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Package 114/462HostnameOS / ArchBUILDCHECKBUILD BIN
crlmm 1.11.2
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm
Last Changed Rev: 55182 / Revision: 55359
Last Changed Date: 2011-04-30 04:38:33 -0700 (Sat, 30 Apr 2011)
wilson2 Linux (openSUSE 11.4) / 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 

Summary

Package: crlmm
Version: 1.11.2
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings crlmm_1.11.2.tar.gz
StartedAt: 2011-05-09 12:09:39 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 12:15:28 -0700 (Mon, 09 May 2011)
EllapsedTime: 349.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: crlmm.Rcheck
Warnings: 1

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/crlmm.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crlmm’ version ‘1.11.2’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘crlmm’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.9Mb
  sub-directories of 1Mb or more:
    scripts   1.6Mb
    doc      10.8Mb
* 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
computeSummary: no visible global function definition for
  ‘summaryStats’
genotypeInf: no visible binding for global variable ‘cdfName’
linesCNSet: no visible global function definition for ‘llines’
preprocess: no visible binding for global variable ‘cdfName’
preprocessInf: no visible binding for global variable ‘cdfName’
updateCors: no visible binding for global variable ‘index’
updateStats: no visible global function definition for ‘Ns.AA’
updateStats: no visible global function definition for ‘Ns.AA<-’
updateStats: no visible binding for global variable ‘k’
updateStats: no visible binding for global variable ‘G.call’
updateStats: no visible global function definition for ‘Ns.AB’
updateStats: no visible global function definition for ‘Ns.AB<-’
updateStats: no visible global function definition for ‘Ns.BB’
updateStats: no visible global function definition for ‘Ns.BB<-’
updateTau: no visible global function definition for ‘summaryStats’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... NOTE
  ================================================================================
  Welcome to oligoClasses version 1.15.0
  ================================================================================
  Large dataset support for 'oligo/crlmm': Disabled
       - Load 'ff'
  ================================================================================
  Parallel computing support for 'oligo/crlmm': Disabled
       - Load 'ff'
       - Load 'snow'
       - Use options(cluster=makeCluster(...))
  ================================================================================
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘crlmm_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Package vignette(s) without corresponding PDF:
   ‘CopyNumberOverview.Rnw’
   ‘genotyping.Rnw’

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/crlmm.Rcheck/00check.log’
for details

crlmm.Rcheck/00install.out:

* installing *source* package ‘crlmm’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c gtypeCaller.c -o gtypeCaller.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c trimmed.c -o trimmed.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c utils.c -o utils.o
utils.c: In function ‘mad_median’:
utils.c:124:15: warning: unused variable ‘n_ignore’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/crlmm.Rcheck/crlmm/libs
** 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")'.

================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
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

Loading package ff2.2-2
- getOption("fftempdir")=="/tmp/Rtmp95Ysft"

- 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

Creating a new generic function for "lines" in "crlmm"
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘AffymetrixPreprocessCN.Rnw’ 
   ‘CopyNumberOverview.Rnw’ 
   ‘IlluminaPreprocessCN.Rnw’ 
   ‘Infrastructure.Rnw’ 
   ‘copynumber.Rnw’ 
   ‘crlmmDownstream.Rnw’ 
   ‘genotyping.Rnw’ 
** testing if installed package can be loaded
================================================================================
Welcome to oligoClasses version 1.15.0
================================================================================
Large dataset support for 'oligo/crlmm': Disabled
     - Load 'ff'
================================================================================
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load 'snow'
     - Use options(cluster=makeCluster(...))
================================================================================
Welcome to crlmm version 1.11.2

* DONE (crlmm)

crlmm.Rcheck/crlmm-Ex.timings:

nameusersystemelapsed
batchStatisticAccessors0.0240.0000.027
constructInf000
copynumberAccessors0.0920.0000.089
crlmm142.261 2.360145.984
crlmmIllumina000
crlmmIlluminaV2000
genotype.Illumina0.0000.0000.001
genotype0.4800.0080.491
genotypeInf000
preprocessInf000
readIdatFiles000
sample.CNSet0.0360.0040.042
snprma28.090 1.45229.681