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Package 181/436HostnameOS / ArchBUILDCHECKBUILD BIN
GGtools 3.9.53
Vince Carey
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GGtools
Last Changed Rev: 53096 / Revision: 53255
Last Changed Date: 2011-02-23 03:35:46 -0800 (Wed, 23 Feb 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ WARNINGS ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  WARNINGS  OK 

Summary

Package: GGtools
Version: 3.9.53
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings GGtools_3.9.53.tar.gz
StartedAt: 2011-02-24 19:57:29 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 20:09:31 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 721.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GGtools.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GGtools/DESCRIPTION’ ... OK
* this is package ‘GGtools’ version ‘3.9.53’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GGtools’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
bestCis: no visible binding for '<<-' assignment to ‘maxgap’
bestCis: no visible global function definition for ‘mclapply’
cisProxScores: no visible binding for global variable ‘mclapply’
diagffCC: no visible global function definition for ‘mclapply’
diagffCC : <anonymous>: no visible binding for '<<-' assignment to ‘ex’
eqtlTests: no visible binding for '<<-' assignment to ‘geneindex’
eqtlTests: no visible global function definition for ‘mclapply’
eqtlTests : <anonymous> : <anonymous>: no visible binding for global
  variable ‘geneindex’
eqtlTests : <anonymous> : <anonymous>: no visible binding for '<<-'
  assignment to ‘geneindex’
eqtlTestsMACH : <anonymous> : <anonymous>: no visible global function
  definition for ‘snp.rhs.testsMACH’
eqtlTestsNofile: no visible binding for '<<-' assignment to ‘geneindex’
eqtlTestsNofile : <anonymous> : <anonymous>: no visible binding for
  global variable ‘geneindex’
eqtlTestsNofile : <anonymous> : <anonymous>: no visible binding for
  '<<-' assignment to ‘geneindex’
fmcisRun: no visible binding for global variable ‘mclapply’
ieqtlTests: no visible global function definition for ‘mclapply’
maxchisq: no visible global function definition for ‘mclapply’
mcisProxScores: no visible binding for global variable ‘mclapply’
meqtlTests: no visible global function definition for ‘mclapply’
meqtlTests2: no visible binding for global variable ‘listOfSmls’
meqtlTests2: no visible binding for global variable ‘summfflist’
restrictProbesToChrom: no visible binding for global variable ‘chr’
sumScores2ff: no visible global function definition for ‘mclapply’
sumScores2ff : <anonymous>: no visible binding for '<<-' assignment to
  ‘ex’
[,cisTransDirector-character-character-ANY: no visible binding for
  global variable ‘mclapply’
[,cisTransDirector-missing-character-ANY: no visible binding for global
  variable ‘mclapply’
min_p_vals,maxchisq-character-character-numeric : mtcorrp: no visible
  global function definition for ‘mt.rawp2adjp’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  eqtlTestsNofile getSNP makeDiagDirector makeMultiDiagDirector
Undocumented S4 methods:
  generic '[' and siglist 'egtSet,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘eqtest.R’
  Running ‘fftest.R’
 OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/GGtools.Rcheck/00check.log’
for details

GGtools.Rcheck/00install.out:

* installing *source* package ‘GGtools’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: snpMatrix2
Loading required package: survival
Loading required package: splines
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

The following object(s) are masked from 'package:base':

    det

Loading required package: RSQLite
Loading required package: DBI
Loading required package: AnnotationDbi

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: RCurl
Loading required package: bitops
Loading required package: tools
Loading required package: bit
Loading package bit1.1-6

package:bit (c) 2008/2009 Jens Oehlschlaegel (GPL-2)

creators: bit bitwhich

coercion: as.logical as.integer as.bit as.bitwhich which

operator: ! & | xor != == 

querying: print length any all min max range sum summary

bit access: length<- [ [<- [[ [[<-

for more help type ?bit


Attaching package: 'bit'

The following object(s) are masked from 'package:base':

    xor

Loading package ff2.2-1

- getOption("fftempdir")=="/tmp/Rtmpa6F6bY"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

Attaching package ff


Attaching package: 'ff'

The following object(s) are masked from 'package:utils':

    write.csv, write.csv2

The following object(s) are masked from 'package:base':

    is.factor, is.ordered

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GGtools)

GGtools.Rcheck/GGtools-Ex.timings:

nameusersystemelapsed
X2chunk23.126 0.43223.776
bestCis000
cisProxScores-class0.0000.0000.002
cisProxScores44.715 0.55645.489
cisRanges0.3600.0080.383
cisSnpTests17.937 0.23618.733
clipPCs62.904 1.60065.548
degnerASE010.0040.0040.011
diagffCC000
egtSet-class2.6920.1802.889
eqtlTests14.309 0.24014.796
eqtlTestsManager-class0.0000.0000.001
ex60.0560.0000.056