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BioC 2.12: CHECK report for GGBase on petty

This page was generated on 2013-10-09 09:39:41 -0700 (Wed, 09 Oct 2013).

Package 278/671HostnameOS / ArchBUILDCHECKBUILD BIN
GGBase 3.22.0
VJ Carey
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/GGBase
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  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: GGBase
Version: 3.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GGBase_3.22.0.tar.gz
StartedAt: 2013-10-08 22:34:18 -0700 (Tue, 08 Oct 2013)
EndedAt: 2013-10-08 22:41:14 -0700 (Tue, 08 Oct 2013)
EllapsedTime: 415.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GGBase.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GGBase.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 'GGBase/DESCRIPTION' ... OK
* this is package 'GGBase' version '3.22.0'
* 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 'GGBase' can be installed ... [31s/31s] 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 ... NOTE
.oldcode : <anonymous>: warning in axis(3, at = genePosition(x@gene,
  annlib = x@annotation), col = "red", lwd = 2, label = " "): partial
  argument match of 'label' to 'labels'
.oldcode : pedinf2df: warning in read.table(fn, h = FALSE): partial
  argument match of 'h' to 'header'
allsnps: warning in dir(system.file("parts", package = packname), full
  = TRUE): partial argument match of 'full' to 'full.names'
.oldcode : genePosition: no visible global function definition for
  'revmap'
.oldcode : featureFilter: no visible global function definition for
  'keys'
.oldcode : sym2pid: no visible global function definition for 'revmap'
.oldcode : <anonymous>: no visible global function definition for
  'revmap'
.oldcode : snpLocs.Hsapiens: no visible global function definition for
  'getSNPlocs'
sym2pid: no visible global function definition for 'revmap'
plot_EvG,genesym-rsid-smlSet: no visible global function definition for
  'revmap'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [40s/45s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
MAFfilter   10.221  0.548  14.749
make_smlSet  6.798  0.378   7.214
plot_EvG     6.426  0.452   6.925
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'MAFfilter.R' [25s/25s]
  Running 'make.R' [25s/25s]
  Running 'plot_EvG.R' [24s/24s]
 [74s/75s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

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

GGBase.Rcheck/00install.out:

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

GGBase.Rcheck/GGBase-Ex.timings:

nameusersystemelapsed
MAFfilter10.221 0.54814.749
clipPCs0.4510.0460.501
externalize0.0040.0070.011
make_smlSet6.7980.3787.214
plot_EvG6.4260.4526.925
rsid-class0.0060.0050.010
smlSet-class0.0040.0060.010