19.3'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'doMPI' 'doSNOW' 'doParallel' 'doRedis'
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.11-bioc/meat/oligoClasses.Rcheck/00_pkg_src/oligoClasses/man/findOverlaps.Rd':
  'RangesMatching-class'

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.

* 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 examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/oligoClasses.Rcheck/00check.log'
for details.

* 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'
Creating a generic function for 'mean' from package 'base' in package 'oligoClasses'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

* DONE (oligoClasses)

name	user	system	elapsed
AlleleSet-class	0.442	0.009	0.462
AssayData-methods	0.668	0.027	0.699
BeadStudioSet-class	0.081	0.001	0.083
CNSet-class	0.081	0.011	0.094
CopyNumberSet-class	0.070	0.001	0.071
FeatureSetExtensions-class	0.271	0.001	0.279
GenomeAnnotatedDataFrame-class	1.183	0.391	9.300
RangedDataCNV-classes	0.002	0.001	0.002
RangedDataCNV-utils	0.546	0.006	0.554
SnpSet-methods	0.076	0.001	0.077
SnpSuperSet-class	0.134	0.001	0.136
affyPlatforms	0.001	0.000	0.001
batch	0.063	0.000	0.063
celfileDate	0.042	0.007	0.098
checkExists	0.008	0.002	0.009
checkOrder	0.422	0.018	0.445
chromosome-methods	0.001	0.000	0.001
chromosome2integer	0	0	0
clusterOpts	0.158	0.045	0.343
data-efsExample	0.003	0.001	0.003
data-scqsExample	0.002	0.001	0.003
data-sfsExample	0.002	0.001	0.003
data-sqsExample	0.003	0.001	0.003
db	0	0	0
ff_matrix	0.000	0.000	0.002
ff_or_matrix-class	0.001	0.000	0.001
fileConnections	0.000	0.000	0.001
findOverlaps	1.378	0.095	1.497
flags	0.452	0.056	0.517
gSet-class	0.002	0.001	0.002
geometry-methods	0.175	0.017	0.194
getBar	0	0	0
i2p_p2i	0.000	0.001	0.000
integerMatrix	0	0	0
is.ffmatrix	0.000	0.001	0.001
isPackageLoaded	0.001	0.000	0.000
kind	0.398	0.020	0.431
largeObjects	0.002	0.001	0.003
ldOpts	0.002	0.000	0.002
library2	0.084	0.006	0.091
list.celfiles	0.043	0.006	0.049
locusLevelData	0.120	0.011	0.140
oligoSetExample	0.176	0.007	0.183
pdPkgFromBioC	0	0	0
requireAnnotation	0.000	0.000	0.001
splitVec	0.017	0.024	0.040