Package: BiocParallel

Version: 0.0.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiocParallel_0.0.12.tar.gz

StartedAt: 2013-03-25 02:55:39 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:56:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 43.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocParallel.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BiocParallel/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiocParallel' version '0.0.12'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'BiocParallel' can be installed ... [3s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck/00_pkg_src/BiocParallel/man/bpcontrols.Rd':
  'DoparParam'

Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck/00_pkg_src/BiocParallel/man/bpschedule.Rd':
  'DoparParam'

Missing link or links in documentation object '/Users/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck/00_pkg_src/BiocParallel/man/register.Rd':
  'DoparParam'

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'DoparParam'
Undocumented S4 classes:
  'DoparParam'
Undocumented S4 methods:
  generic 'bpisup' and siglist 'DoparParam'
  generic 'bplapply' and siglist 'ANY,DoparParam'
  generic 'bpworkers' and siglist 'DoparParam'
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 ... OK
* checking examples ... [2s/4s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'test.R' [2s/7s]
 [3s/7s] OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck/00check.log'
for details.

* installing *source* package 'BiocParallel' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BiocParallel)

name	user	system	elapsed
AllClasses	0.014	0.001	0.014
MulticoreParam-class	0.050	0.078	0.116
SerialParam-class	0.015	0.001	0.016
SnowParam-class	0.089	0.023	2.266
bpcontrols	0.014	0.000	0.015
bplapply	0.099	0.098	0.112
bpschedule	0.029	0.036	0.047
bpvec	0.090	0.064	0.136
bpvectorize	0.025	0.050	0.047
register	0.027	0.007	0.033