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BioC 2.13: CHECK report for annmap on zin1

This page was generated on 2014-04-05 09:48:20 -0700 (Sat, 05 Apr 2014).

Package 36/750HostnameOS / ArchBUILDCHECKBUILD BIN
annmap 1.4.1
Tim Yates
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/annmap
Last Changed Rev: 84838 / Revision: 88450
Last Changed Date: 2013-12-18 01:40:32 -0800 (Wed, 18 Dec 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: annmap
Version: 1.4.1
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings annmap_1.4.1.tar.gz
StartedAt: 2014-04-04 23:28:01 -0700 (Fri, 04 Apr 2014)
EndedAt: 2014-04-04 23:30:45 -0700 (Fri, 04 Apr 2014)
EllapsedTime: 164.2 seconds
RetCode: 0
Status:  OK 
CheckDir: annmap.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/annmap.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘annmap/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘annmap’ version ‘1.4.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘annmap’ can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.make.hash’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [15s/24s]
 [15s/24s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/annmap.Rcheck/00check.log’
for details.

annmap.Rcheck/00install.out:

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

annmap.Rcheck/annmap-Ex.timings:

nameusersystemelapsed
annmap.all0.0040.0000.005
annmap.coords0.0120.0000.010
annmap.details0.0040.0000.002
annmap.env0.0040.0000.003
annmap.filters0.0080.0000.007
annmap.range0.0080.0080.016
annmap.seqname0.0040.0000.003
annmap.spliceIndex0.0040.0000.005
annmap.to0.0080.0000.008
annmap.utils0.0080.0000.006
annmap.utr0.0000.0040.004