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Package 41/98HostnameOS / ArchBUILDCHECKBUILD BIN
ggtut 0.0.20
VJ Carey
Snapshot Date: 2011-07-01 11:15:06 -0700 (Fri, 01 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/ggtut
Last Changed Rev: 1658 / Revision: 1675
Last Changed Date: 2011-06-21 08:13:54 -0700 (Tue, 21 Jun 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.7) / i386  OK [ WARNINGS ] OK 

Summary

Package: ggtut
Version: 0.0.20
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ggtut_0.0.20.tar.gz
StartedAt: 2011-07-01 12:50:15 -0700 (Fri, 01 Jul 2011)
EndedAt: 2011-07-01 13:00:14 -0700 (Fri, 01 Jul 2011)
EllapsedTime: 598.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ggtut.Rcheck
Warnings: 2

Command output

* using log directory '/Users/biocbuild/bbs-2.9-data-experiment/meat/ggtut.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ggtut/DESCRIPTION' ... OK
* this is package 'ggtut' version '0.0.20'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ggtut' can be installed ... WARNING
Found the following significant warnings:
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
  Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
See '/Users/biocbuild/bbs-2.9-data-experiment/meat/ggtut.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 236.1Mb
  sub-directories of 1Mb or more:
    bam          15.1Mb
    data         31.3Mb
    doc           7.0Mb
    ffarchives  129.9Mb
    ffobjects     1.6Mb
    images       12.9Mb
    sqlite       38.0Mb
* 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
  'permsb1' 'rsb2_list' 'rsb2_perm_list' 'sb1'
All user-level objects in a package 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK

WARNING: There were 2 warnings, see
  '/Users/biocbuild/bbs-2.9-data-experiment/meat/ggtut.Rcheck/00check.log'
for details

ggtut.Rcheck/00install.out:

* installing *source* package 'ggtut' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase

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: GGBase
Loading required package: snpStats
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: annotate
Loading required package: AnnotationDbi
Loading required package: IRanges

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: rtracklayer
Loading required package: RCurl
Loading required package: bitops
Loading required package: org.Hs.eg.db

Loading required package: GenomicRanges
Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package bit1.1-7

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

Warning: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
Loading package ff2.2-2
- getOption("fftempdir")=="/tmp/Rtmpp71VkD"

- 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: 'GGtools'

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

    geneNames

Loading required package: tools
Loading required package: bit

Attaching package: 'bit'

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

    xor

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

Loading required package: illuminaHumanv1.db

To get a tailored smlSet, use getSS("GGdata", [chrvec]) 
available chromosomes are named  1 10 ... X Y 
Loading required package: biomaRt

Attaching package: 'biomaRt'

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

    getGO

Loading required package: multtest
Loading required package: Biostrings

Attaching package: 'Biostrings'

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

    mismatch, pattern

Loading required package: BSgenome

Attaching package: 'BSgenome'

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

    organism

Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db

Loading required package: limma
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
To get a tailored smlSet, use getSS("GGdata", [chrvec]) 
available chromosomes are named  1 10 ... X Y 
Warning messages:
1: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 
2: 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible 

* DONE (ggtut)

ggtut.Rcheck/ggtut-Ex.timings:

nameusersystemelapsed
c17imp1.0130.0371.059
g17rngsnr0.1480.0060.154
ggtut-package0.4810.0140.496
observed17ceu0.3210.0270.350
rules.n436.3080.0926.399
snpgr171.3460.0721.418