Package: biocDatasets

Version: 1.7.1

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch biocDatasets_1.7.1.tar.gz

StartedAt: 2011-03-17 17:29:27 -0700 (Thu, 17 Mar 2011)

EndedAt: 2011-03-17 17:31:27 -0700 (Thu, 17 Mar 2011)

EllapsedTime: 119.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: biocDatasets.Rcheck

Warnings: 1

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/biocDatasets.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocDatasets/DESCRIPTION’ ... OK
* this is package ‘biocDatasets’ version ‘1.7.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘biocDatasets’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in documentation object '/Users/biocbuild/bbs-2.8-bioc/meat/biocDatasets.Rcheck/00_pkg_src/biocDatasets/man/msubseq.Rd':
  ‘[IRanges:Sequence-class]{Sequence}’

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 ... NOTE
'library' or 'require' call not declared from: lattice
* checking sizes of PDF files under inst/doc ... NOTE
  'qpdf' made some significant size reductions:
     compacted ‘synthetic_arrays.pdf’ from 587Kb to 162Kb
  consider running tools::compactPDF() on these files
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/Users/biocbuild/bbs-2.8-bioc/meat/biocDatasets.Rcheck/00check.log’
for details

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

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (biocDatasets)

name	user	system	elapsed
createProbeCoords	0.332	0.020	0.359
expression_arraywide	0.356	0.018	0.378
msubseq	0.215	0.001	0.216
randomDNASequences	0.003	0.000	0.003
randomIRanges	0.137	0.003	0.140
tilingProbes	0.055	0.000	0.055