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 |
* checking for working pdflatex ... OK
* using log directory 'E:/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
* install options are ' --no-html'
* installing *source* package 'crlmm' ...
** libs
making DLL ...
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c gtypeCaller.c -o gtypeCaller.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c init.c -o init.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c trimmed.c -o trimmed.o
gcc -I"E:/biocbld/bbs-2.6-bioc/R/include" -O3 -Wall -std=gnu99 -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
gcc -shared -s -static-libgcc -o crlmm.dll tmp.def gtypeCaller.o init.o trimmed.o utils.o -LE:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to E:/biocbld/bbs-2.6-bioc/meat/crlmm.Rcheck/crlmm/libs
... 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")=="E:/biocbld/bbs-2.6-bioc/tmpdir/RtmptBQUN4"
- 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")==16095641.6 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==804782080 -- 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)