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Package 91/389HostnameOS / ArchBUILDCHECKBUILD BIN
crlmm 1.6.6
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/crlmm
Last Changed Rev: 49659 / Revision: 49923
Last Changed Date: 2010-09-27 18:36:19 -0700 (Mon, 27 Sep 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK [ OK ] OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: crlmm
Version: 1.6.6
Command: D:\biocbld\bbs-2.6-bioc\R\bin\R.exe CMD check --no-vignettes --timings crlmm_1.6.6.tar.gz
StartedAt: 2010-10-04 16:27:20 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 16:32:38 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 317.8 seconds
RetCode: 0
Status:  OK  
CheckDir: crlmm.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'D:/biocbld/bbs-2.6-bioc/meat/crlmm.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'crlmm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'crlmm' version '1.6.6'
* 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 package directory ... OK
* checking for portable file names ... 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
bias2: no visible binding for global variable 'emit'
biasAdjust: no visible binding for global variable 'normal'
biasAdjust: no visible binding for global variable 'emit'
crlmmCopynumber: no visible global function definition for 'physical'
crlmmIlluminaRS: no visible global function definition for 'clone'
fit.lm1: no visible global function definition for 'physical'
fit.lm2: no visible global function definition for 'physical'
fit.lm3: no visible global function definition for 'physical'
fit.lm4: no visible global function definition for 'physical'
getFeatureData.Affy: no visible binding for global variable 'snpProbes'
getPhenoData: no visible binding for global variable 'sep'
getPhenoData: no visible binding for global variable 'highDensity'
getPhenoData: no visible binding for global variable 'fileExt'
getPhenoData: no visible binding for global variable 'path'
[,CNSetLM: no visible global function definition for 'physical'
open,CNSetLM: no visible global function definition for 'physical'
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

crlmm.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'crlmm' ...
** libs
  making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c gtypeCaller.c -o gtypeCaller.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c init.c -o init.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c trimmed.c -o trimmed.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include"         -O2 -Wall  -std=gnu99 -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
x86_64-w64-mingw32-gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/crlmm.Rcheck/crlmm/libs/x64
  ... done
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

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

================================================================================
Welcome to oligoClasses version 1.10.0
================================================================================
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 bit1.1-6

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

Loading package ff2.2-0

- getOption("fftempdir")=="D:/biocbld/bbs-2.6-bioc/tmpdir/RtmpTh5czb"

- 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")==42928701.44 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==2146435072 -- consider a different value for tuning your system

Creating a new generic function for "ellipse" in "crlmm"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Welcome to crlmm version 1.6.6

* DONE (crlmm)

crlmm.Rcheck/crlmm-Ex.timings:

nameusersystemelapsed
CNSetLM-class000
crlmm153.72 1.94157.76
crlmmCopynumber000
crlmmIllumina000
genotype0.650.030.69
readIdatFiles000
sample.CNSetLM0.380.000.45
snprma22.01 0.8623.00