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BioC 2.12: CHECK report for BiocGenerics on petty

This page was generated on 2013-10-09 09:40:06 -0700 (Wed, 09 Oct 2013).

Package 71/671HostnameOS / ArchBUILDCHECKBUILD BIN
BiocGenerics 0.6.0
Bioconductor Package Maintainer
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/BiocGenerics
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  WARNINGS 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ WARNINGS ] OK 

Summary

Package: BiocGenerics
Version: 0.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BiocGenerics_0.6.0.tar.gz
StartedAt: 2013-10-08 21:42:45 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 21:44:16 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 90.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/BiocGenerics.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.6.0'
* 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 'BiocGenerics' can be installed ... [5s/5s] 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/BiocGenerics.Rcheck/00_pkg_src/BiocGenerics/man/rank.Rd':
  '[IRanges]{rank,Vector-method}'

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 ... NOTE
S3 methods shown with full name in documentation object 'rep':
  'rep.int'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [10s/10s] OK
Examples with CPU or elapsed time > 5s
       user system elapsed
strand 5.12  0.087   5.238
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'BiocGenerics_unit_tests.R' [3s/3s]
 [4s/4s] OK
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.

BiocGenerics.Rcheck/00install.out:

* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'as.data.frame' in package 'BiocGenerics'
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rank' in package 'BiocGenerics'
Creating a new generic function for 'rep.int' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'sort' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'unlist' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Warning in getPackageName(environment(fdef)) :
  Created a package name, '2013-10-08 21:42:48', when none found
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' in package 'BiocGenerics'
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (BiocGenerics)

BiocGenerics.Rcheck/BiocGenerics-Ex.timings:

nameusersystemelapsed
BiocGenerics-package0.0090.0020.010
Extremes0.0980.0030.102
annotation0.7590.0250.787
as.data.frame0.0160.0000.017
boxplot0.0090.0000.010
cbind0.0130.0000.014
clusterApply0.0820.0050.088
combine0.2020.0050.208
density0.0100.0010.011
duplicated0.0280.0010.029
eval0.0130.0010.014
funprog0.0430.0030.044
get0.0170.0010.018
image0.0080.0010.010
lapply0.0190.0010.020
mapply0.0170.0000.018
match0.0110.0010.011
nrow0.0220.0010.023
order0.0120.0010.012
paste0.0090.0000.010
rank0.0120.0010.012
rep0.0120.0010.012
residuals0.0120.0010.012
row_colnames0.0150.0010.016
sets0.0220.0010.023
sort0.0110.0010.012
strand5.1200.0875.238
table0.2240.0030.248
tapply0.0110.0010.012
unique0.0160.0010.016
unlist0.2140.0020.217
updateObject0.5550.0420.601
weights0.0190.0020.020
xtabs0.0120.0020.014