Package: BiocParallel

Version: 0.0.9

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings BiocParallel_0.0.9.tar.gz

StartedAt: 2013-01-16 00:59:43 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 01:00:12 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 29.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocParallel.Rcheck

Warnings: 2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocParallel/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BiocParallel’ version ‘0.0.9’
* 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 ... 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 ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck/00_pkg_src/BiocParallel/man/bpcontrols.Rd’:
  ‘DoparParam’ ‘register’

Missing link or links in documentation object ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/BiocParallel.Rcheck/00_pkg_src/BiocParallel/man/bpschedule.Rd’:
  ‘DoparParam’ ‘register’

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

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘DoparParam’ ‘register’ ‘registered’
Undocumented S4 classes:
  ‘DoparParam’
Undocumented S4 methods:
  generic 'bpisup' and siglist 'DoparParam'
  generic 'bplapply' and siglist 'ANY,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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘test.R’
 OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
See
  ‘/loc/home/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	0.024	0.000	0.024
MulticoreParam-class	0.052	0.044	0.100
SerialParam-class	0.008	0.004	0.015
SnowParam-class	0.120	0.024	1.669
bpcontrols	0.016	0.000	0.017
bplapply	0.072	0.032	0.107
bpschedule	0.012	0.020	0.038
bpvec	0.076	0.020	0.104
bpvectorize	0.016	0.024	0.059